Citrus Sinensis ID: 018689

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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--
Protein Sequence
MSFSGGNFGGAAAAAPPQQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELETPNPSVNPNPNPMDAFLLDDLSTLLGMGPTRSFTDPSEFNPFVFLQNYLQNLRANGASIQFVVENNSNVDPAAGGAGAAFRLPANLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYEQRRNGNGNGNNNSNNNNSMNQSFNLGFGFGGGGSGGNDGESGGNAETPRTVERRLRISLPWPFNAFASRAETSGNSGSGSGGTNDGDSTSGNRGSEPRQEDLD
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccEEcccccEEEEcccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccHHHHHHHHHHccccccccHHHHcccccccccccccccccccccccccccccHHHHHHHHHHHHccccccccccccHHHHHHcccEEccccccccccccccccccccccccccEEcccccccccccHHHHHHHcccccccccccccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccEEEEEccEEEEEccccccccEccccccccEEEcccccccccccccccccHHcccHHHcccccccccccccccccccEEcccccccccccccccccccccccccccccccccccccccccccHHcccccHHHHHHHHHHccccccccccccHHHHHcccEEEEEHHHcccccccccccHccccccHHHcccccccccccccEcHHHHHccccccEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
msfsggnfggaaaaappqqepqmyfchqcnrtvrvtpspssdlvcpscnggfieeletpnpsvnpnpnpmdaFLLDDLStllgmgptrsftdpsefnpFVFLQNYLQNLRANGASIQFVVEnnsnvdpaaggagaafrlpanlgdyfigpGLEQLIQQLAendpnrygtppasksaiealpsikineammssdssqcavckdsfeLNEEarqmpckhiyhpdcimpwlelhnscpvcryelptddpdyeqrrngngngnnnsnnnnsmnqsfnlgfgfggggsggndgesggnaetprtVERRLRIslpwpfnafasraetsgnsgsgsggtndgdstsgnrgseprqedld
Flexible Loop (DISEMBL)
MSFSGGNFGGAAAAAPPQQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELETPNPSVNPNPNPMDAFLLDDLSTLLGMGPTRSFTDPSEFNPFVFLQNYLQNLRANGASIQFVVENNSNVDPAAGGAGAAFRLPANLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYEQRRNGNGNGNNNSNNNNSMNQSFNLGFGFGGGGSGGNDGESGGNAETPRTVERRLRISLPWPFNAFASRaetsgnsgsgsggtndgdstsgnrgseprqedld
Low Complexity Region (SEG)
MSFSGGNFGGaaaaappqqepqMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELETpnpsvnpnpnpMDAFLLDDLSTLLGMGPTRSFTDPSEFNPFVFLQNYLQNLRANGASIQFVVENNSNVDPAAGGAGAAFRLPANLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYEQRRngngngnnnsnnnnsmnqsfnlgfgfggggsggndgesggnAETPRTVERRLRISLPWPFNAFASRAEtsgnsgsgsggtndgdstsgnRGSEPRQEDLD
Disordered region (IsUnstruct)
**********************MYFCHQCNRTVRVT*****DLVCPSCNGGFI******************AFLLDDLSTLLGMGPTRSFTDPSEFNPFVFLQNYLQNLRANGASIQFVVENNSNVDPAAGGAGAAFRLPANLGDYFIGPGLEQLIQQ***************************************AVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYEL***************************************************************RISLPWPFNA**************************************
Disordered Region (DISOPRED)
**********************MYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELETPNPSVNPNPNPMDAFLLDDLSTLLGMGPTRS***********************************************FRLPANLGDYFIGPGLEQ********************SAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP**************************************************************************************************************
Disordered Region (DISEMBL)
*****************QQEPQMYFCHQCNRTVR*********VCPSCNGGFIEELETPNPSVNPNPNPMDAFLLDDLSTLLGMGPTRSFTDPSEFNPFVFLQNYLQNLRANGASIQFVVENNSNVDPAAGGAGAAFRLPANLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAM********AVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYEQRRNGNGNGNNNSNNNNSMNQSFNLGFGFGGGGSGG*************TVERRLRISLPWPFNAFASRAE********************************
Disordered Region (DISPRO)
********************PQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELET****************LDDLSTLLGMGPTRSFTDPSEFNPFVFLQNYLQNLRANGASIQFVVENNSNVDPAAGGAGAAFRLPANLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYEL*************************************************************RLRISLPWPFNA**************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSFSGGNFGGAAAAAPPQQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELETPNPSVNPNPNPMDAFLLDDLSTLLGMGPTRSFTDPSEFNPFVFLQNYLQNLRANGASIQFVVENNSNVDPAAGGAGAAFRLPANLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYEQRRNGNGNGNNNSNNNNSMNQSFNLGFGFGGGGSGGNDGESGGNAETPRTVERRLRISLPWPFNAFASRAETSGNSGSGSGGTNDGDSTSGNRGSEPRQEDLD
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	352	2.2.26 [Sep-21-2011]
P0CH30	338	E3 ubiquitin-protein liga	N/A	no	0.846	0.881	0.485	3e-84
Q8LPN7	328	E3 ubiquitin-protein liga	yes	no	0.761	0.817	0.466	1e-74
Q91YL2	313	RING finger protein 126 O	yes	no	0.605	0.680	0.324	1e-22
Q9Y4L5	304	E3 ubiquitin-protein liga	yes	no	0.684	0.792	0.277	7e-22
Q8RXD3	310	E3 ubiquitin-protein liga	no	no	0.301	0.341	0.419	1e-20
Q9SPL2	334	E3 ubiquitin-protein liga	no	no	0.315	0.332	0.456	1e-20
Q9BV68	326	RING finger protein 126 O	no	no	0.616	0.665	0.312	2e-20
Q9D0C1	305	E3 ubiquitin-protein liga	no	no	0.377	0.436	0.350	3e-20
Q6DIP3	311	RING finger protein 126 O	no	no	0.306	0.347	0.450	7e-20
Q0II22	313	RING finger protein 126 O	no	no	0.306	0.345	0.459	2e-19

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

 Score =  312 bits (799), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 188/387 (48%), Positives = 227/387 (58%), Gaps = 89/387 (22%)

Query: 4   SGGNFGGAAAAAPPQQEPQMYFCHQCNRTVRVTPSP-SSDLVCPSCNGGFIEELETPNPS 62
           S GN  G   A       + +FC+QCNRTV VT SP SSD  CP CN GF+EE + PNP+
Sbjct: 3   SDGNVTGGGGANTVGVTNKPFFCYQCNRTVNVTISPPSSDPTCPICNEGFLEEYDNPNPN 62

Query: 63  -----VNPNPNPM---DAFLL--DDLSTLLGM------------------------GPTR 88
                +NPNPN +   D FL   D  ++LL +                        GPTR
Sbjct: 63  QGSGFLNPNPNSIPFHDLFLTLSDPFASLLPLLFPSSSSTTTSSSASIDPNNPSLSGPTR 122

Query: 89  SFT-DPSEFNPFVFLQNYLQNLRANGASIQFVVENNSNVDPAAGGAGAAFRLPANLGDYF 147
           S   DP  F+PF F+QN+L +LR++GA I+FV++NN         +   FRLPAN+GDYF
Sbjct: 123 SGRGDPFAFDPFTFIQNHLNDLRSSGAQIEFVIQNNP--------SDQGFRLPANIGDYF 174

Query: 148 IGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELN 207
           IGPGLEQLIQQLAENDPNRYGTPPASKSAIEALP + I ++ ++S+ +QCAVC D FE  
Sbjct: 175 IGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPLVNITKSNLNSEFNQCAVCMDDFEEG 234

Query: 208 EEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYEQRRNGNGNGNNNSNNNNS 267
            EA+QMPCKH+YH DC++PWLELHNSCPVCR+ELPTDDPDYE+R  G             
Sbjct: 235 TEAKQMPCKHLYHKDCLLPWLELHNSCPVCRHELPTDDPDYERRVRG------------- 281

Query: 268 MNQSFNLGFGFGGGGSGGNDGESGGNAETP--RTVERRLRISLPWPFNAFASRAETSGNS 325
                        G SGGNDG++ G       RTVER  RISLPWPF A           
Sbjct: 282 -----------AQGTSGGNDGDNSGQRSDGDNRTVERSFRISLPWPFQARGP-------- 322

Query: 326 GSGSGGTNDGDSTSGNRGSEPRQEDLD 352
                G   GD+      +E RQEDLD
Sbjct: 323 -----GPAPGDN------AETRQEDLD 338

E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Promotes polyubiquitination of target proteins.
Gossypium hirsutum (taxid: 3635)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

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

 Score =  280 bits (715), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 158/339 (46%), Positives = 200/339 (58%), Gaps = 71/339 (20%)

Query: 4   SGGNFGGAAAAAPPQQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELETPNP-- 61
           SG N  G+AAAAP  +  +M+FC+QCN+TV ++ S S+D  CP CN GF+EE E PNP  
Sbjct: 3   SGVNSTGSAAAAP--EVDKMFFCYQCNQTVTISISSSADPFCPICNQGFLEEYEDPNPNQ 60

Query: 62  SVNPNPNPMDAF--LLDDLSTLLGMGPTRSFTDPS------------------------- 94
           S+N NPN  D+F  + D  STLL +    S   PS                         
Sbjct: 61  SLNFNPNSSDSFFPMADPFSTLLPLIFGSSAAAPSGMDFMSLFGPSMQPQARSTQQNPQS 120

Query: 95  -EFNPFVFLQNYLQNLRANGASIQFVVENNSNVDPAAGGAGAAFRLPANLGDYFIGPGLE 153
             F+PF FLQN+LQ LR++G   +FV+EN+ + DP         R+P N GDYF GPGLE
Sbjct: 121 DAFDPFTFLQNHLQTLRSSGTHFEFVIENHPS-DPGN-------RMPGNFGDYFFGPGLE 172

Query: 154 QLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQM 213
           QLIQQLAENDPNRYGTPPASKSAI+ALP++K+ + M+ S+ +QCAVC D FE   + +QM
Sbjct: 173 QLIQQLAENDPNRYGTPPASKSAIDALPTVKVTKDMLKSEMNQCAVCMDEFEDGSDVKQM 232

Query: 214 PCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYEQRRNGNGNGNNNSNNNNSMNQSFN 273
           PCKH++H DC++PWLELHNSCPVCR+ELPTDDPDYE R  G+    +   +         
Sbjct: 233 PCKHVFHQDCLLPWLELHNSCPVCRFELPTDDPDYENRSQGSQGSGDGQGSVEGQ----- 287

Query: 274 LGFGFGGGGSGGNDGESGGNAETPRTVERRLRISLPWPF 312
                                +TPR       I LPWPF
Sbjct: 288 ---------------------QTPR-----FSIQLPWPF 300

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

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score =  107 bits (267), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 94/290 (32%), Positives = 125/290 (43%), Gaps = 77/290 (26%)

Query: 13  AAAPPQQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEEL--ETPN------PSVN 64
           A A PQ  P  YFCH C  +V + P    D +CP C  GFIEEL  ET N      PS  
Sbjct: 2   AEASPQ--PGRYFCHCC--SVEIVPR-LPDYICPRCESGFIEELPEETRNTENGSAPSTA 56

Query: 65  PNPNPMDAFLLDDLSTLLGMGPTRSFTDPSEFNPFVF----------------------- 101
           P       F  +++   L       FT P  ++ F F                       
Sbjct: 57  PTDQNRQPF--ENVDQHL-------FTLPQGYSQFAFGIFDDSFEIPTFPPGAQADDGRD 107

Query: 102 -----------LQNY--------LQNLRANGA-----SIQFVVENNSN--VDPAAG---G 132
                         Y        L   RA G      +++ +++   N  + PAA    G
Sbjct: 108 PESRREREHQSRHRYGARQPRARLTARRATGRHEGVPTLEGIIQQLVNGIISPAAVPSLG 167

Query: 133 AGAAFRLPANLGDYFIGP-GLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMS 191
            G    L +N  DY  G  GL+ +I QL  N     G PPA K  I+ALP++ + E  + 
Sbjct: 168 LGPWGVLHSNPMDYAWGANGLDTIITQLL-NQFENTGPPPADKEKIQALPTVPVTEEHVG 226

Query: 192 SDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYEL 241
           S   +C VCK+ + L E  RQ+PC H++H  CI+PWLE H+SCPVCR  L
Sbjct: 227 S-GLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSL 275

Mus musculus (taxid: 10090)

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

 Score =  105 bits (261), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 82/295 (27%), Positives = 133/295 (45%), Gaps = 54/295 (18%)

Query: 24  YFCHQCNRTVRVTPSPS-SDLVCPSCNGGFIEELETPNPSVNPNPNPMDAFLLDDLSTLL 82
           +FCH C   V    SP   + +CP C  GFIEE+   +  +    + +D       + L 
Sbjct: 20  FFCHFCKGEV----SPKLPEYICPRCESGFIEEVTDDSSFLGGGGSRIDNTTTTHFAELW 75

Query: 83  G-MGPTRSFTDPSEFNPFVFLQNYLQNLRAN-----------GA---------------- 114
           G +  T  F D   F PF+      Q+ RAN           GA                
Sbjct: 76  GHLDHTMFFQD---FRPFLSSSPLDQDNRANERGHQTHTDFWGARPPRLPLGRRYRSRGS 132

Query: 115 -------SIQFVVEN-------NSNVDPAAGGAGAAFRLPANLGDYFIG-PGLEQLIQQL 159
                  +I+ ++++       NS +  +      +  L +N GDY  G  GL+ ++ QL
Sbjct: 133 SRPDRSPAIEGILQHIFAGFFANSAIPGSPHPFSWSGMLHSNPGDYAWGQTGLDAIVTQL 192

Query: 160 AENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIY 219
                N  G PPA K  I +LP++ + +  +     +C VCK+ + + EE RQ+PC H +
Sbjct: 193 LGQLENT-GPPPADKEKITSLPTVTVTQEQVDM-GLECPVCKEDYTVEEEVRQLPCNHFF 250

Query: 220 HPDCIMPWLELHNSCPVCRYELPTDDPDYEQRRNGNGNGNNNSNNNNSMNQSFNL 274
           H  CI+PWLELH++CPVCR  L  +D    Q ++   + +N  +N++ ++  +  
Sbjct: 251 HSSCIVPWLELHDTCPVCRKSLNGED-STRQSQSTEASASNRFSNDSQLHDRWTF 304

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

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score =  101 bits (251), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 47/112 (41%), Positives = 71/112 (63%), Gaps = 6/112 (5%)

Query: 141 ANLGDYFIGPGLEQLIQQLAEND-PNRYGTPPASKSAIEALPSIKINEAMMSS--DSSQC 197
           ANL    I  GL+ +I  + ++  P R   PPASK  +E LP I   E ++      ++C
Sbjct: 174 ANLMQELIN-GLDMIIPDILDDGGPPR--APPASKEVVEKLPVIIFTEELLKKFGAEAEC 230

Query: 198 AVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYE 249
            +CK++  + ++ +++PCKH +HP C+ PWL+ HNSCP+CR+ELPTDD  YE
Sbjct: 231 CICKENLVIGDKMQELPCKHTFHPPCLKPWLDEHNSCPICRHELPTDDQKYE 282

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

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9SPL2|CIP8_ARATH E3 ubiquitin-protein ligase CIP8 OS=Arabidopsis thaliana GN=CIP8 PE=1 SV=1

 Score =  100 bits (250), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 57/125 (45%), Positives = 73/125 (58%), Gaps = 14/125 (11%)

Query: 138 RLPANLGDYFI-GPGLEQLIQQLAENDPNRYG----TPPASKSAIEALPSIKIN----EA 188
           R   N  DY     G E L+Q LAE D    G     PPA+KSAIEAL + +++    E 
Sbjct: 194 RYAGNPADYIDDAAGYEALLQNLAEGDGGGGGGRRGAPPAAKSAIEALETFEVSSSEGEM 253

Query: 189 MMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDY 248
           +M      CAVCKD   + E  +++PC H YH DCI+PWL   NSCPVCR++L TDD +Y
Sbjct: 254 VMV-----CAVCKDGMVMGETGKKLPCGHCYHGDCIVPWLGTRNSCPVCRFQLETDDAEY 308

Query: 249 EQRRN 253
           E+ R 
Sbjct: 309 EEERK 313

E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins. Probably forms a minimal ubiquitin ligase complex in cooperation with the E2 enzyme UBC8. Its interaction with COP1 suggests that it may participate in proteasome-mediated degradation of HY5 in vivo.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score =  100 bits (249), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 85/272 (31%), Positives = 114/272 (41%), Gaps = 55/272 (20%)

Query: 20  EPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFI----EELETPNPSVNPNPNPMD---- 71
            P  YFCH C  +V + P    D +CP C  GFI    EE  +      P+  P D    
Sbjct: 7   HPGRYFCHCC--SVEIVPR-LPDYICPRCESGFIEELPEETRSTENGSAPSTAPTDQSRP 63

Query: 72  -------------------AF-LLDDLSTLLGMGP------------TRSFTDPSEF--- 96
                              AF + DD   +    P             R    PS     
Sbjct: 64  PLEHVDQHLFTLPQGYGQFAFGIFDDSFEIPTFPPGAQADDGRDPESRRERDHPSRHRYG 123

Query: 97  --NPFVFLQNYLQNLRANGA-SIQFVVEN--NSNVDPAA-GGAGAAFRLPANLGDYFIGP 150
              P   L       R  G  +++ +++   N  + PA     G    L +N  DY  G 
Sbjct: 124 ARQPRARLTTRRATGRHEGVPTLEGIIQQLVNGIITPATIPSLGPWGVLHSNPMDYAWGA 183

Query: 151 -GLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEE 209
            GL+ +I QL  N     G PPA K  I+ALP++ + E  + S   +C VCKD + L E 
Sbjct: 184 NGLDAIITQLL-NQFENTGPPPADKEKIQALPTVPVTEEHVGS-GLECPVCKDDYALGER 241

Query: 210 ARQMPCKHIYHPDCIMPWLELHNSCPVCRYEL 241
            RQ+PC H++H  CI+PWLE H+SCPVCR  L
Sbjct: 242 VRQLPCNHLFHDGCIVPWLEQHDSCPVCRKSL 273

Homo sapiens (taxid: 9606)

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

 Score = 99.8 bits (247), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 48/137 (35%), Positives = 81/137 (59%), Gaps = 4/137 (2%)

Query: 139 LPANLGDYFIG-PGLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQC 197
           L +N GDY  G  GL+ ++ QL     N  G PPA K  I +LP++ + +  +++   +C
Sbjct: 172 LHSNPGDYAWGQTGLDAIVTQLLGQLENT-GPPPADKEKITSLPTVTVTQEQVNT-GLEC 229

Query: 198 AVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYEQRRNGNGN 257
            VCK+ + + E+ RQ+PC H +H  CI+PWLELH++CPVCR  L  +D    Q ++   +
Sbjct: 230 PVCKEDYTVEEKVRQLPCNHFFHSSCIVPWLELHDTCPVCRKSLNGED-STRQTQSSEAS 288

Query: 258 GNNNSNNNNSMNQSFNL 274
            +N  +N++ ++  +  
Sbjct: 289 ASNRFSNDSQLHDRWTF 305

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

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score = 98.6 bits (244), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 50/111 (45%), Positives = 67/111 (60%), Gaps = 3/111 (2%)

Query: 132 GAGAAFRLPANLGDYFIGP-GLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMM 190
           G G    L +N  DY  G  GL+ +I QL  N     G PPA    I+ALP+I+I E  +
Sbjct: 163 GVGPWGVLHSNPMDYAWGANGLDTIITQLL-NQFENTGPPPADTEKIQALPTIQITEEHV 221

Query: 191 SSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYEL 241
            S   +C VCK+ + + E  RQ+PC H++H DCI+PWLE H++CPVCR  L
Sbjct: 222 GS-GLECPVCKEDYTVGESVRQLPCNHLFHNDCIIPWLEQHDTCPVCRKSL 271

Xenopus tropicalis (taxid: 8364)

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

 Score = 97.1 bits (240), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 51/111 (45%), Positives = 66/111 (59%), Gaps = 3/111 (2%)

Query: 132 GAGAAFRLPANLGDYFIGP-GLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMM 190
           G G    L +N  DY  G  GL+ +I QL  N     G PPA K  I+ALP++ + E  +
Sbjct: 168 GLGPWGVLHSNPMDYAWGANGLDAIITQLL-NQFENTGPPPADKEKIQALPTVPVTEEHV 226

Query: 191 SSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYEL 241
            S   +C VCKD + L E  RQ+PC H++H  CI+PWLE H+SCPVCR  L
Sbjct: 227 GS-GLECPVCKDDYGLGEHVRQLPCNHLFHDGCIVPWLEQHDSCPVCRKSL 276

Bos taurus (taxid: 9913)

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	352
251829631	340	zinc finger protein [Carica papaya]	0.886	0.917	0.621	1e-105
224125824	345	predicted protein [Populus trichocarpa]	0.875	0.892	0.584	1e-101
224118084	323	predicted protein [Populus trichocarpa]	0.826	0.900	0.563	5e-94
225457493	369	PREDICTED: E3 ubiquitin-protein ligase R	0.906	0.864	0.532	9e-90
147854704	371	hypothetical protein VITISV_042386 [Viti	0.892	0.846	0.533	9e-90
449439501	378	PREDICTED: E3 ubiquitin-protein ligase R	0.886	0.825	0.515	9e-88
302595801	338	RecName: Full=E3 ubiquitin-protein ligas	0.846	0.881	0.485	2e-82
356561816	369	PREDICTED: E3 ubiquitin-protein ligase R	0.931	0.888	0.498	4e-82
356531052	376	PREDICTED: E3 ubiquitin-protein ligase R	0.801	0.75	0.529	3e-78
297830662	330	zinc finger family protein [Arabidopsis	0.761	0.812	0.475	2e-75

>gi|251829631|gb|ACT21194.1| zinc finger protein [Carica papaya]

 Score =  386 bits (992), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 220/354 (62%), Positives = 248/354 (70%), Gaps = 42/354 (11%)

Query: 22  QMYFCHQCNRTVRVTPSP--SSDLVCPSCNGGFIEELETPNPSVNP-NPNPMDA---FL- 74
           Q YFC+QCNRTVR++PSP  SSDL+CP+CNGGF+EELE PNP+    N NP D+   FL 
Sbjct: 6   QPYFCYQCNRTVRISPSPCPSSDLLCPTCNGGFLEELENPNPNQQTLNLNPFDSPFPFLS 65

Query: 75  -------LDDLSTLLG-MGPTRSFT----DPSEFNPFVFLQNYLQNLRANGASIQFVVEN 122
                   DDLS   G M P  S T    D   FNPF+FLQNYLQ LRANGA+IQFV+EN
Sbjct: 66  SPNSPHPFDDLSAFFGGMVPPPSATARPNDTEVFNPFLFLQNYLQTLRANGANIQFVIEN 125

Query: 123 NSNVDPAAGGAGAAFRLPA--NLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAIEAL 180
           NS   P   G   AFRLP   NLGDYF+GPGLEQLIQQLAENDPNR+GTPPASKSAIEAL
Sbjct: 126 NS---PGGSGPSGAFRLPGSLNLGDYFLGPGLEQLIQQLAENDPNRHGTPPASKSAIEAL 182

Query: 181 PSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYE 240
           P+IKI + M  SDSSQCAVCKDSF L EEA+QMPCKHIYH  CI+PWLELHNSCPVCRYE
Sbjct: 183 PTIKIFQEMPDSDSSQCAVCKDSFALAEEAKQMPCKHIYHSQCILPWLELHNSCPVCRYE 242

Query: 241 LPTDDPDYEQRRNGNGN-GNNNSNNNNSMNQSFNLGFGFGGGGSGGNDGESGGNAETPRT 299
           LPTDD DYE R   N     N S + +++N           G +G  D     N ETPR+
Sbjct: 243 LPTDDADYEHRTRANRTPAQNVSGSTDAVN-------AVADGNAGNRD-----NPETPRS 290

Query: 300 VERRLRISLPWPF-NAFASRAETSGNSGSGSGGTNDGDSTSGNRGSEPRQEDLD 352
           VERR RI LPWPF ++F S AETS NSG+  G   D D+  G+RGSEPR EDLD
Sbjct: 291 VERRFRIFLPWPFRSSFGSGAETS-NSGTSGG---DADTNPGSRGSEPRHEDLD 340

Source: Carica papaya

Species: Carica papaya

Genus: Carica

Family: Caricaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224125824|ref|XP_002329726.1| predicted protein [Populus trichocarpa] gi|118486397|gb|ABK95038.1| unknown [Populus trichocarpa] gi|222870634|gb|EEF07765.1| predicted protein [Populus trichocarpa]

 Score =  374 bits (959), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 210/359 (58%), Positives = 246/359 (68%), Gaps = 51/359 (14%)

Query: 22  QMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELETPNPSVNPNPNPMDA-----FLLD 76
           Q+YFC+QCNRTV +TP P++ L CP+C+ GF+EEL++PNPS    PNP DA      LLD
Sbjct: 10  QLYFCYQCNRTVTITP-PTTALSCPNCHEGFLEELDSPNPS----PNPFDAGLGPALLLD 64

Query: 77  DLSTLLG-MGPTRS-----------------FTDPSEFNPFVFLQNYLQNLRANGASIQF 118
           D +++ G M PT                   F DP  FNPFVFLQNYLQ +RA GA+IQF
Sbjct: 65  DFASIFGGMNPTPRSSTTSTTATNSSSASPLFQDPDGFNPFVFLQNYLQTMRAGGANIQF 124

Query: 119 VVENNSNVDPAAGGAG-AAFRLPANLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAI 177
           V+ENN    P  GG     FR+PANLGDYFIGPGLEQLIQQLAENDPNRYGTPPA+KSA+
Sbjct: 125 VIENN----PGMGGMDPTGFRVPANLGDYFIGPGLEQLIQQLAENDPNRYGTPPAAKSAV 180

Query: 178 EALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVC 237
           E LP +K+ E +M SDSSQCAVCKDSFEL E A+Q+PCKHIYH DCIMPWLELHNSCPVC
Sbjct: 181 ENLPDVKVTEELMQSDSSQCAVCKDSFELGEVAKQIPCKHIYHKDCIMPWLELHNSCPVC 240

Query: 238 RYELPTDDPDYEQRRNGNGNGNNNSNNNNSMNQSFNLGFGFGGGGSGGNDGE-SGGNAET 296
           RYELPTDD DYEQR+   GNG+N  N N     +          G   +DG+ S GNA+T
Sbjct: 241 RYELPTDDQDYEQRK---GNGSNGVNQNVGGGIN---------SGGSISDGDNSDGNAQT 288

Query: 297 PRTVERRLRISLPWPFNAFASRAETSG--NSGSGSGGTNDGDST-SGNRGSEPRQEDLD 352
           PR  ERR RI  PWPF++   R+  S    S S SG  NDGDS  + N GS+ R+EDLD
Sbjct: 289 PR--ERRFRIPFPWPFSSGTGRSAGSSAEASNSRSGNNNDGDSRGNTNFGSDTREEDLD 345

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224118084|ref|XP_002317728.1| predicted protein [Populus trichocarpa] gi|222858401|gb|EEE95948.1| predicted protein [Populus trichocarpa]

 Score =  350 bits (898), Expect = 5e-94,   Method: Compositional matrix adjust.
 Identities = 200/355 (56%), Positives = 234/355 (65%), Gaps = 64/355 (18%)

Query: 21  PQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELETPNPSVNPNPNPMD-AFLLDDLS 79
           PQ+YFC+QC+RTV +TPSP+SDL CP+C  GF+EE E+PNPS NP  + +  A LLD+ +
Sbjct: 10  PQLYFCYQCDRTVTITPSPTSDLSCPNCQEGFLEECESPNPSSNPVDSGLGPAILLDEFA 69

Query: 80  TLLG-MGPTRS----------------FTDPSEFNPFVFLQNYLQNLRANGASIQFVVEN 122
           ++ G M PT                  F DP  FNPF FLQNYLQ +RA GA+IQFV+EN
Sbjct: 70  SIFGGMAPTPRSSNNSTTTNSSSASPLFQDPDGFNPFAFLQNYLQTMRAGGANIQFVIEN 129

Query: 123 NSNVDPAAGGAGAAFRLPANLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPS 182
           NS +    G     FRLPANLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSA+E LP 
Sbjct: 130 NSGM---GGMDTTGFRLPANLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAVENLPD 186

Query: 183 IKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP 242
           IK+ + ++ SDSSQCAVCKDSFEL EEA+Q+PCKHIYH DCI PWLELHNSCPVCRYELP
Sbjct: 187 IKVTKELLESDSSQCAVCKDSFELGEEAKQIPCKHIYHKDCITPWLELHNSCPVCRYELP 246

Query: 243 TDDPDYEQRRNGNGNGNNNSNNNNSMNQSFNLGFGFGGGGSGGNDGESGGNAETPRTVER 302
           TDDPDYEQR+ GNGN                                   +  TPR  +R
Sbjct: 247 TDDPDYEQRK-GNGN-----------------------------------DVVTPR--DR 268

Query: 303 RLRISLPWPF----NAFASRAETSGNSGSGSGGTNDGDST-SGNRGSEPRQEDLD 352
           R RI+  WPF     +  S   ++G S SGSG  ND DS  + N GSE R+EDLD
Sbjct: 269 RFRIAFQWPFSSGSGSGRSVGSSAGASNSGSGNNNDEDSRGNTNFGSETREEDLD 323

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225457493|ref|XP_002267134.1| PREDICTED: E3 ubiquitin-protein ligase RING1 isoform 1 [Vitis vinifera] gi|359491811|ref|XP_003634328.1| PREDICTED: E3 ubiquitin-protein ligase RING1 isoform 2 [Vitis vinifera]

 Score =  336 bits (862), Expect = 9e-90,   Method: Compositional matrix adjust.
 Identities = 190/357 (53%), Positives = 222/357 (62%), Gaps = 38/357 (10%)

Query: 21  PQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELETPNPSVNPNPNPMDAFLLDDLST 80
           PQ YFC+QCN TV +TPSP+SD +CP CN GF+EE+E PNP+  P P P       DL +
Sbjct: 22  PQSYFCYQCNLTVSITPSPTSDPLCPHCNDGFLEEVENPNPNPIPVPIPNPFLGFSDLPS 81

Query: 81  LLGMGPTRSF---------------------------TDPSEFNPFVFLQNYLQNLRANG 113
           L   G T +                             DP  F+PF FLQNYLQ LRA G
Sbjct: 82  LSAAGATATAFPPLVFSTAAGGSIDLQNSVDFPGLFGADPDAFHPFAFLQNYLQTLRAGG 141

Query: 114 ASIQFVVENNSNVDPAAGGAGAAFRLPANLGDYFIGPGLEQLIQQLAENDPNRYGTPPAS 173
            ++QFV++ NS            FRL  NLGDYFIGPGLEQLIQQLAENDPNRYGTPPAS
Sbjct: 142 TNVQFVIDGNS--------PEGTFRLSPNLGDYFIGPGLEQLIQQLAENDPNRYGTPPAS 193

Query: 174 KSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNS 233
           KSAIE LP+I+I   ++ +DSSQCAVCKDSFEL+EEA+QMPCKHIYH DCI+PWLELHNS
Sbjct: 194 KSAIEGLPTIRITVELLGTDSSQCAVCKDSFELDEEAKQMPCKHIYHNDCILPWLELHNS 253

Query: 234 CPVCRYELPTDDPDYEQRRNGNGNGNNNSNNNNSMNQSFNLGFGFGGGGSGGNDGESGGN 293
           CPVCRYELPTDDPDYE R  G G  N    N  ++  +        G   G        N
Sbjct: 254 CPVCRYELPTDDPDYEHRTRG-GQVNQTGGNAAAVAAAGAASNSASGAAGGAAVSGENPN 312

Query: 294 AETPRTVERRLRISLPWPFNAFASRAETSGNSGSGSGGTNDGDSTSGNRGSEPRQED 350
            +TPRT +R  RIS PWPF  F S AETS  + +  GG+N G+  +   GSE RQ D
Sbjct: 313 PQTPRTADRMFRISFPWPFRTFGSPAETS--NSNNDGGSNPGNRANQESGSENRQGD 367

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147854704|emb|CAN79596.1| hypothetical protein VITISV_042386 [Vitis vinifera]

 Score =  336 bits (862), Expect = 9e-90,   Method: Compositional matrix adjust.
 Identities = 193/362 (53%), Positives = 223/362 (61%), Gaps = 48/362 (13%)

Query: 21  PQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELETPNPSVNPNPNPMDAFLLDDLST 80
           PQ YFC+QCN TV +TPSP+SD +CP CN GF+EE+E PNP+  P P P       DL +
Sbjct: 24  PQSYFCYQCNLTVSITPSPTSDPLCPHCNDGFLEEVENPNPNPIPVPIPNPFLGFSDLPS 83

Query: 81  LLGMGPTRSF---------------------------TDPSEFNPFVFLQNYLQNLRANG 113
           L   G T +                             DP  F+PF FLQNYLQ LRA G
Sbjct: 84  LSAAGATATAFPPLVFSTAAGGSIDLQNSVDFPGLFGADPDAFHPFAFLQNYLQTLRAGG 143

Query: 114 ASIQFVVENNSNVDPAAGGAGAAFRLPANLGDYFIGPGLEQLIQQLAENDPNRYGTPPAS 173
            ++QFV++ NS            FRL  NLGDYFIGPGLEQLIQQLAENDPNRYGTPPAS
Sbjct: 144 TNVQFVIDGNS--------PEGTFRLSPNLGDYFIGPGLEQLIQQLAENDPNRYGTPPAS 195

Query: 174 KSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNS 233
           KSAIE LP+I+I   ++ +DSSQCAVCKDSFEL+EEA+QMPCKHIYH DCI+PWLELHNS
Sbjct: 196 KSAIEGLPTIRITVELLGTDSSQCAVCKDSFELDEEAKQMPCKHIYHNDCILPWLELHNS 255

Query: 234 CPVCRYELPTDDPDYEQRRNGNGNGNNNSNNNNSMNQSFNLGFGFGGGGSGGNDGESGGN 293
           CPVCRYELPTDDPDYE R  G G  N    N  ++  +        G   G        N
Sbjct: 256 CPVCRYELPTDDPDYEHRTRG-GQVNQTGGNAAAVAAAGAASNSASGAAGGAAVSGENPN 314

Query: 294 AETPRTVERRLRISLPWPFNAFASRAETSGNSGSGSGGTNDGDSTSGNR-----GSEPRQ 348
            +TPRT +R  RIS PWPF  F S AETS ++       NDG+S  GNR     GSE RQ
Sbjct: 315 PQTPRTADRMFRISFPWPFRTFGSPAETSNSN-------NDGESNPGNRANQESGSENRQ 367

Query: 349 ED 350
            D
Sbjct: 368 GD 369

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449439501|ref|XP_004137524.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like isoform 1 [Cucumis sativus] gi|449439503|ref|XP_004137525.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like isoform 2 [Cucumis sativus] gi|449439505|ref|XP_004137526.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like isoform 3 [Cucumis sativus] gi|449503086|ref|XP_004161827.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like isoform 1 [Cucumis sativus] gi|449503089|ref|XP_004161828.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like isoform 2 [Cucumis sativus] gi|449503091|ref|XP_004161829.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like isoform 3 [Cucumis sativus]

 Score =  330 bits (845), Expect = 9e-88,   Method: Compositional matrix adjust.
 Identities = 195/378 (51%), Positives = 241/378 (63%), Gaps = 66/378 (17%)

Query: 21  PQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELETPNPSVNPNPNPMDAF------- 73
           PQ+YFC+ CNRTV +TPS SSDL+CP+CN  F+EE+E+PNP+ +P  NP  +F       
Sbjct: 21  PQLYFCYTCNRTVTITPSSSSDLLCPNCNDSFVEEMESPNPNPSPVSNPFLSFTSEAFPP 80

Query: 74  -----------------------------LLDDLSTLLGMGPTRSFT---DPSEFNPFVF 101
                                        +++DLS LLG G  RS +   +P  FNP +F
Sbjct: 81  FSTGGGGNGGFPIIFSTTSSSGGIGGGGSMMNDLSALLGGGSLRSSSSLQNPDGFNPLLF 140

Query: 102 LQNYLQNLRANGASIQFVVENNSNVDPAAGGAGAAFRLPAN--LGDYFIGPGLEQLIQQL 159
           LQNYLQ+     A++Q V++N          +G AF  P+N  LGDYF GPGLEQLIQQL
Sbjct: 141 LQNYLQS-----ANVQLVIQN---------ASGEAFHPPSNFNLGDYFFGPGLEQLIQQL 186

Query: 160 AENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIY 219
           AENDPNRYGTPPASKSAIE LP IKI E ++++DSSQCAVCKD+FEL+E A+ MPCKHIY
Sbjct: 187 AENDPNRYGTPPASKSAIEGLPDIKITEELLATDSSQCAVCKDTFELDEVAKLMPCKHIY 246

Query: 220 HPDCIMPWLELHNSCPVCRYELPTDDPDYEQRRNGNGNGNNNSNNNNSMNQSFNLGFGFG 279
           H DCI+PWLELHNSCPVCRYELPTDDPDYEQR  G+   N + + +     S       G
Sbjct: 247 HADCIIPWLELHNSCPVCRYELPTDDPDYEQRTRGSSAPNRSQSESQPFGDS-----STG 301

Query: 280 GGGSGGNDGESGGNAETPRTVERRL-RISLPWPFNAFASRAETSGNSGSGSGGTNDGDST 338
           G    G+D  S  N++T +  ERR+ RI+ PWPF  F S AETS + G  + G ND + +
Sbjct: 302 GENVVGSDPNSDENSQTQQMGERRVRRIAFPWPFRGFGSAAETSNSGGGNNSGNND-EPS 360

Query: 339 SGNRG----SEPRQEDLD 352
           S NRG    SEP QEDLD
Sbjct: 361 SRNRGSQGSSEPMQEDLD 378

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302595801|sp|P0CH30.1|RING1_GOSHI RecName: Full=E3 ubiquitin-protein ligase RING1; AltName: Full=RING finger protein 1 gi|298155591|gb|ADI58769.1| RING-type ubiquitin E3 ligase [Gossypium hirsutum]

 Score =  312 bits (799), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 188/387 (48%), Positives = 227/387 (58%), Gaps = 89/387 (22%)

Query: 4   SGGNFGGAAAAAPPQQEPQMYFCHQCNRTVRVTPSP-SSDLVCPSCNGGFIEELETPNPS 62
           S GN  G   A       + +FC+QCNRTV VT SP SSD  CP CN GF+EE + PNP+
Sbjct: 3   SDGNVTGGGGANTVGVTNKPFFCYQCNRTVNVTISPPSSDPTCPICNEGFLEEYDNPNPN 62

Query: 63  -----VNPNPNPM---DAFLL--DDLSTLLGM------------------------GPTR 88
                +NPNPN +   D FL   D  ++LL +                        GPTR
Sbjct: 63  QGSGFLNPNPNSIPFHDLFLTLSDPFASLLPLLFPSSSSTTTSSSASIDPNNPSLSGPTR 122

Query: 89  SFT-DPSEFNPFVFLQNYLQNLRANGASIQFVVENNSNVDPAAGGAGAAFRLPANLGDYF 147
           S   DP  F+PF F+QN+L +LR++GA I+FV++NN         +   FRLPAN+GDYF
Sbjct: 123 SGRGDPFAFDPFTFIQNHLNDLRSSGAQIEFVIQNNP--------SDQGFRLPANIGDYF 174

Query: 148 IGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELN 207
           IGPGLEQLIQQLAENDPNRYGTPPASKSAIEALP + I ++ ++S+ +QCAVC D FE  
Sbjct: 175 IGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPLVNITKSNLNSEFNQCAVCMDDFEEG 234

Query: 208 EEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYEQRRNGNGNGNNNSNNNNS 267
            EA+QMPCKH+YH DC++PWLELHNSCPVCR+ELPTDDPDYE+R  G             
Sbjct: 235 TEAKQMPCKHLYHKDCLLPWLELHNSCPVCRHELPTDDPDYERRVRG------------- 281

Query: 268 MNQSFNLGFGFGGGGSGGNDGESGGNAETP--RTVERRLRISLPWPFNAFASRAETSGNS 325
                        G SGGNDG++ G       RTVER  RISLPWPF A           
Sbjct: 282 -----------AQGTSGGNDGDNSGQRSDGDNRTVERSFRISLPWPFQARGP-------- 322

Query: 326 GSGSGGTNDGDSTSGNRGSEPRQEDLD 352
                G   GD+      +E RQEDLD
Sbjct: 323 -----GPAPGDN------AETRQEDLD 338

Source: Gossypium hirsutum

Species: Gossypium hirsutum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356561816|ref|XP_003549174.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like [Glycine max]

 Score =  311 bits (796), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 196/393 (49%), Positives = 235/393 (59%), Gaps = 65/393 (16%)

Query: 1   MSFSGGNFGGAAAAAPPQQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELETPN 60
           MS +GG+ GG A +  P+Q    YFCHQCNRTV ++PSPSSDL+CP+CNGGF+EELE P 
Sbjct: 1   MSSAGGDRGGGATSGDPRQ----YFCHQCNRTVSISPSPSSDLLCPTCNGGFLEELEFPI 56

Query: 61  -----------------------PSVNPNPNPMDAFLLDDLSTLLGMGPTRSFTDPSEFN 97
                                  P V P       F  +DLS L G  P  +      FN
Sbjct: 57  PNPNPNPPNPFFPDFPLAGAATIPLVLPGAAASPPF--EDLSALFGNRPDAA---ADAFN 111

Query: 98  PFVFLQNYLQNLRANGASIQFVVENNSNVDPAAGGAGAAFRLP-ANLGDYFIGPGLEQLI 156
           P VFLQNY Q LRA G ++Q V+E        +G  G AFR P    GDYF GPGLE+LI
Sbjct: 112 PLVFLQNYFQTLRA-GGNLQLVIE--------SGDPGGAFRFPGVTHGDYFFGPGLEELI 162

Query: 157 QQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCK 216
           Q LAENDPNRYGTPPASKS +E LP + + E +++SDSSQCAVCKD+FEL E A+Q+PCK
Sbjct: 163 QHLAENDPNRYGTPPASKSVVEGLPDVSVTEELLASDSSQCAVCKDTFELGETAKQIPCK 222

Query: 217 HIYHPDCIMPWLELHNSCPVCRYELPTDDPDYEQRRNGNGNGNNNSNNNNSMNQ-SFNLG 275
           HIYH DCI+PWLELHNSCPVCRYELPTDDPDYEQR    G+G   +  + +  Q ++N+ 
Sbjct: 223 HIYHADCILPWLELHNSCPVCRYELPTDDPDYEQRARRGGSGGGGAAGSGAAPQVNWNMA 282

Query: 276 FGFGGGGSGGNDGESGGNAETPRTVERRLRISLPWPFNAFASRAET-----------SGN 324
                    G   +S G+     +  RR R+SLPWPF  FA  +             + N
Sbjct: 283 L------GSGGSADSSGSGGGDNSQRRRFRVSLPWPFRQFAETSNVGSGNNDSNNNNNSN 336

Query: 325 SGSGSGGTNDGDSTSGNRG-----SEPRQEDLD 352
           S S S G N G S SGNRG     SE RQEDLD
Sbjct: 337 SNSDSSGNNGGQSNSGNRGNQNFDSETRQEDLD 369

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356531052|ref|XP_003534092.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like isoform 1 [Glycine max] gi|356531054|ref|XP_003534093.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like isoform 2 [Glycine max]

 Score =  298 bits (763), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 171/323 (52%), Positives = 203/323 (62%), Gaps = 41/323 (12%)

Query: 20  EPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELETPN------------------- 60
           EP+ YFCHQCNRTV ++PSPSSDL+CP+CNGGF+EELE P                    
Sbjct: 16  EPRQYFCHQCNRTVSISPSPSSDLLCPTCNGGFLEELEIPIPDPNPPNPFFSDFPLGGAA 75

Query: 61  --PSVNPNPNPMDAFLLDDLSTLLGMGPTRSFTDPSEFNPFVFLQNYLQNLRANGA-SIQ 117
             P V P       F   DLS L G     + +D   FNP VFLQNY Q LRA G  ++Q
Sbjct: 76  TIPLVLPGAATSPPF--GDLSALFGDRSDAAASD--AFNPLVFLQNYFQTLRAGGGGNLQ 131

Query: 118 FVVENNSNVDPAAGGAGAAFRLP-ANLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSA 176
            V+E        +G  G  FR P    GDYF GPGLE+LIQ LAENDPNRYGTPPASKSA
Sbjct: 132 LVIE--------SGDPGGVFRFPGVTHGDYFFGPGLEELIQHLAENDPNRYGTPPASKSA 183

Query: 177 IEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPV 236
           +E LP + + E +++SDSSQCAVCKD+FEL E A+Q+PCKHIYH DCI+PWLELHNSCPV
Sbjct: 184 VEGLPDVSVTEELLASDSSQCAVCKDTFELGETAKQIPCKHIYHADCILPWLELHNSCPV 243

Query: 237 CRYELPTDDPDYEQRRNGNGNGNNNSNNNNSM---NQSFNLGFGFGGGGSGGNDGESGGN 293
           CRYELPTDDPDYEQR    G G +  +   S      ++N+  G  GG +  + G   G 
Sbjct: 244 CRYELPTDDPDYEQRARRGGGGGSGGDGAGSGAAPQVNWNMALGPAGGSADSSGGGGSGG 303

Query: 294 AETPRTVERRLRISLPWPFNAFA 316
             + R   RR R+SLPWPF  FA
Sbjct: 304 DSSQR---RRFRVSLPWPFRQFA 323

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297830662|ref|XP_002883213.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata] gi|297329053|gb|EFH59472.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  288 bits (738), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 162/341 (47%), Positives = 205/341 (60%), Gaps = 73/341 (21%)

Query: 4   SGGNFGGAAAAAPPQQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELE--TPNP 61
           SG N  G+AA  P  +  +M+FC+QCNRTV ++ S S+D  CP CN GF+EE E   PNP
Sbjct: 3   SGVNSTGSAATEP--EVDKMFFCYQCNRTVTISISSSADPFCPICNQGFLEEYEDPNPNP 60

Query: 62  SVNPNPNPMDAF--LLDDLSTLLGM-------GPT------RSFTDPS------------ 94
           S+N NPN +D+   + D  STLL +        P+       SF  PS            
Sbjct: 61  SLNFNPNSVDSLFPMADPFSTLLPLLFGSSAASPSGIDLMSSSFFAPSMQPQARSTQQNP 120

Query: 95  ---EFNPFVFLQNYLQNLRANGASIQFVVENNSNVDPAAGGAGAAFRLPANLGDYFIGPG 151
               F+PF FLQN+LQNLR++G  +QFV+EN+    P+  G     R+P N GDYF GPG
Sbjct: 121 QSDAFDPFTFLQNHLQNLRSSGTHVQFVIENH----PSDLGN----RMPGNFGDYFFGPG 172

Query: 152 LEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEAR 211
           LEQLIQQLAENDPNRYGTPPASKSAI+ LP++K+ + M+ S+ +QCAVC D FE   + +
Sbjct: 173 LEQLIQQLAENDPNRYGTPPASKSAIDGLPTVKVTKDMLKSEMNQCAVCMDEFEDGSDVK 232

Query: 212 QMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYEQRRNGNGNGNNNSNNNNSMNQS 271
           QMPCKH++H DC++PWL+LHNSCPVCR+ELPTDDPDYE R  G                 
Sbjct: 233 QMPCKHVFHQDCLLPWLQLHNSCPVCRFELPTDDPDYENRTQG----------------- 275

Query: 272 FNLGFGFGGGGSGGNDGESGGNAETPRTVERRLRISLPWPF 312
                   G G G  +G+     +TPR       I LPWPF
Sbjct: 276 ----IQASGDGQGSVEGQ-----QTPR-----FSIQLPWPF 302

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	352
TAIR|locus:2092231	328	AT3G19950 [Arabidopsis thalian	0.602	0.646	0.518	1.6e-59
TAIR|locus:2193874	351	AT1G55530 [Arabidopsis thalian	0.343	0.344	0.554	4.8e-48
TAIR|locus:2161058	396	ATCRT1 [Arabidopsis thaliana (	0.284	0.252	0.638	9.5e-46
TAIR|locus:2092895	315	AT3G13430 [Arabidopsis thalian	0.286	0.320	0.626	2e-41
TAIR|locus:2131463	356	AT4G26400 [Arabidopsis thalian	0.275	0.272	0.524	1.3e-39
TAIR|locus:2102569	320	RZF1 "AT3G56580" [Arabidopsis	0.613	0.675	0.414	3.7e-39
TAIR|locus:2058465	328	RHC1A "RING-H2 finger C1A" [Ar	0.627	0.673	0.384	3e-37
TAIR|locus:2195573	327	AT1G60360 [Arabidopsis thalian	0.306	0.330	0.513	1.2e-35
TAIR|locus:2075175	395	RDUF1 "RING and Domain of Unkn	0.613	0.546	0.354	1.1e-34
TAIR|locus:2148318	407	RDUF2 "RING and Domain of Unkn	0.619	0.535	0.357	2.8e-34

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

 Score = 585 (211.0 bits), Expect = 1.6e-59, Sum P(2) = 1.6e-59
 Identities = 115/222 (51%), Positives = 145/222 (65%)

Query:    30 NRTVRVTPSPSSDLVCPSCNGGFIEELETXXXXXXXXXXXMDAFLLDDLSTLLGMGPTRS 89
             N+++   P+ SSD   P  +  F   L             MD   L   S       T+ 
Sbjct:    59 NQSLNFNPN-SSDSFFPMADP-FSTLLPLIFGSSAAAPSGMDFMSLFGPSMQPQARSTQQ 116

Query:    90 FTDPSEFNPFVFLQNYLQNLRANGASIQFVVENNSNVDPAAGGAGAAFRLPANLGDYFIG 149
                   F+PF FLQN+LQ LR++G   +FV+EN+ + DP  G      R+P N GDYF G
Sbjct:   117 NPQSDAFDPFTFLQNHLQTLRSSGTHFEFVIENHPS-DP--GN-----RMPGNFGDYFFG 168

Query:   150 PGLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEE 209
             PGLEQLIQQLAENDPNRYGTPPASKSAI+ALP++K+ + M+ S+ +QCAVC D FE   +
Sbjct:   169 PGLEQLIQQLAENDPNRYGTPPASKSAIDALPTVKVTKDMLKSEMNQCAVCMDEFEDGSD 228

Query:   210 ARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYEQR 251
              +QMPCKH++H DC++PWLELHNSCPVCR+ELPTDDPDYE R
Sbjct:   229 VKQMPCKHVFHQDCLLPWLELHNSCPVCRFELPTDDPDYENR 270

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

GO:0010200 "response to chitin" evidence=RCA

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

 Score = 393 (143.4 bits), Expect = 4.8e-48, Sum P(3) = 4.8e-48
 Identities = 71/128 (55%), Positives = 91/128 (71%)

Query:   119 VVENNSNVDPAAGGAGAAFRLPA-NLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAI 177
             ++ N SN       +     +PA +LGDYFIGPG E L+Q+LAENDPNRYGTPPA K A+
Sbjct:   150 ILINTSNQTITVQNSADMDSVPAGSLGDYFIGPGFEMLLQRLAENDPNRYGTPPAKKEAV 209

Query:   178 EALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVC 237
             EAL ++KI E +      QC+VC D FE+  EA+ MPC H +H DC++PWLELH+SCPVC
Sbjct:   210 EALATVKIEETL------QCSVCLDDFEIGTEAKLMPCTHKFHSDCLLPWLELHSSCPVC 263

Query:   238 RYELPTDD 245
             RY+LP D+
Sbjct:   264 RYQLPADE 271

GO:0005737 "cytoplasm" evidence=ISM

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

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

 Score = 377 (137.8 bits), Expect = 9.5e-46, Sum P(3) = 9.5e-46
 Identities = 69/108 (63%), Positives = 84/108 (77%)

Query:   142 NLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCK 201
             +LGDYFIGPGL+ L+Q LAENDPNR GTPPA K A+EALP++KI E +      QC+VC 
Sbjct:   210 SLGDYFIGPGLDLLLQHLAENDPNRQGTPPARKEAVEALPTVKIMEPL------QCSVCL 263

Query:   202 DSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPT--DDPD 247
             D FE   EA++MPCKH +H  CI+PWLELH+SCPVCR+ELP+  DD D
Sbjct:   264 DDFEKGTEAKEMPCKHKFHVRCIVPWLELHSSCPVCRFELPSSADDDD 311

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

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

 Score = 380 (138.8 bits), Expect = 2.0e-41, Sum P(2) = 2.0e-41
 Identities = 67/107 (62%), Positives = 85/107 (79%)

Query:   142 NLGDYFIGPGLEQLIQQLAEND-PNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVC 200
             +LGDYFIGPG E L+Q+LAEND  NRYGTPPA+K A+EAL  +KI ++++     QC+VC
Sbjct:   174 SLGDYFIGPGFETLLQRLAENDLNNRYGTPPATKEAVEALAMVKIEDSLL-----QCSVC 228

Query:   201 KDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPD 247
              D FE+  EA++MPCKH +H DC++PWLELH+SCPVCRY LPT D D
Sbjct:   229 LDDFEIGMEAKEMPCKHKFHSDCLLPWLELHSSCPVCRYLLPTGDDD 275

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0006944 "cellular membrane fusion" evidence=RCA

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

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

 Score = 323 (118.8 bits), Expect = 1.3e-39, Sum P(3) = 1.3e-39
 Identities = 54/103 (52%), Positives = 77/103 (74%)

Query:   143 LGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKD 202
             +GDYF+G  L+ L++ LA+ND  R+G+ PA K  ++ LP++KI+E++      QC++C D
Sbjct:   193 IGDYFVGSSLDHLLEHLADNDSIRHGSLPARKEVVDNLPTVKISESL------QCSICLD 246

Query:   203 SFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD 245
              F+   EA++MPCKH +H  CI+PWLELH+SCPVCRYELP DD
Sbjct:   247 DFDKGSEAKEMPCKHKFHIRCIVPWLELHSSCPVCRYELPPDD 289

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

GO:0010200 "response to chitin" evidence=IEP

GO:0000303 "response to superoxide" evidence=RCA

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

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

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

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

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

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

 Score = 418 (152.2 bits), Expect = 3.7e-39, P = 3.7e-39
 Identities = 95/229 (41%), Positives = 121/229 (52%)

Query:    24 YFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELETXXXXXXX------XXXXMDAFLLDD 77
             ++CH+C R V +    + D VC  C GGF+EE++                  M+AF    
Sbjct:     8 HWCHRCQRAVWLR---ARDAVCSYCGGGFVEEIDIGPSRAHRDVERDPTFDLMEAFSAFM 64

Query:    78 LSTLLGMGPTRSFTDPSEFNPFVFLQNYLQNLRANG-ASIQFVVENNSNVDPAAGGA--G 134
              S L      R  +            N    L   G A  +    +NS+V+    GA  G
Sbjct:    65 RSRLAERSYDREISGRLGSAGSESFSNLAPLLIFGGQAPFRLAGGDNSSVEAFVNGAAPG 124

Query:   135 AAFRLPANLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDS 194
                    N GDYF GPGLE+LI+QL+    +R G PPA KS+I+ALP+IKI +  + S  
Sbjct:   125 IGIARGTNAGDYFFGPGLEELIEQLSSGTHHR-GPPPAPKSSIDALPTIKITQKHLKSSD 183

Query:   195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPT 243
             S C VCKD FEL  EA+QMPC HIYH DCI+PWL  HNSCPVCR ELP+
Sbjct:   184 SHCPVCKDEFELKSEAKQMPCHHIYHSDCIVPWLVQHNSCPVCRKELPS 232

GO:0005575 "cellular_component" evidence=ND

GO:0008270 "zinc ion binding" evidence=ISS

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

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

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

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

 Score = 400 (145.9 bits), Expect = 3.0e-37, P = 3.0e-37
 Identities = 95/247 (38%), Positives = 125/247 (50%)

Query:    24 YFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELETXXXX-------------XXXXXXXM 70
             ++CH+C R VR+      + VC  C GGF+EEL+                         M
Sbjct:     8 HWCHRCQRAVRLH---GQEPVCFYCGGGFVEELDMAQASPFDMFRSHRGVVERDQTFDLM 64

Query:    71 DAFLLDDLSTLLGMGPTRSFTDPS-EFNPFVFLQNY--LQNLRANGASIQFVVENNSNVD 127
             DAF +   + L      R     +    P    +N+  L  L   G  + + +  ++ V+
Sbjct:    65 DAFSVFMRNRLAERSHDREIRGRTISSGP----ENFPGLAPLLIFGGQVPYRLTGDNAVE 120

Query:   128 PAAGGAGAAFRLP-ANLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKIN 186
                 G      +   N GDYF GPGLE+L +QL+     R G PPA +SAI+ALP+IKI 
Sbjct:   121 ALFNGGSPGIGITRGNTGDYFFGPGLEELFEQLSAGTTRR-GPPPAPRSAIDALPTIKIA 179

Query:   187 EAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPT-DD 245
             +  + S  S C VCKD FEL  EA+QMPC HIYH DCI+PWL  HNSCPVCR ELP+   
Sbjct:   180 QRHLRSSDSNCPVCKDEFELGSEAKQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPSASG 239

Query:   246 PDYEQRR 252
             P   Q R
Sbjct:   240 PSSSQNR 246

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

GO:0005618 "cell wall" evidence=IDA

TAIR|locus:2195573 AT1G60360 [Arabidopsis thaliana (taxid:3702)]

 Score = 305 (112.4 bits), Expect = 1.2e-35, Sum P(2) = 1.2e-35
 Identities = 57/111 (51%), Positives = 76/111 (68%)

Query:   142 NLGDYFIGPG-LEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVC 200
             N  DYF G   LEQLI+QL ++D  R G PPAS+  I +LPS+KI    +++D SQC VC
Sbjct:   170 NSHDYFTGASSLEQLIEQLTQDD--RPGPPPASEPTINSLPSVKITPQHLTNDMSQCTVC 227

Query:   201 KDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYEQR 251
              + F +  +A ++PCKHIYH DCI+PWL L+NSCP+CR +LP  +   E R
Sbjct:   228 MEEFIVGGDATELPCKHIYHKDCIVPWLRLNNSCPICRRDLPLVNTVAESR 278

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

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

 Score = 376 (137.4 bits), Expect = 1.1e-34, P = 1.1e-34
 Identities = 84/237 (35%), Positives = 128/237 (54%)

Query:    24 YFCHQCNRTVRVTPSPSSD--LVCPSCNGGFIEELETXXXXXXXXXXXMDAFLLDDLSTL 81
             Y+C+ C R + V     ++  ++CP CNGGFIEE+E                +     T 
Sbjct:    31 YWCYSCTRFISVWEDQDANAGVLCPYCNGGFIEEIEDSSNSTVAAIPASTPEVRSVEETH 90

Query:    82 LGMGPTRSFTDPSEFNPFVFLQN--------YLQNLRANGASIQFVVENNSNVDPAAGGA 133
               +   R     + FNP + L           ++N   +GA+     E  +       G+
Sbjct:    91 RSIIRRRRSNRRTSFNPVIVLHGGGGGGAGERVENEEGDGATR----ERRAYEFYYDDGS 146

Query:   134 GAAFR-LPANLGDYFIGPGLEQLIQQLAE-----NDPNRYGTPPASKSAIEALPSIKINE 187
             G+  R LP ++ +  +G G E+L++QL++     N   R G PPASKSAIE+LP ++I++
Sbjct:   147 GSGLRPLPDSVSEILMGSGFERLLEQLSQIEASGNGIGRSGNPPASKSAIESLPRVEISD 206

Query:   188 AMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTD 244
                 ++++ CAVC + FE   E R+MPCKHI+H DCI+PWL + NSCPVCR+ELP+D
Sbjct:   207 CHTKAEAN-CAVCTEVFEAGIEGREMPCKHIFHGDCIVPWLSIRNSCPVCRFELPSD 262

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

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

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

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

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

GO:0051865 "protein autoubiquitination" evidence=IDA

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

GO:0009611 "response to wounding" evidence=RCA

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

GO:0009693 "ethylene biosynthetic process" evidence=RCA

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

GO:0035556 "intracellular signal transduction" evidence=RCA

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

 Score = 372 (136.0 bits), Expect = 2.8e-34, P = 2.8e-34
 Identities = 83/232 (35%), Positives = 126/232 (54%)

Query:    24 YFCHQCNRTVRVTPSPSSDLV----CPSCNGGFIEELETXXXXXXXXXXXMDAFLLDDLS 79
             Y+C+ C R V V     +  V    CP C+GGFIE++                 +    +
Sbjct:    18 YWCYSCTRFVSVWADQGTTTVGSVACPHCDGGFIEQINDSSSAATELTIPASTEVRSINN 77

Query:    80 TLLGM-GPTRSFTDPSEFNPFVFLQNYLQNLRANGASIQFVVENNSNVDPAAGGAGAAFR 138
                 +    RS   PS FNP + LQ      R  G       +  +       G+G+  R
Sbjct:    78 NRRSVIRRRRSGRRPS-FNPVIVLQGGAGE-REEGEEGDAARDRRAFEFYYDDGSGSGLR 135

Query:   139 -LPANLGDYFIGPGLEQLIQQLAENDPN-----RYGTPPASKSAIEALPSIKINEAMMSS 192
              LP ++ +  +G G E+L++QL++ + +     R G PPASKSAIE+LP ++I++  + S
Sbjct:   136 PLPDSVSEILMGSGFERLLEQLSQIEASATGIGRSGNPPASKSAIESLPRVEISDCHIGS 195

Query:   193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTD 244
             +++ CAVC + FE   EAR+MPCKH++H DCI+PWL + NSCPVCR+ELP++
Sbjct:   196 EAN-CAVCTEIFETETEAREMPCKHLFHDDCIVPWLSIRNSCPVCRFELPSE 246

GO:0005634 "nucleus" evidence=ISM

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

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

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

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

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

GO:0051865 "protein autoubiquitination" evidence=IDA

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

GO:0009693 "ethylene biosynthetic process" evidence=RCA

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

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

GO:0035556 "intracellular signal transduction" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: estExt_fgenesh4_pg.C_1220024 SubName- Full=Putative uncharacterized protein; (345 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	352
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	1e-17
pfam14369	34	pfam14369, zf-RING_3, zinc-finger	7e-15
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	4e-12
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	2e-09
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	3e-09
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	3e-09
smart00184	40	smart00184, RING, Ring finger	2e-08
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	2e-06
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	6e-06
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	7e-06
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	4e-04
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	5e-04

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

 Score = 75.5 bits (186), Expect = 1e-17
 Identities = 19/43 (44%), Positives = 28/43 (65%)

Query: 196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCR 238
           +C +C D FE  EE   +PC H++H +C+  WL   N+CP+CR
Sbjct: 2   ECPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCR 44

Length = 46

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

 Score = 67.2 bits (165), Expect = 7e-15
 Identities = 20/35 (57%), Positives = 26/35 (74%), Gaps = 1/35 (2%)

Query: 22 QMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEEL 56
            Y+C+QC+R VR+ PS  SD VCP C GGF+EE+
Sbjct: 1  SRYWCYQCDRFVRIAPSGDSD-VCPRCGGGFVEEI 34

Length = 34

>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 = 60.2 bits (146), Expect = 4e-12
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 3/47 (6%)

Query: 196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYEL 241
           +C +C + F   E    +PC H++   CI  WL+   N+CP+CR  +
Sbjct: 1   ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 52.8 bits (127), Expect = 2e-09
 Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 10/52 (19%)

Query: 197 CAVCKDSFE--------LNEEA--RQMPCKHIYHPDCIMPWLELHNSCPVCR 238
           CA+C++ F+          ++       C H +H  CI  WL+  N+CP+CR
Sbjct: 22  CAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73

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

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

 Score = 57.7 bits (139), Expect = 3e-09
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 10/78 (12%)

Query: 175 SAIEALPSIKINEAMM-SSDSS--------QCAVCKDSFELNEEARQMPCKHIYHPDCIM 225
           S+ EA+P+     ++   S           +CA+C  +F  N+  R +PC H +H  C+ 
Sbjct: 295 SSSEAIPTTTTKGSLKPLSIERAVEADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVD 354

Query: 226 PWLELH-NSCPVCRYELP 242
            WL  + N CPVCR  +P
Sbjct: 355 KWLLGYSNKCPVCRTAIP 372

Length = 374

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

 Score = 51.7 bits (124), Expect = 3e-09
 Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 2/47 (4%)

Query: 193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRY 239
           +  +C +C D   L +     PC H++  +CI+ +L+  + CP+CR 
Sbjct: 1   EELECPICLD--LLRDPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 49.4 bits (118), Expect = 2e-08
 Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 3/42 (7%)

Query: 197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHN-SCPVC 237
           C +C + +   ++   +PC H +   CI  WLE  N +CP+C
Sbjct: 1   CPICLEEYL--KDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40

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

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

 Score = 49.2 bits (117), Expect = 2e-06
 Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 10/64 (15%)

Query: 185 INEAMMSSDSSQCAVCKDSF----------ELNEEARQMPCKHIYHPDCIMPWLELHNSC 234
             E  +++    C +C D             L+   +++PC HI H  C+  WLE   +C
Sbjct: 278 ATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTC 337

Query: 235 PVCR 238
           P+CR
Sbjct: 338 PICR 341

Length = 491

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

 Score = 42.5 bits (100), Expect = 6e-06
 Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 3/42 (7%)

Query: 197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-HNSCPVC 237
           C +C +  +  +    +PC H++   CI+ WLE  + +CP+C
Sbjct: 1   CPICLEEPK--DPVTILPCGHLFCSKCILSWLESGNVTCPLC 40

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

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

 Score = 47.7 bits (113), Expect = 7e-06
 Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 10/76 (13%)

Query: 175  SAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMP------CKHIYHPDCIMPWL 228
            S ++ L   K N     S   +CA+C     L+   R +P      CK+ +H  C+  W 
Sbjct: 1450 SFMDLLGLWKKNIDEKFSGHEECAIC--YSVLDMVDRSLPSKRCATCKNKFHTRCLYKWF 1507

Query: 229  ELHNS--CPVCRYELP 242
                   CP+CR E+ 
Sbjct: 1508 ASSARSNCPLCRSEIT 1523

Length = 1525

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

 Score = 38.6 bits (90), Expect = 4e-04
 Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 3/34 (8%)

Query: 215 CKHIYHPDCIMPWLELHNS---CPVCRYELPTDD 245
           CKH +H  CI+ WL    S   CP+CR      +
Sbjct: 52  CKHNFHMHCILKWLATETSKGLCPMCRQTFVFAE 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 = 38.3 bits (89), Expect = 5e-04
 Identities = 10/24 (41%), Positives = 13/24 (54%)

Query: 215 CKHIYHPDCIMPWLELHNSCPVCR 238
           C H +H  CI  WL+    CP+ R
Sbjct: 54  CNHAFHDHCIYRWLDTKGVCPLDR 77

Length = 88

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	352
PF14369	35	zf-RING_3: zinc-finger	99.65
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.6
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.49
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.33
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.2
PHA02929	238	N1R/p28-like protein; Provisional	99.2
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.2
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.93
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.89
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	98.88
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.86
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	98.85
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.82
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.78
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.76
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.74
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.72
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.67
PF14634	44	zf-RING_5: zinc-RING finger domain	98.67
PHA02926	242	zinc finger-like protein; Provisional	98.66
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.64
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.6
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.49
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.47
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.32
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.28
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.27
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.22
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.22
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.21
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.15
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.15
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.14
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.14
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	97.98
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	97.96
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.96
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	97.88
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	97.85
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.73
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.66
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.66
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.65
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.58
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.48
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.47
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.43
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.18
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.18
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.17
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.13
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.07
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	96.95
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	96.89
KOG0297	391	consensus TNF receptor-associated factor [Signal t	96.84
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	96.72
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.63
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	96.62
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	96.44
KOG2660	331	consensus Locus-specific chromosome binding protei	96.44
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.02
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.0
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	95.93
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	95.88
KOG1002	791	consensus Nucleotide excision repair protein RAD16	95.86
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	95.73
COG5152	259	Uncharacterized conserved protein, contains RING a	95.71
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	95.63
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.54
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	95.52
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	95.52
KOG3039	303	consensus Uncharacterized conserved protein [Funct	95.44
PHA02862	156	5L protein; Provisional	95.37
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	95.28
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	95.27
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	95.2
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	95.15
PHA02825	162	LAP/PHD finger-like protein; Provisional	94.87
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	94.79
PF04641	260	Rtf2: Rtf2 RING-finger	94.74
COG5236	493	Uncharacterized conserved protein, contains RING Z	94.42
COG0375	115	HybF Zn finger protein HypA/HybF (possibly regulat	93.79
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	93.74
PHA03096	284	p28-like protein; Provisional	93.73
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	93.72
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	93.44
KOG4739	233	consensus Uncharacterized protein involved in syna	93.39
COG5222	427	Uncharacterized conserved protein, contains RING Z	93.31
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	93.1
KOG1940	276	consensus Zn-finger protein [General function pred	93.0
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	92.76
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	92.28
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	91.84
KOG0298	1394	consensus DEAD box-containing helicase-like transc	91.52
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	91.4
KOG3002	299	consensus Zn finger protein [General function pred	91.14
TIGR00100	115	hypA hydrogenase nickel insertion protein HypA. In	89.87
COG5175	480	MOT2 Transcriptional repressor [Transcription]	89.68
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	89.41
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	88.85
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	88.79
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	88.64
KOG1001	674	consensus Helicase-like transcription factor HLTF/	87.94
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	87.37
PRK12380	113	hydrogenase nickel incorporation protein HybF; Pro	87.19
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	86.9
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	86.69
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	86.68
PRK00564	117	hypA hydrogenase nickel incorporation protein; Pro	86.53
KOG3053	293	consensus Uncharacterized conserved protein [Funct	86.25
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	86.13
PF01155	113	HypA: Hydrogenase expression/synthesis hypA family	85.74
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	84.43
KOG1609	323	consensus Protein involved in mRNA turnover and st	83.65
PRK00762	124	hypA hydrogenase nickel incorporation protein; Pro	82.9
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	82.65
COG2093	64	DNA-directed RNA polymerase, subunit E'' [Transcri	82.6
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	82.21
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	81.87
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	81.65
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	81.08
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	80.48
COG5270	202	PUA domain (predicted RNA-binding domain) [Transla	80.38
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	80.1

>PF14369 zf-RING_3: zinc-finger

Probab=99.65  E-value=7.4e-17  Score=106.66  Aligned_cols=35  Identities=66%  Similarity=1.462  Sum_probs=31.2

Q ss_pred             CceeeecCCcccccCCCCCCCCcCCCCCCCceEEc
Q 018689           22 QMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEEL   56 (352)
Q Consensus        22 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi   56 (352)
                      ++||||+|+|+|++.+...++++||+|++||||||
T Consensus         1 ~~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFvEei   35 (35)
T PF14369_consen    1 QRYWCHQCNRFVRIAPSPDSDVACPRCHGGFVEEI   35 (35)
T ss_pred             CCEeCccCCCEeEeCcCCCCCcCCcCCCCcEeEeC
Confidence            58999999999999776666777999999999997

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

Probab=99.60  E-value=5.8e-16  Score=150.31  Aligned_cols=80  Identities=29%  Similarity=0.695  Sum_probs=68.3

Q ss_pred             CCCCCCHHHHhhCCcceeccccccCCCCccccccccccccCCceEcccCceecccchHHHhhcCC-CCCccCCCCCCCCh
Q 018689          168 GTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHN-SCPVCRYELPTDDP  246 (352)
Q Consensus       168 g~~pas~~~i~~lp~~~~~~~~~~~~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~-sCP~CR~~l~~~~~  246 (352)
                      ....+.+..++++|..+++..........|+||+|+|+.++++++|||+|.||..||++||.++. .||+||.++.+...
T Consensus       203 ~~~r~~k~~l~~~p~~~f~~~~~~~~~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~~  282 (348)
T KOG4628|consen  203 RRNRLIKRLLKKLPVRTFTKGDDEDATDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDSG  282 (348)
T ss_pred             hhhhhHHHHHhhCCcEEeccccccCCCceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCCCC
Confidence            45578899999999999987655333359999999999999999999999999999999998775 59999999876554


Q ss_pred             h
Q 018689          247 D  247 (352)
Q Consensus       247 ~  247 (352)
                      .
T Consensus       283 ~  283 (348)
T KOG4628|consen  283 S  283 (348)
T ss_pred             C
Confidence            3

>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=99.49  E-value=5.5e-15  Score=102.71  Aligned_cols=44  Identities=45%  Similarity=1.196  Sum_probs=40.6

Q ss_pred             CccccccccccccCCceEcccCceecccchHHHhhcCCCCCccC
Q 018689          195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCR  238 (352)
Q Consensus       195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR  238 (352)
                      .+|+||++.|..++.++.|+|+|+||..||.+|++.+.+||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence            37999999999999999999999999999999999999999997

...

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

Probab=99.33  E-value=2.7e-12  Score=123.88  Aligned_cols=70  Identities=29%  Similarity=0.760  Sum_probs=53.1

Q ss_pred             CHHHHhhCCcceeccccccCCCCcccccccc-cccc---------CCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689          173 SKSAIEALPSIKINEAMMSSDSSQCAVCKDS-FELN---------EEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       173 s~~~i~~lp~~~~~~~~~~~~~~~C~IC~e~-~~~~---------~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      .|+.-+.+|++..+  ....++..|.||+++ |+.+         .++++|||||+||.+|++.|++++.+||+||.++.
T Consensus       268 ~kdl~~~~~t~t~e--ql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~i  345 (491)
T COG5243         268 TKDLNAMYPTATEE--QLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVI  345 (491)
T ss_pred             hhHHHhhcchhhhh--hhcCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccc
Confidence            34444445544433  334557899999999 5443         35799999999999999999999999999999965


Q ss_pred             CC
Q 018689          243 TD  244 (352)
Q Consensus       243 ~~  244 (352)
                      -+
T Consensus       346 fd  347 (491)
T COG5243         346 FD  347 (491)
T ss_pred             cc
Confidence            43

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

Probab=99.20  E-value=5.4e-12  Score=119.08  Aligned_cols=50  Identities=40%  Similarity=1.022  Sum_probs=46.8

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhh-cCCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLE-LHNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~-~~~sCP~CR~~l~~  243 (352)
                      .-+|+|||+.|..+++++.|||.|.||..||++|+. -++.||+||.++|+
T Consensus       323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            579999999999999999999999999999999997 67899999999985

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.20  E-value=7e-12  Score=116.94  Aligned_cols=71  Identities=27%  Similarity=0.593  Sum_probs=55.3

Q ss_pred             CCHHHHhhCCcceeccccc--cCCCCccccccccccccCC-----ceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689          172 ASKSAIEALPSIKINEAMM--SSDSSQCAVCKDSFELNEE-----ARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       172 as~~~i~~lp~~~~~~~~~--~~~~~~C~IC~e~~~~~~~-----~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      .++..++.+|.+...-+..  ...+.+|+||++.+.....     .+.++|+|.||..||.+|++.+.+||+||..+.
T Consensus       150 ~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~  227 (238)
T PHA02929        150 NYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI  227 (238)
T ss_pred             hhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence            3888899999886543322  2335899999999865431     244569999999999999999999999999875

>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=99.20  E-value=9e-12  Score=96.07  Aligned_cols=45  Identities=40%  Similarity=1.001  Sum_probs=36.0

Q ss_pred             CCcccccccccccc----------CCceEcccCceecccchHHHhhcCCCCCccC
Q 018689          194 SSQCAVCKDSFELN----------EEARQMPCKHIYHPDCIMPWLELHNSCPVCR  238 (352)
Q Consensus       194 ~~~C~IC~e~~~~~----------~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR  238 (352)
                      ...|+||++.|...          -.+...+|+|.||..||.+||+.+.+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            45699999999332          2344557999999999999999999999998

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 ....

>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=98.93  E-value=4.3e-10  Score=80.15  Aligned_cols=46  Identities=24%  Similarity=0.753  Sum_probs=39.9

Q ss_pred             CCccccccccccccCCceEcccCce-ecccchHHHhhcCCCCCccCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHI-YHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      +..|.||++....   +..+||||. |+..|+..|++....||+||+++.
T Consensus         2 ~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRD---VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSS---EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCCc---eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            4689999998655   889999999 999999999999999999999874

...

>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=98.89  E-value=7.3e-10  Score=75.39  Aligned_cols=44  Identities=36%  Similarity=1.073  Sum_probs=36.5

Q ss_pred             ccccccccccccCCceEcccCceecccchHHHhhc-CCCCCccCCCC
Q 018689          196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYEL  241 (352)
Q Consensus       196 ~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l  241 (352)
                      +|+||++.+.  .....++|+|.||..|++.|++. ...||+||..+
T Consensus         1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhh--CceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            5999999982  33555559999999999999987 77899999864

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=98.88  E-value=9e-10  Score=99.25  Aligned_cols=50  Identities=24%  Similarity=0.634  Sum_probs=41.8

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhc----------------CCCCCccCCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL----------------HNSCPVCRYELPTDD  245 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~----------------~~sCP~CR~~l~~~~  245 (352)
                      +..+|+||++.++.   +++++|||.||..||.+|+..                +..||+||..+...+
T Consensus        17 ~~~~CpICld~~~d---PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~   82 (193)
T PLN03208         17 GDFDCNICLDQVRD---PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT   82 (193)
T ss_pred             CccCCccCCCcCCC---cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence            35899999999865   678899999999999999852                347999999996544

>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=98.86  E-value=1.1e-09  Score=74.14  Aligned_cols=39  Identities=36%  Similarity=0.923  Sum_probs=33.4

Q ss_pred             cccccccccccCCceEcccCceecccchHHHhhcCCCCCcc
Q 018689          197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVC  237 (352)
Q Consensus       197 C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~C  237 (352)
                      |+||++.+..  .++.++|||.||..||.+|++.+.+||+|
T Consensus         1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC--cCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence            8999999877  34788999999999999999998999998

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

Probab=98.85  E-value=8.6e-10  Score=103.97  Aligned_cols=49  Identities=27%  Similarity=0.800  Sum_probs=44.0

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD  245 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~  245 (352)
                      ...|.||++....   +..+||||+||..||..|+..+..||+||.++.+.+
T Consensus       239 ~~kC~LCLe~~~~---pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~psk  287 (293)
T KOG0317|consen  239 TRKCSLCLENRSN---PSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSK  287 (293)
T ss_pred             CCceEEEecCCCC---CCcCcCcchHHHHHHHHHHccccCCCcccccCCCcc
Confidence            5799999998655   789999999999999999999999999999987654

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

Probab=98.82  E-value=7.8e-10  Score=115.18  Aligned_cols=50  Identities=30%  Similarity=0.935  Sum_probs=45.0

Q ss_pred             CCCccccccccccccCC--ceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689          193 DSSQCAVCKDSFELNEE--ARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~--~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      ....|+||+|.+..+.+  +++|+|+|+||..|++.|+++.++||+||..+.
T Consensus       290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~  341 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLY  341 (543)
T ss_pred             cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhh
Confidence            36899999999988655  899999999999999999999999999999543

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

Probab=98.78  E-value=2.3e-09  Score=98.42  Aligned_cols=49  Identities=29%  Similarity=0.717  Sum_probs=41.9

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhc---CCCCCccCCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL---HNSCPVCRYELPTDD  245 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~---~~sCP~CR~~l~~~~  245 (352)
                      ..+|.|||+.-++   +++..|||.||..||.+||..   .+.||+||..|..+.
T Consensus        47 ~FdCNICLd~akd---PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~   98 (230)
T KOG0823|consen   47 FFDCNICLDLAKD---PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDT   98 (230)
T ss_pred             ceeeeeeccccCC---CEEeecccceehHHHHHHHhhcCCCeeCCccccccccce
Confidence            5899999998555   888889999999999999975   446999999987654

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

Probab=98.76  E-value=2.5e-09  Score=84.11  Aligned_cols=50  Identities=28%  Similarity=0.822  Sum_probs=38.8

Q ss_pred             CCccccccccccc--------cCC-ceEc-ccCceecccchHHHhhc---CCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFEL--------NEE-ARQM-PCKHIYHPDCIMPWLEL---HNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~--------~~~-~~~l-pC~H~FH~~Ci~~Wl~~---~~sCP~CR~~l~~  243 (352)
                      ++.|.||+..|..        ++. +.++ .|+|.||..||.+||..   +..||+||+++..
T Consensus        21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~   83 (85)
T PF12861_consen   21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF   83 (85)
T ss_pred             CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence            5789999999862        222 3333 49999999999999975   4689999998753

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

Probab=98.74  E-value=4.3e-09  Score=72.55  Aligned_cols=38  Identities=32%  Similarity=0.816  Sum_probs=30.2

Q ss_pred             cccccccccccCCceEcccCceecccchHHHhhcC----CCCCcc
Q 018689          197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH----NSCPVC  237 (352)
Q Consensus       197 C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~----~sCP~C  237 (352)
                      |+||++.|..   ++.|+|||.|+..||..|++..    ..||+|
T Consensus         1 CpiC~~~~~~---Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKD---PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SS---EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCC---ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            8999999988   8999999999999999999653    369988

>smart00504 Ubox Modified RING finger domain

Probab=98.72  E-value=8.7e-09  Score=76.28  Aligned_cols=47  Identities=21%  Similarity=0.399  Sum_probs=42.0

Q ss_pred             CccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689          195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      ..|+||++.+..   ++.++|||+|++.||.+|++.+.+||+|+..+...
T Consensus         2 ~~Cpi~~~~~~~---Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~   48 (63)
T smart00504        2 FLCPISLEVMKD---PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHE   48 (63)
T ss_pred             cCCcCCCCcCCC---CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChh
Confidence            579999999877   68889999999999999998899999999988543

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

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

Probab=98.67  E-value=5.7e-09  Score=92.17  Aligned_cols=50  Identities=28%  Similarity=0.689  Sum_probs=42.2

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPT  243 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~  243 (352)
                      ....|+|||+.+.... +....|||+||+.||+.-|+....||+|+++|..
T Consensus       130 ~~~~CPiCl~~~sek~-~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~  179 (187)
T KOG0320|consen  130 GTYKCPICLDSVSEKV-PVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH  179 (187)
T ss_pred             cccCCCceecchhhcc-ccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence            3589999999997732 2346799999999999999999999999997754

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.67  E-value=8.2e-09  Score=71.68  Aligned_cols=44  Identities=25%  Similarity=0.748  Sum_probs=39.0

Q ss_pred             ccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCC
Q 018689          196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRY  239 (352)
Q Consensus       196 ~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~  239 (352)
                      .|.||++.|.......+++|||+|+..||..+......||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            49999999966667899999999999999999866778999985

>PHA02926 zinc finger-like protein; Provisional

Probab=98.66  E-value=6.2e-09  Score=95.11  Aligned_cols=52  Identities=25%  Similarity=0.701  Sum_probs=38.7

Q ss_pred             cCCCCcccccccccccc-----CCceEc-ccCceecccchHHHhhcC------CCCCccCCCCC
Q 018689          191 SSDSSQCAVCKDSFELN-----EEARQM-PCKHIYHPDCIMPWLELH------NSCPVCRYELP  242 (352)
Q Consensus       191 ~~~~~~C~IC~e~~~~~-----~~~~~l-pC~H~FH~~Ci~~Wl~~~------~sCP~CR~~l~  242 (352)
                      .+.+.+|+||++.+-..     ....+| +|+|.||..||..|.+.+      .+||+||..+.
T Consensus       167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            34468999999986332     122344 599999999999999753      46999999764

>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=98.64  E-value=1.5e-08  Score=68.90  Aligned_cols=39  Identities=38%  Similarity=1.036  Sum_probs=33.7

Q ss_pred             cccccccccccCCceEcccCceecccchHHHhh--cCCCCCcc
Q 018689          197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWLE--LHNSCPVC  237 (352)
Q Consensus       197 C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~--~~~sCP~C  237 (352)
                      |+||++.+...  ...++|+|.||..||.+|++  ....||+|
T Consensus         1 C~iC~~~~~~~--~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDP--VILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSE--EEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCC--CEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            89999998772  35889999999999999998  46689998

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=98.60  E-value=1.6e-08  Score=66.31  Aligned_cols=38  Identities=34%  Similarity=1.121  Sum_probs=33.2

Q ss_pred             cccccccccccCCceEcccCceecccchHHHhh-cCCCCCcc
Q 018689          197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWLE-LHNSCPVC  237 (352)
Q Consensus       197 C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~-~~~sCP~C  237 (352)
                      |+||++..   .....++|+|.||..|++.|++ ....||+|
T Consensus         1 C~iC~~~~---~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEEL---KDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCC---CCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            88999883   4588899999999999999998 66789998

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)

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.49  E-value=5.7e-08  Score=96.96  Aligned_cols=48  Identities=33%  Similarity=0.732  Sum_probs=42.7

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      ...|+||++.|..   +++++|+|.||..||..||.....||+||..+...
T Consensus        26 ~l~C~IC~d~~~~---PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~   73 (397)
T TIGR00599        26 SLRCHICKDFFDV---PVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES   73 (397)
T ss_pred             ccCCCcCchhhhC---ccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence            5899999999866   66889999999999999998888999999988653

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

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

Probab=98.47  E-value=5.2e-08  Score=75.10  Aligned_cols=47  Identities=28%  Similarity=0.723  Sum_probs=34.3

Q ss_pred             cccccccccccCCceEc-c-cCceecccchHHHhhcCCCCCccCCCCCC
Q 018689          197 CAVCKDSFELNEEARQM-P-CKHIYHPDCIMPWLELHNSCPVCRYELPT  243 (352)
Q Consensus       197 C~IC~e~~~~~~~~~~l-p-C~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~  243 (352)
                      |+-|.-.+..+++..+. . |.|.||..||.+||..++.||++|++...
T Consensus        34 C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~   82 (88)
T COG5194          34 CPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVL   82 (88)
T ss_pred             CcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence            33333333344444333 3 99999999999999999999999998753

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

Probab=98.32  E-value=6.4e-08  Score=74.03  Aligned_cols=49  Identities=29%  Similarity=0.887  Sum_probs=38.0

Q ss_pred             CCccccccccccc--------cCC-ceEcc-cCceecccchHHHhhc---CCCCCccCCCCC
Q 018689          194 SSQCAVCKDSFEL--------NEE-ARQMP-CKHIYHPDCIMPWLEL---HNSCPVCRYELP  242 (352)
Q Consensus       194 ~~~C~IC~e~~~~--------~~~-~~~lp-C~H~FH~~Ci~~Wl~~---~~sCP~CR~~l~  242 (352)
                      ++.|-||...|..        ++. +.++. |.|.||..||.+||..   +..||+||+++.
T Consensus        20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            5699999999853        333 33444 9999999999999954   457999999864

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

Probab=98.28  E-value=3.4e-07  Score=63.39  Aligned_cols=38  Identities=29%  Similarity=0.871  Sum_probs=22.9

Q ss_pred             cccccccccc-cCCceEcccCceecccchHHHhhcC----CCCC
Q 018689          197 CAVCKDSFEL-NEEARQMPCKHIYHPDCIMPWLELH----NSCP  235 (352)
Q Consensus       197 C~IC~e~~~~-~~~~~~lpC~H~FH~~Ci~~Wl~~~----~sCP  235 (352)
                      |+||++ |.. ...+++|+|||+|+++||.+|++..    ..||
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 744 4557889999999999999999753    2576

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

Probab=98.27  E-value=1.6e-07  Score=87.82  Aligned_cols=49  Identities=29%  Similarity=0.836  Sum_probs=41.6

Q ss_pred             CCccccccccccccC-------CceEcccCceecccchHHHh--hcCCCCCccCCCCC
Q 018689          194 SSQCAVCKDSFELNE-------EARQMPCKHIYHPDCIMPWL--ELHNSCPVCRYELP  242 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~-------~~~~lpC~H~FH~~Ci~~Wl--~~~~sCP~CR~~l~  242 (352)
                      +..|+||-..+....       +.-+|.|+|+||..||+-|.  -++.+||.|+..+.
T Consensus       224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd  281 (328)
T KOG1734|consen  224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD  281 (328)
T ss_pred             cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence            479999998886544       67889999999999999995  56789999988774

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

Probab=98.22  E-value=3.4e-07  Score=85.61  Aligned_cols=48  Identities=25%  Similarity=0.779  Sum_probs=41.1

Q ss_pred             CCccccccccccccCCceEcccCceecccchHH-HhhcCCC-CCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMP-WLELHNS-CPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~-Wl~~~~s-CP~CR~~l~~~  244 (352)
                      +..|+||++..+.   +..++|||+||..||.. |-.++.- ||+||+.+..+
T Consensus       215 d~kC~lC~e~~~~---ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk  264 (271)
T COG5574         215 DYKCFLCLEEPEV---PSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPK  264 (271)
T ss_pred             ccceeeeecccCC---cccccccchhhHHHHHHHHHhhccccCchhhhhccch
Confidence            5789999998666   88999999999999999 9766655 99999987654

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

Probab=98.22  E-value=5e-07  Score=69.55  Aligned_cols=49  Identities=24%  Similarity=0.443  Sum_probs=39.6

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhc-CCCCCccCCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYELPTDD  245 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~~~~  245 (352)
                      ...|+||.+.|.+   +++++|||.|.+.||..||+. +.+||+|+..+...+
T Consensus         4 ~f~CpIt~~lM~d---PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~   53 (73)
T PF04564_consen    4 EFLCPITGELMRD---PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESD   53 (73)
T ss_dssp             GGB-TTTSSB-SS---EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGG
T ss_pred             ccCCcCcCcHhhC---ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCccc
Confidence            4789999999988   889999999999999999988 889999999887644

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 ....

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

Probab=98.21  E-value=5e-07  Score=64.31  Aligned_cols=42  Identities=24%  Similarity=0.838  Sum_probs=33.7

Q ss_pred             ccccccccccccCCceEcccC-----ceecccchHHHhhc--CCCCCccC
Q 018689          196 QCAVCKDSFELNEEARQMPCK-----HIYHPDCIMPWLEL--HNSCPVCR  238 (352)
Q Consensus       196 ~C~IC~e~~~~~~~~~~lpC~-----H~FH~~Ci~~Wl~~--~~sCP~CR  238 (352)
                      .|.||++ ...++...++||.     |.+|..|+.+|+..  +.+||+|+
T Consensus         1 ~CrIC~~-~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHD-EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCC-CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4899999 4445566788985     89999999999955  44899995

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

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

Probab=98.15  E-value=4.6e-07  Score=87.24  Aligned_cols=49  Identities=27%  Similarity=0.735  Sum_probs=45.0

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD  245 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~  245 (352)
                      ...|-||.+.|..   +.+.||+|.||.-||..+|..+..||.|+.++...+
T Consensus        23 lLRC~IC~eyf~i---p~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~   71 (442)
T KOG0287|consen   23 LLRCGICFEYFNI---PMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESD   71 (442)
T ss_pred             HHHHhHHHHHhcC---ceeccccchHHHHHHHHHhccCCCCCceecccchhh
Confidence            4789999999988   789999999999999999999999999999987654

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

Probab=98.15  E-value=2.8e-07  Score=98.02  Aligned_cols=68  Identities=26%  Similarity=0.670  Sum_probs=47.6

Q ss_pred             HHHhhCCcceeccccccCCCCccccccccccccC---CceEcc-cCceecccchHHHhhc--CCCCCccCCCCC
Q 018689          175 SAIEALPSIKINEAMMSSDSSQCAVCKDSFELNE---EARQMP-CKHIYHPDCIMPWLEL--HNSCPVCRYELP  242 (352)
Q Consensus       175 ~~i~~lp~~~~~~~~~~~~~~~C~IC~e~~~~~~---~~~~lp-C~H~FH~~Ci~~Wl~~--~~sCP~CR~~l~  242 (352)
                      +..+.|...+......-+..++|+||+..+..-+   .-+..+ |+|.||..|+.+|++.  +++||+||.+++
T Consensus      1450 s~~D~l~l~kkNi~~~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1450 SFMDLLGLWKKNIDEKFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             hHHHHHHHHHhhhhhhcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            3445555555555444455789999998876211   122333 9999999999999976  568999998875

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

Probab=98.14  E-value=8.5e-07  Score=89.65  Aligned_cols=49  Identities=29%  Similarity=0.765  Sum_probs=40.2

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhc-----CCCCCccCCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-----HNSCPVCRYELPTDD  245 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-----~~sCP~CR~~l~~~~  245 (352)
                      +..|+||++....   +..+.|||+||..||.++|..     ...||+||..|-.++
T Consensus       186 ~~~CPICL~~~~~---p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kd  239 (513)
T KOG2164|consen  186 DMQCPICLEPPSV---PVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKD  239 (513)
T ss_pred             CCcCCcccCCCCc---ccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccc
Confidence            4799999998665   566669999999999998754     457999999886644

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

Probab=98.14  E-value=5.4e-07  Score=90.36  Aligned_cols=51  Identities=33%  Similarity=1.004  Sum_probs=40.8

Q ss_pred             CCCccccccccccccC--------------CceEcccCceecccchHHHhh-cCCCCCccCCCCCC
Q 018689          193 DSSQCAVCKDSFELNE--------------EARQMPCKHIYHPDCIMPWLE-LHNSCPVCRYELPT  243 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~--------------~~~~lpC~H~FH~~Ci~~Wl~-~~~sCP~CR~~l~~  243 (352)
                      ....|+||+..+..-.              .-...||.|+||..|+..|.. .+-.||+||..|+.
T Consensus       570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             ccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            3578999999875321              134559999999999999998 55699999999874

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

Probab=97.98  E-value=2.1e-06  Score=81.26  Aligned_cols=46  Identities=26%  Similarity=0.614  Sum_probs=41.8

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      ...|-||.+.|..   ....+|||.||.-||+..|..+..||+||.+..
T Consensus        25 ~lrC~IC~~~i~i---p~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~   70 (391)
T COG5432          25 MLRCRICDCRISI---PCETTCGHTFCSLCIRRHLGTQPFCPVCREDPC   70 (391)
T ss_pred             HHHhhhhhheeec---ceecccccchhHHHHHHHhcCCCCCccccccHH
Confidence            4789999999887   678889999999999999999999999998753

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=97.96  E-value=3.9e-06  Score=80.98  Aligned_cols=50  Identities=24%  Similarity=0.436  Sum_probs=37.1

Q ss_pred             CCccccccccccccCCc--eEcccCceecccchHHHh-hcCCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEA--RQMPCKHIYHPDCIMPWL-ELHNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~--~~lpC~H~FH~~Ci~~Wl-~~~~sCP~CR~~l~~  243 (352)
                      +..|+||+..--.....  .+.+|||.||..||+..+ .....||.|+..+..
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk   55 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRK   55 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence            46899999964333333  333799999999999965 445689999987754

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).

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

Probab=97.96  E-value=1.7e-06  Score=66.10  Aligned_cols=49  Identities=20%  Similarity=0.539  Sum_probs=22.9

Q ss_pred             CCcccccccccc-ccCCc-eEc---ccCceecccchHHHhhc----C-------CCCCccCCCCC
Q 018689          194 SSQCAVCKDSFE-LNEEA-RQM---PCKHIYHPDCIMPWLEL----H-------NSCPVCRYELP  242 (352)
Q Consensus       194 ~~~C~IC~e~~~-~~~~~-~~l---pC~H~FH~~Ci~~Wl~~----~-------~sCP~CR~~l~  242 (352)
                      +.+|.||+..+. .++.+ ...   .|++.||..||.+||..    +       ..||.|+.+|.
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~   66 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS   66 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence            368999999876 32222 222   49999999999999953    1       14999999874

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

Probab=97.88  E-value=3.7e-06  Score=68.06  Aligned_cols=49  Identities=33%  Similarity=0.742  Sum_probs=37.5

Q ss_pred             CCccccccccccc------------cCCc-eEcc-cCceecccchHHHhhcCCCCCccCCCCC
Q 018689          194 SSQCAVCKDSFEL------------NEEA-RQMP-CKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       194 ~~~C~IC~e~~~~------------~~~~-~~lp-C~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      .+.|+||...+-+            .++. +... |.|.||..||.+||+.++.||+|.++..
T Consensus        46 vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~  108 (114)
T KOG2930|consen   46 VDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWV  108 (114)
T ss_pred             echhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCccee
Confidence            4689999876521            1223 3333 9999999999999999999999988754

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

Probab=97.85  E-value=3.9e-06  Score=78.03  Aligned_cols=44  Identities=32%  Similarity=0.714  Sum_probs=39.0

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRY  239 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~  239 (352)
                      +...|+||++.|...   ++++|+|.||..||..|+.....||.||.
T Consensus        12 ~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   12 EELTCPICLEYFREP---VLLPCGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             ccccChhhHHHhhcC---ccccccchHhHHHHHHhcCCCcCCcccCC
Confidence            468999999999884   89999999999999999885568999993

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

Probab=97.73  E-value=1e-05  Score=80.61  Aligned_cols=48  Identities=33%  Similarity=0.901  Sum_probs=38.8

Q ss_pred             CCCccccccccccccC-CceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689          193 DSSQCAVCKDSFELNE-EARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~-~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      +..+|+||||.+...- .++...|.|.||..|+.+|.  ..+||+||.-..
T Consensus       174 ELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~  222 (493)
T KOG0804|consen  174 ELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS  222 (493)
T ss_pred             cCCCcchhHhhcCccccceeeeecccccchHHHhhcc--cCcChhhhhhcC
Confidence            4579999999997643 24555699999999999994  457999999765

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

Probab=97.66  E-value=2.3e-05  Score=58.49  Aligned_cols=47  Identities=28%  Similarity=0.654  Sum_probs=24.9

Q ss_pred             CCccccccccccccCCceEc-ccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQM-PCKHIYHPDCIMPWLELHNSCPVCRYELPTDD  245 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~  245 (352)
                      ...|++|.+.++.   ++.| .|.|+|+..||..-+..  .||+|+.+.-..|
T Consensus         7 lLrCs~C~~~l~~---pv~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD   54 (65)
T PF14835_consen    7 LLRCSICFDILKE---PVCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQD   54 (65)
T ss_dssp             TTS-SSS-S--SS----B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS
T ss_pred             hcCCcHHHHHhcC---CceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHH
Confidence            4689999999876   5444 59999999999986653  4999998765443

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

Probab=97.66  E-value=1.2e-05  Score=78.84  Aligned_cols=47  Identities=32%  Similarity=0.930  Sum_probs=36.9

Q ss_pred             CccccccccccccCCceEcc-cCceecccchHHHhhc---CCCCCccCCCC
Q 018689          195 SQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLEL---HNSCPVCRYEL  241 (352)
Q Consensus       195 ~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~---~~sCP~CR~~l  241 (352)
                      ..|.||.+-+-...++.-+. |||+||..|+.+|++.   ...||+|+-.+
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~   55 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKL   55 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecc
Confidence            58999966555555566666 9999999999999976   34799999444

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

Probab=97.65  E-value=2.1e-05  Score=76.61  Aligned_cols=47  Identities=23%  Similarity=0.678  Sum_probs=40.9

Q ss_pred             CCccccccccccccCCceEcccCce-ecccchHHHhhcCCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHI-YHPDCIMPWLELHNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~sCP~CR~~l~~  243 (352)
                      ..+|.||+.+-++   ..+|||.|. .|..|.+..--+++.||+||+.+..
T Consensus       290 gkeCVIClse~rd---t~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~  337 (349)
T KOG4265|consen  290 GKECVICLSESRD---TVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEE  337 (349)
T ss_pred             CCeeEEEecCCcc---eEEecchhhehhHhHHHHHHHhhcCCCccccchHh
Confidence            6799999999666   899999997 7899999876778999999998853

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

Probab=97.58  E-value=1.1e-05  Score=84.91  Aligned_cols=50  Identities=26%  Similarity=0.536  Sum_probs=44.5

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~  243 (352)
                      ...|+||+..+.+.......+|+|+||..||..|-+.-++||+||.++..
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~  172 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGE  172 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhhe
Confidence            46899999999887777777899999999999999999999999998743

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

Probab=97.48  E-value=4.1e-05  Score=73.04  Aligned_cols=48  Identities=21%  Similarity=0.557  Sum_probs=40.0

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhc-CCCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~~~  244 (352)
                      ..+|+||+.....   ++.|+|+|.||..||+--... +.+|++||.+|...
T Consensus         7 ~~eC~IC~nt~n~---Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    7 KKECLICYNTGNC---PVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDST   55 (324)
T ss_pred             CCcceeeeccCCc---CccccccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence            4689999998554   688999999999999987655 55799999999653

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

Probab=97.47  E-value=1.1e-05  Score=78.50  Aligned_cols=47  Identities=30%  Similarity=0.656  Sum_probs=38.9

Q ss_pred             CCccccccccccccCCceEcc-cCceecccchHHHhhc-CCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLEL-HNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~~  243 (352)
                      +..|+||++.++.   .+..+ |.|.||..||.+-|+. .++||.||+.+..
T Consensus        43 ~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S   91 (381)
T KOG0311|consen   43 QVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS   91 (381)
T ss_pred             hhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence            5799999999876   34444 9999999999998865 7799999998743

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

Probab=97.43  E-value=5.6e-05  Score=74.35  Aligned_cols=48  Identities=27%  Similarity=0.799  Sum_probs=37.1

Q ss_pred             CCccccccccccccC----CceEcc-cCceecccchHHHh--hc-----CCCCCccCCCC
Q 018689          194 SSQCAVCKDSFELNE----EARQMP-CKHIYHPDCIMPWL--EL-----HNSCPVCRYEL  241 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~----~~~~lp-C~H~FH~~Ci~~Wl--~~-----~~sCP~CR~~l  241 (352)
                      +..|.||++.+....    .-.+|| |.|.||..||..|-  .+     ...||.||...
T Consensus       161 ~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s  220 (344)
T KOG1039|consen  161 EKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPS  220 (344)
T ss_pred             cccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcc
Confidence            589999999875532    122345 99999999999997  44     46899999865

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

Probab=97.18  E-value=0.00017  Score=71.31  Aligned_cols=48  Identities=27%  Similarity=0.800  Sum_probs=38.1

Q ss_pred             CCccccccccccccC--CceEcccCceecccchHHHhhc--CCCCCccCCCC
Q 018689          194 SSQCAVCKDSFELNE--EARQMPCKHIYHPDCIMPWLEL--HNSCPVCRYEL  241 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~--~~~~lpC~H~FH~~Ci~~Wl~~--~~sCP~CR~~l  241 (352)
                      ..+|+||++.++..-  ....+.|||.|-..||++||-+  ...||.|..+.
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka   55 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA   55 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence            478999999997543  3555569999999999999942  34799997765

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

Probab=97.18  E-value=6.2e-05  Score=71.75  Aligned_cols=90  Identities=22%  Similarity=0.446  Sum_probs=57.9

Q ss_pred             cHHHHHHHHHhcCCCCCCCCCCCHHHHhhCCcceeccccccCCCCccccccccccccCCceEcccCceecccchHHHhhc
Q 018689          151 GLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL  230 (352)
Q Consensus       151 ~le~li~~L~~~~~~~~g~~pas~~~i~~lp~~~~~~~~~~~~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~  230 (352)
                      .|..|..++...-....+ -|.--..|+....+.....   -...+|.|||--|..++...+.+|-|.||..|+.++|..
T Consensus        76 ~~~~i~~~~~~iikq~~g-~pii~~lie~~~e~LT~nn---~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~  151 (368)
T KOG4445|consen   76 EFREIQRQIQEIIKQNSG-MPIICQLIEHCSEFLTENN---HPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTE  151 (368)
T ss_pred             HHHHHHHHHHHHHHhcCC-CchhHHHHHHHHHHcccCC---CCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHH
Confidence            455666665554333444 2333334433222211111   124689999999999998999999999999999887621


Q ss_pred             -----------------------CCCCCccCCCCCCC
Q 018689          231 -----------------------HNSCPVCRYELPTD  244 (352)
Q Consensus       231 -----------------------~~sCP~CR~~l~~~  244 (352)
                                             ...||+||..|..+
T Consensus       152 ~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e  188 (368)
T KOG4445|consen  152 CLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIE  188 (368)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccc
Confidence                                   12599999988544

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

Probab=97.17  E-value=0.0001  Score=72.63  Aligned_cols=48  Identities=25%  Similarity=0.894  Sum_probs=40.1

Q ss_pred             CccccccccccccCCceEcccCceecccchHHHhhc--CCCCCccCCCCCCCC
Q 018689          195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL--HNSCPVCRYELPTDD  245 (352)
Q Consensus       195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~--~~sCP~CR~~l~~~~  245 (352)
                      ..|.||-|.   +..+++-||||..|..|+..|-..  .++||.||.+|.-.+
T Consensus       370 eLCKICaen---dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte  419 (563)
T KOG1785|consen  370 ELCKICAEN---DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTE  419 (563)
T ss_pred             HHHHHhhcc---CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEecccc
Confidence            579999887   445888899999999999999733  679999999986544

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

Probab=97.13  E-value=0.0001  Score=78.04  Aligned_cols=48  Identities=23%  Similarity=0.655  Sum_probs=40.1

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhh-cCCCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLE-LHNSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~-~~~sCP~CR~~l~~~  244 (352)
                      -..|++|-..+++   +++..|+|+||..||.+-+. ++..||.|...+-.-
T Consensus       643 ~LkCs~Cn~R~Kd---~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan  691 (698)
T KOG0978|consen  643 LLKCSVCNTRWKD---AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAN  691 (698)
T ss_pred             ceeCCCccCchhh---HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence            4689999988766   66677999999999999995 577899998887543

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

Probab=97.07  E-value=3.3e-05  Score=55.62  Aligned_cols=47  Identities=26%  Similarity=0.622  Sum_probs=35.1

Q ss_pred             CCccccccccccccCCceEcccCce-ecccchHHHh-hcCCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHI-YHPDCIMPWL-ELHNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~-FH~~Ci~~Wl-~~~~sCP~CR~~l~~  243 (352)
                      ..+|.||+|.-.+   .++..|||+ .|..|-.+.+ ..+..||+||.++..
T Consensus         7 ~dECTICye~pvd---sVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~d   55 (62)
T KOG4172|consen    7 SDECTICYEHPVD---SVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKD   55 (62)
T ss_pred             ccceeeeccCcch---HHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHH
Confidence            3789999987544   445569997 6788855544 478999999998753

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

Probab=96.95  E-value=0.00033  Score=61.38  Aligned_cols=42  Identities=26%  Similarity=0.786  Sum_probs=36.1

Q ss_pred             CcceeccccccCCCCccccccccccccCCceEcccCceeccc
Q 018689          181 PSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPD  222 (352)
Q Consensus       181 p~~~~~~~~~~~~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~  222 (352)
                      |.+.+.+..+..+..+|.||+|+++.++.+..|||-.+||+.
T Consensus       164 PrlsYNdDVL~ddkGECvICLEdL~~GdtIARLPCLCIYHK~  205 (205)
T KOG0801|consen  164 PRLSYNDDVLKDDKGECVICLEDLEAGDTIARLPCLCIYHKQ  205 (205)
T ss_pred             cccccccchhcccCCcEEEEhhhccCCCceeccceEEEeecC
Confidence            455666666677788999999999999999999999999973

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

Probab=96.89  E-value=0.00036  Score=70.07  Aligned_cols=47  Identities=30%  Similarity=0.708  Sum_probs=42.0

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~  243 (352)
                      +..|.||+..+..   ++.+||||.||..||++-+.....||+||..+..
T Consensus        84 ef~c~vc~~~l~~---pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   84 EFECCVCSRALYP---PVVTPCGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             hhhhhhhHhhcCC---CccccccccccHHHHHHHhccCCCCccccccccc
Confidence            5899999888776   7888999999999999988878889999999974

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

Probab=96.84  E-value=0.00055  Score=68.87  Aligned_cols=49  Identities=31%  Similarity=0.729  Sum_probs=42.0

Q ss_pred             CCCccccccccccccCCceE-cccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQ-MPCKHIYHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~-lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      ++..|+||...+.+   +.. ..|+|.||..|+..|+..+..||.|+..+...
T Consensus        20 ~~l~C~~C~~vl~~---p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~   69 (391)
T KOG0297|consen   20 ENLLCPICMSVLRD---PVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQA   69 (391)
T ss_pred             ccccCccccccccC---CCCCCCCCCcccccccchhhccCcCCcccccccchh
Confidence            35899999999887   444 57999999999999999999999998887543

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

Probab=96.72  E-value=0.00068  Score=75.46  Aligned_cols=70  Identities=26%  Similarity=0.562  Sum_probs=50.8

Q ss_pred             HHHHhhCCcceeccccc-cCCCCccccccccccccCCceEcccCceecccchHHHhhcC----------CCCCccCCCCC
Q 018689          174 KSAIEALPSIKINEAMM-SSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH----------NSCPVCRYELP  242 (352)
Q Consensus       174 ~~~i~~lp~~~~~~~~~-~~~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~----------~sCP~CR~~l~  242 (352)
                      +..-..||......+.. ...+..|.||+.+--.....+.|.|+|+||..|...-|++.          .+||+|+.+|.
T Consensus      3465 kNEE~CLPCl~Cdks~tkQD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3465 KNEEHCLPCLHCDKSATKQDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             cchhhcccccccChhhhhcccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            33445666665544333 22368999999886666778999999999999998876542          27999999874


Q ss_pred             C
Q 018689          243 T  243 (352)
Q Consensus       243 ~  243 (352)
                      .
T Consensus      3545 H 3545 (3738)
T KOG1428|consen 3545 H 3545 (3738)
T ss_pred             h
Confidence            3

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

Probab=96.63  E-value=0.00036  Score=68.74  Aligned_cols=46  Identities=39%  Similarity=0.908  Sum_probs=38.7

Q ss_pred             CCcccccccccccc-CCceEcccCceecccchHHHhhcC--CCCCccCC
Q 018689          194 SSQCAVCKDSFELN-EEARQMPCKHIYHPDCIMPWLELH--NSCPVCRY  239 (352)
Q Consensus       194 ~~~C~IC~e~~~~~-~~~~~lpC~H~FH~~Ci~~Wl~~~--~sCP~CR~  239 (352)
                      ..-|-.|-+.+... +....|||.|+||..|+...|+++  .+||.||+
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            46899999988654 457889999999999999999664  58999994

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

Probab=96.62  E-value=0.00076  Score=49.50  Aligned_cols=41  Identities=24%  Similarity=0.668  Sum_probs=28.1

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhc--CCCCCc
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL--HNSCPV  236 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~--~~sCP~  236 (352)
                      ...|+|.+..|+.  .++...|+|+|-+..|..||+.  ...||+
T Consensus        11 ~~~CPiT~~~~~~--PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   11 SLKCPITLQPFED--PVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             -SB-TTTSSB-SS--EEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             ccCCCCcCChhhC--CcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            4799999999876  3555679999999999999944  447998

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

Probab=96.44  E-value=0.0021  Score=45.22  Aligned_cols=40  Identities=28%  Similarity=0.861  Sum_probs=27.5

Q ss_pred             cccccccccccCCceEcccC-----ceecccchHHHhhc--CCCCCcc
Q 018689          197 CAVCKDSFELNEEARQMPCK-----HIYHPDCIMPWLEL--HNSCPVC  237 (352)
Q Consensus       197 C~IC~e~~~~~~~~~~lpC~-----H~FH~~Ci~~Wl~~--~~sCP~C  237 (352)
                      |-||++.-.... ..+.||.     ...|..|+.+|+..  ..+|++|
T Consensus         1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            779999876654 5667863     37899999999964  5679988

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

Probab=96.44  E-value=0.00052  Score=66.43  Aligned_cols=46  Identities=26%  Similarity=0.662  Sum_probs=39.6

Q ss_pred             CCccccccccccccCCceEcc-cCceecccchHHHhhcCCCCCccCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      ..+|.+|...|.+   +..+. |-|.||+.||.+.|+..++||.|...|-
T Consensus        15 ~itC~LC~GYliD---ATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih   61 (331)
T KOG2660|consen   15 HITCRLCGGYLID---ATTITECLHTFCKSCIVKYLEESKYCPTCDIVIH   61 (331)
T ss_pred             ceehhhccceeec---chhHHHHHHHHHHHHHHHHHHHhccCCccceecc
Confidence            5799999988877   44455 9999999999999999999999988664

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

Probab=96.02  E-value=0.0029  Score=61.82  Aligned_cols=51  Identities=24%  Similarity=0.406  Sum_probs=43.1

Q ss_pred             CCCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689          192 SDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD  245 (352)
Q Consensus       192 ~~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~  245 (352)
                      .++..|+||+..-   -.++..||+|.=|+.||.+.|...+.|=.|+..+.+..
T Consensus       420 sEd~lCpICyA~p---i~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~~~  470 (489)
T KOG4692|consen  420 SEDNLCPICYAGP---INAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVIDVI  470 (489)
T ss_pred             cccccCcceeccc---chhhccCCCCchHHHHHHHHHhcCCeeeEecceeeehh
Confidence            4568999998763   34778899999999999999999999999999887533

>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=96.00  E-value=0.0037  Score=50.59  Aligned_cols=31  Identities=32%  Similarity=0.734  Sum_probs=27.0

Q ss_pred             CCccccccccccccCCceEcccCceecccchH
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIM  225 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~  225 (352)
                      ...|+||...+.. ......||+|+||..|+.
T Consensus        78 ~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   78 STKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence            5789999999876 567788999999999985

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 [].

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

Probab=95.93  E-value=0.0016  Score=55.71  Aligned_cols=35  Identities=20%  Similarity=0.561  Sum_probs=30.6

Q ss_pred             CCccccccccccccCCceEcccC------ceecccchHHHh
Q 018689          194 SSQCAVCKDSFELNEEARQMPCK------HIYHPDCIMPWL  228 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~------H~FH~~Ci~~Wl  228 (352)
                      ..+|.||++.+...+.++.++|+      |+||..|+++|-
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~   66 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWR   66 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence            46899999999886678888886      899999999994

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

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

Probab=95.88  E-value=0.0034  Score=44.39  Aligned_cols=44  Identities=25%  Similarity=0.588  Sum_probs=21.9

Q ss_pred             cccccccccccCCceEcc--cCceecccchHHHhh-cCCCCCccCCCC
Q 018689          197 CAVCKDSFELNEEARQMP--CKHIYHPDCIMPWLE-LHNSCPVCRYEL  241 (352)
Q Consensus       197 C~IC~e~~~~~~~~~~lp--C~H~FH~~Ci~~Wl~-~~~sCP~CR~~l  241 (352)
                      |++|.+++.. .....+|  |++.++..|...-++ ....||-||.+.
T Consensus         1 cp~C~e~~d~-~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDE-TDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--C-CCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCccccccc-CCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            7899999833 2334555  899999999888775 477899999864

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

Probab=95.86  E-value=0.0033  Score=64.31  Aligned_cols=49  Identities=31%  Similarity=0.676  Sum_probs=39.9

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhc-----CCCCCccCCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-----HNSCPVCRYELPTDD  245 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-----~~sCP~CR~~l~~~~  245 (352)
                      ...|.+|-+.-++   .+...|.|.||+.||..++..     .-+||+|...|..+.
T Consensus       536 ~~~C~lc~d~aed---~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDl  589 (791)
T KOG1002|consen  536 EVECGLCHDPAED---YIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDL  589 (791)
T ss_pred             ceeecccCChhhh---hHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccc
Confidence            5789999987444   778889999999999998743     458999988886554

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

Probab=95.73  E-value=0.009  Score=56.70  Aligned_cols=49  Identities=24%  Similarity=0.535  Sum_probs=37.5

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhc--CCCCCccCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL--HNSCPVCRYELPT  243 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~--~~sCP~CR~~l~~  243 (352)
                      .+.+|++|-+.-..  .....+|+|+||.-||..-+..  ..+||.|-..+.+
T Consensus       238 ~~~~C~~Cg~~Pti--P~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~  288 (298)
T KOG2879|consen  238 SDTECPVCGEPPTI--PHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEP  288 (298)
T ss_pred             CCceeeccCCCCCC--CeeeccccceeehhhhhhhhcchhhcccCccCCCCcc
Confidence            36899999887544  2445569999999999987653  4689999887753

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

Probab=95.71  E-value=0.0024  Score=57.88  Aligned_cols=45  Identities=22%  Similarity=0.547  Sum_probs=39.6

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYEL  241 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l  241 (352)
                      ...|.||.++|+.   +++..|||.||..|...-++....|-+|-+..
T Consensus       196 PF~C~iCKkdy~s---pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t  240 (259)
T COG5152         196 PFLCGICKKDYES---PVVTECGHSFCSLCAIRKYQKGDECGVCGKAT  240 (259)
T ss_pred             ceeehhchhhccc---hhhhhcchhHHHHHHHHHhccCCcceecchhh
Confidence            4689999999988   77888999999999988888888999997754

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

Probab=95.63  E-value=0.0036  Score=67.15  Aligned_cols=51  Identities=24%  Similarity=0.683  Sum_probs=38.2

Q ss_pred             cCCCCccccccccccccCCceEcc-cCceecccchHHHhhcC-------CCCCccCCCC
Q 018689          191 SSDSSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELH-------NSCPVCRYEL  241 (352)
Q Consensus       191 ~~~~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~-------~sCP~CR~~l  241 (352)
                      .....+|.||++.+.....+.... |-|+||..||.+|-+..       -.||.|+...
T Consensus       188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~  246 (950)
T KOG1952|consen  188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVS  246 (950)
T ss_pred             hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchh
Confidence            344689999999998755444333 88999999999997541       1599998543

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

Probab=95.54  E-value=0.004  Score=61.98  Aligned_cols=46  Identities=17%  Similarity=0.569  Sum_probs=38.1

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcC--------CCCCccCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH--------NSCPVCRY  239 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~--------~sCP~CR~  239 (352)
                      ...|.||+++..-....+.|||+|+||+.|++.++..+        -.||-|.-
T Consensus       184 lf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  184 LFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             cccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            57999999998776789999999999999999998543        25876654

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

Probab=95.52  E-value=0.0067  Score=56.01  Aligned_cols=50  Identities=20%  Similarity=0.614  Sum_probs=40.5

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhc--------CCCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL--------HNSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~--------~~sCP~CR~~l~~~  244 (352)
                      ...|..|.-.+..++.+ .|-|-|+||.+|+..|-..        ...||.|..+|.+.
T Consensus        50 ~pNC~LC~t~La~gdt~-RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp  107 (299)
T KOG3970|consen   50 NPNCRLCNTPLASGDTT-RLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP  107 (299)
T ss_pred             CCCCceeCCccccCcce-eehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence            46799999998887654 6779999999999999643        23699999998653

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=95.52  E-value=0.011  Score=42.90  Aligned_cols=46  Identities=28%  Similarity=0.681  Sum_probs=35.0

Q ss_pred             CccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689          195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD  245 (352)
Q Consensus       195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~  245 (352)
                      ..|..|...   +.+-.++||+|+.+..|..-  ++-+-||+|-+++..++
T Consensus         8 ~~~~~~~~~---~~~~~~~pCgH~I~~~~f~~--~rYngCPfC~~~~~~~~   53 (55)
T PF14447_consen    8 QPCVFCGFV---GTKGTVLPCGHLICDNCFPG--ERYNGCPFCGTPFEFDD   53 (55)
T ss_pred             eeEEEcccc---ccccccccccceeeccccCh--hhccCCCCCCCcccCCC
Confidence            456666554   44578899999999999664  56778999999886554

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.44  E-value=0.0074  Score=56.43  Aligned_cols=58  Identities=19%  Similarity=0.276  Sum_probs=48.3

Q ss_pred             CCCccccccccccccCCceEc-ccCceecccchHHHhhcCCCCCccCCCCCCCChhHHH
Q 018689          193 DSSQCAVCKDSFELNEEARQM-PCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYEQ  250 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~~~~e~  250 (352)
                      ....|+||.+.+.....+..| ||||+|+..|+.+.+.....||+|-.++...+...-+
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~Lq  278 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIGLQ  278 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEeee
Confidence            357899999999887766666 4999999999999999999999999998776554433

>PHA02862 5L protein; Provisional

Probab=95.37  E-value=0.0054  Score=52.97  Aligned_cols=45  Identities=20%  Similarity=0.676  Sum_probs=34.5

Q ss_pred             CccccccccccccCCceEcccC-----ceecccchHHHhhc--CCCCCccCCCCCC
Q 018689          195 SQCAVCKDSFELNEEARQMPCK-----HIYHPDCIMPWLEL--HNSCPVCRYELPT  243 (352)
Q Consensus       195 ~~C~IC~e~~~~~~~~~~lpC~-----H~FH~~Ci~~Wl~~--~~sCP~CR~~l~~  243 (352)
                      ..|-||+++-++  .  .-||.     ...|..|+.+|+..  +.+|++|+.+...
T Consensus         3 diCWIC~~~~~e--~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I   54 (156)
T PHA02862          3 DICWICNDVCDE--R--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI   54 (156)
T ss_pred             CEEEEecCcCCC--C--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence            589999998433  2  35653     57899999999954  5689999998754

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

Probab=95.28  E-value=0.0011  Score=65.45  Aligned_cols=52  Identities=31%  Similarity=0.708  Sum_probs=45.4

Q ss_pred             CCcccccccccccc-CCceEcccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689          194 SSQCAVCKDSFELN-EEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD  245 (352)
Q Consensus       194 ~~~C~IC~e~~~~~-~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~  245 (352)
                      ...|+||.+.++.. +++..+-|||.+|..||.+||.....||.|+.+|+...
T Consensus       196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~~  248 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPKNG  248 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhhhh
Confidence            46899999999876 66778889999999999999999889999999986543

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

Probab=95.27  E-value=0.0035  Score=59.89  Aligned_cols=42  Identities=29%  Similarity=0.645  Sum_probs=33.1

Q ss_pred             CCccccccccccccCCceEcccCcee-cccchHHHhhcCCCCCccCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIY-HPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~F-H~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      ...|+||++.-.+   ...|+|||.. |..|-+.    -+.||+||+.|.
T Consensus       300 ~~LC~ICmDaP~D---CvfLeCGHmVtCt~CGkr----m~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAPRD---CVFLECGHMVTCTKCGKR----MNECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCCcc---eEEeecCcEEeehhhccc----cccCchHHHHHH
Confidence            4689999998655   8999999974 6677554    458999998764

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

Probab=95.20  E-value=0.0072  Score=57.89  Aligned_cols=46  Identities=20%  Similarity=0.478  Sum_probs=40.6

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      ...|-||...|..   .++..|+|.||..|...-++....|.+|-+.+.
T Consensus       241 Pf~c~icr~~f~~---pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~  286 (313)
T KOG1813|consen  241 PFKCFICRKYFYR---PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTH  286 (313)
T ss_pred             Ccccccccccccc---chhhcCCceeehhhhccccccCCcceecccccc
Confidence            3679999999987   778889999999999998888899999988764

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

Probab=95.15  E-value=0.0098  Score=58.40  Aligned_cols=43  Identities=33%  Similarity=0.712  Sum_probs=33.4

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      ...|.||+++...   .+.+||||+-|  |+.-- +.-.+||+||..+.
T Consensus       305 p~lcVVcl~e~~~---~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI~  347 (355)
T KOG1571|consen  305 PDLCVVCLDEPKS---AVFVPCGHVCC--CTLCS-KHLPQCPVCRQRIR  347 (355)
T ss_pred             CCceEEecCCccc---eeeecCCcEEE--chHHH-hhCCCCchhHHHHH
Confidence            5789999999766   88999999976  66543 23345999998774

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=94.87  E-value=0.012  Score=51.68  Aligned_cols=47  Identities=28%  Similarity=0.762  Sum_probs=34.6

Q ss_pred             CCCccccccccccccCCceEccc--Cc---eecccchHHHhhc--CCCCCccCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPC--KH---IYHPDCIMPWLEL--HNSCPVCRYELPT  243 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC--~H---~FH~~Ci~~Wl~~--~~sCP~CR~~l~~  243 (352)
                      .+..|-||.++-..    ..-||  ..   ..|..|+..|+..  ..+|++|+++...
T Consensus         7 ~~~~CRIC~~~~~~----~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i   60 (162)
T PHA02825          7 MDKCCWICKDEYDV----VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNI   60 (162)
T ss_pred             CCCeeEecCCCCCC----ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEE
Confidence            35799999988432    23465  44   5699999999964  4589999987753

>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=94.79  E-value=0.01  Score=40.98  Aligned_cols=41  Identities=24%  Similarity=0.729  Sum_probs=24.3

Q ss_pred             cccccccccccCCceEcccCceecccchHHHhhcCC--CCCcc
Q 018689          197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHN--SCPVC  237 (352)
Q Consensus       197 C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~--sCP~C  237 (352)
                      |.+|.+.+..+.....-.|+=.+|..|+..+++...  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            778888887765444445999999999999997655  79988

; PDB: 3NW0_A 2CT0_A.

>PF04641 Rtf2: Rtf2 RING-finger

Probab=94.74  E-value=0.049  Score=51.85  Aligned_cols=92  Identities=21%  Similarity=0.385  Sum_probs=57.8

Q ss_pred             cHHHHHHHHHhcCCCCCCCCCCCHHHHh---hCCcceecccc-----------ccCCCCccccccccccccCCceE-ccc
Q 018689          151 GLEQLIQQLAENDPNRYGTPPASKSAIE---ALPSIKINEAM-----------MSSDSSQCAVCKDSFELNEEARQ-MPC  215 (352)
Q Consensus       151 ~le~li~~L~~~~~~~~g~~pas~~~i~---~lp~~~~~~~~-----------~~~~~~~C~IC~e~~~~~~~~~~-lpC  215 (352)
                      ..+.||+-|..-...  +..+..-.-|.   .|-.++++...           .......|||...+|......+. .+|
T Consensus        58 nKeaile~Ll~~~~~--~~~~~~~~hI~~LKDl~~l~~~~n~~~~~~~~~~~~~~~~~~~CPvt~~~~~~~~~fv~l~~c  135 (260)
T PF04641_consen   58 NKEAILEFLLDKKKN--KDLPKTFSHIKSLKDLVELKFTKNPSYKEEDKSSGDNSEGRFICPVTGKEFNGKHKFVYLRPC  135 (260)
T ss_pred             cHHHHHHHHHhcCcC--CCCccccccccCccceeeEEeEecCccccccccccccCCceeECCCCCcccCCceeEEEEcCC
Confidence            578888888865432  11222222333   33334444331           12336899999999965544444 479


Q ss_pred             CceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689          216 KHIYHPDCIMPWLELHNSCPVCRYELPTDD  245 (352)
Q Consensus       216 ~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~  245 (352)
                      ||+|...+|..- .....||+|-.++...|
T Consensus       136 G~V~s~~alke~-k~~~~Cp~c~~~f~~~D  164 (260)
T PF04641_consen  136 GCVFSEKALKEL-KKSKKCPVCGKPFTEED  164 (260)
T ss_pred             CCEeeHHHHHhh-cccccccccCCccccCC
Confidence            999999999986 33557999999875443

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

Probab=94.42  E-value=0.022  Score=55.74  Aligned_cols=47  Identities=28%  Similarity=0.736  Sum_probs=38.8

Q ss_pred             CCCCccccccccccccCCceEcccCceecccchHHH--hhcCCCCCccCCCC
Q 018689          192 SDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPW--LELHNSCPVCRYEL  241 (352)
Q Consensus       192 ~~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~W--l~~~~sCP~CR~~l  241 (352)
                      .+...|.||-+.+.-   ..++||+|..|..|....  |-..+.||+||.+.
T Consensus        59 Een~~C~ICA~~~TY---s~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~  107 (493)
T COG5236          59 EENMNCQICAGSTTY---SARYPCGHQICHACAVRLRALYMQKGCPLCRTET  107 (493)
T ss_pred             cccceeEEecCCceE---EEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence            346789999988665   788999999999997665  45688999999875

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

Probab=93.79  E-value=0.042  Score=45.99  Aligned_cols=37  Identities=24%  Similarity=0.618  Sum_probs=29.4

Q ss_pred             CCCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEccC
Q 018689           19 QEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELET   58 (352)
Q Consensus        19 ~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~~   58 (352)
                      -.+...||..|+..|....   .+..||.|+|..+.-+..
T Consensus        66 ~~p~~~~C~~C~~~~~~e~---~~~~CP~C~s~~~~i~~G  102 (115)
T COG0375          66 EEPAECWCLDCGQEVELEE---LDYRCPKCGSINLRIIGG  102 (115)
T ss_pred             EeccEEEeccCCCeecchh---heeECCCCCCCceEEecC
Confidence            4567899999999986443   567799999999887654

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

Probab=93.74  E-value=0.032  Score=54.20  Aligned_cols=49  Identities=20%  Similarity=0.474  Sum_probs=38.4

Q ss_pred             cCCCCccccccccccccCCceEcc-cCceecccchHHHhhcCCCCCccCCCCC
Q 018689          191 SSDSSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       191 ~~~~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      ..+...|+||+.....   ..++. -|-+||..||...+..++.||+=-.++.
T Consensus       297 ~~~~~~CpvClk~r~N---ptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~  346 (357)
T KOG0826|consen  297 PPDREVCPVCLKKRQN---PTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPAS  346 (357)
T ss_pred             CCccccChhHHhccCC---CceEEecceEEeHHHHHHHHHhcCCCCccCCcch
Confidence            3446899999987544   33444 5999999999999999999999766553

>PHA03096 p28-like protein; Provisional

Probab=93.73  E-value=0.021  Score=55.15  Aligned_cols=45  Identities=20%  Similarity=0.458  Sum_probs=32.2

Q ss_pred             Ccccccccccccc----CCceEcc-cCceecccchHHHhhc---CCCCCccCC
Q 018689          195 SQCAVCKDSFELN----EEARQMP-CKHIYHPDCIMPWLEL---HNSCPVCRY  239 (352)
Q Consensus       195 ~~C~IC~e~~~~~----~~~~~lp-C~H~FH~~Ci~~Wl~~---~~sCP~CR~  239 (352)
                      ..|.||++.....    ..-..|+ |.|.||..||..|...   ..+||.||.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            6899999987643    2345566 9999999999999743   234444443

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

Probab=93.72  E-value=0.028  Score=50.26  Aligned_cols=50  Identities=20%  Similarity=0.568  Sum_probs=35.5

Q ss_pred             CCcccccccccccc----CCceEcccCceecccchHHHhhcC-----------CCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELN----EEARQMPCKHIYHPDCIMPWLELH-----------NSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~----~~~~~lpC~H~FH~~Ci~~Wl~~~-----------~sCP~CR~~l~~  243 (352)
                      ...|-||+..--.+    ...--..|+.-||.-|+..||+.-           ..||.|..++..
T Consensus       165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pial  229 (234)
T KOG3268|consen  165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIAL  229 (234)
T ss_pred             hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCccee
Confidence            45788887654333    233445699999999999999641           159999888753

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

Probab=93.44  E-value=0.059  Score=51.87  Aligned_cols=47  Identities=23%  Similarity=0.660  Sum_probs=39.1

Q ss_pred             CccccccccccccC---CceEcccCceecccchHHHhhc-CCCCCccCCCC
Q 018689          195 SQCAVCKDSFELNE---EARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYEL  241 (352)
Q Consensus       195 ~~C~IC~e~~~~~~---~~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l  241 (352)
                      ..|-||-++|...+   .++.|.|||.|+..|+.+.+.. ...||.||...
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            57999999998763   4777889999999999987754 45799999985

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

Probab=93.39  E-value=0.026  Score=52.68  Aligned_cols=44  Identities=18%  Similarity=0.580  Sum_probs=32.8

Q ss_pred             CccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCC
Q 018689          195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYEL  241 (352)
Q Consensus       195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l  241 (352)
                      ..|-.|...-. .+...++.|.|+||..|...-.  ...||+|++.|
T Consensus         4 VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~--~~~C~lCkk~i   47 (233)
T KOG4739|consen    4 VHCNKCFRFPS-QDPFFLTACRHVFCEPCLKASS--PDVCPLCKKSI   47 (233)
T ss_pred             EEeccccccCC-CCceeeeechhhhhhhhcccCC--cccccccccee
Confidence            35777765443 6677778899999999976532  22899999976

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

Probab=93.31  E-value=0.04  Score=52.93  Aligned_cols=43  Identities=28%  Similarity=0.675  Sum_probs=34.2

Q ss_pred             CCccccccccccccCCceEcc-cCceecccchHHHh-hcCCCCCccCC
Q 018689          194 SSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWL-ELHNSCPVCRY  239 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl-~~~~sCP~CR~  239 (352)
                      ...|+.|..-+..   +.+.| |+|.||..||..-| .....||.|..
T Consensus       274 ~LkCplc~~Llrn---p~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         274 SLKCPLCHCLLRN---PMKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             cccCcchhhhhhC---cccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            3789999887665   45556 99999999999776 56778999944

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=93.10  E-value=0.062  Score=38.95  Aligned_cols=39  Identities=28%  Similarity=0.675  Sum_probs=32.3

Q ss_pred             CCccccccccccccCCceEcc-cCceecccchHHHhhcCCCCCc
Q 018689          194 SSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHNSCPV  236 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~sCP~  236 (352)
                      ...|.+|-+.|+.++.+++-| |+-.||+.|..+    ...|-+
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~   44 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCIN   44 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEe
Confidence            468999999999888999999 999999999543    445544

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

Probab=93.00  E-value=0.038  Score=52.96  Aligned_cols=45  Identities=29%  Similarity=0.721  Sum_probs=38.3

Q ss_pred             Ccccccccccccc-CCceEcccCceecccchHHHhhcCCCCCccCC
Q 018689          195 SQCAVCKDSFELN-EEARQMPCKHIYHPDCIMPWLELHNSCPVCRY  239 (352)
Q Consensus       195 ~~C~IC~e~~~~~-~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~  239 (352)
                      ..|+||.+.+... ..+..++|||.-|..|+......+-+||+|.+
T Consensus       159 ~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  159 FNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             CCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence            4599999987665 35778899999999999988877799999988

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

Probab=92.76  E-value=0.086  Score=46.36  Aligned_cols=54  Identities=20%  Similarity=0.445  Sum_probs=36.3

Q ss_pred             CCccccccccccccCCceEcccC-------------ceecccchHHHhhc------------------------------
Q 018689          194 SSQCAVCKDSFELNEEARQMPCK-------------HIYHPDCIMPWLEL------------------------------  230 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~-------------H~FH~~Ci~~Wl~~------------------------------  230 (352)
                      +..|+||||.-..   +++|-|.             -.-|..|++++-+.                              
T Consensus         2 d~~CpICme~PHN---AVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (162)
T PF07800_consen    2 DVTCPICMEHPHN---AVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQ   78 (162)
T ss_pred             CccCceeccCCCc---eEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCccccccccccc
Confidence            4789999997433   6666552             22478899987532                              


Q ss_pred             -CCCCCccCCCCCCCChhHHH
Q 018689          231 -HNSCPVCRYELPTDDPDYEQ  250 (352)
Q Consensus       231 -~~sCP~CR~~l~~~~~~~e~  250 (352)
                       +-.||+||.+|.......+.
T Consensus        79 ~~L~CPLCRG~V~GWtvve~A   99 (162)
T PF07800_consen   79 PELACPLCRGEVKGWTVVEPA   99 (162)
T ss_pred             ccccCccccCceeceEEchHH
Confidence             11499999999766544443

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

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

Probab=92.28  E-value=0.045  Score=52.89  Aligned_cols=43  Identities=26%  Similarity=0.764  Sum_probs=31.0

Q ss_pred             CccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCC
Q 018689          195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYEL  241 (352)
Q Consensus       195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l  241 (352)
                      -.|--|-..+..  .-+.+||+|+||.+|...  ...+.||.|-..|
T Consensus        91 HfCd~Cd~PI~I--YGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen   91 HFCDRCDFPIAI--YGRMIPCKHVFCLECARS--DSDKICPLCDDRV  133 (389)
T ss_pred             EeecccCCccee--eecccccchhhhhhhhhc--CccccCcCcccHH
Confidence            356667555444  567889999999999653  3466899997665

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

Probab=91.84  E-value=0.052  Score=58.56  Aligned_cols=43  Identities=33%  Similarity=0.849  Sum_probs=34.4

Q ss_pred             CccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689          195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      ..|..|--.+..  ..+..-|||.||..|+.   .....||.|+.++.
T Consensus       841 skCs~C~~~Ldl--P~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~~  883 (933)
T KOG2114|consen  841 SKCSACEGTLDL--PFVHFLCGHSYHQHCLE---DKEDKCPKCLPELR  883 (933)
T ss_pred             eeecccCCcccc--ceeeeecccHHHHHhhc---cCcccCCccchhhh
Confidence            589999887765  45666799999999988   44568999998654

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

Probab=91.52  E-value=0.07  Score=59.98  Aligned_cols=45  Identities=24%  Similarity=0.554  Sum_probs=38.0

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYE  240 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~  240 (352)
                      ...|.||++.+..  ...+..|+|.||..|+..|+..+..||+|+..
T Consensus      1153 ~~~c~ic~dil~~--~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi 1197 (1394)
T KOG0298|consen 1153 HFVCEICLDILRN--QGGIAGCGHEPCCRCDELWLYASSRCPICKSI 1197 (1394)
T ss_pred             ccchHHHHHHHHh--cCCeeeechhHhhhHHHHHHHHhccCcchhhh
Confidence            4589999999874  23455699999999999999999999999753

>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=91.40  E-value=0.062  Score=37.82  Aligned_cols=44  Identities=27%  Similarity=0.652  Sum_probs=25.6

Q ss_pred             ccccccccccccCCceEccc-CceecccchHHHhhcCCCCCccCCCCCCC
Q 018689          196 QCAVCKDSFELNEEARQMPC-KHIYHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       196 ~C~IC~e~~~~~~~~~~lpC-~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      .|.-|.-..     ...+.| .|..|..|+...|.....||+|.++||+.
T Consensus         4 nCKsCWf~~-----k~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen    4 NCKSCWFAN-----KGLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK   48 (50)
T ss_dssp             ---SS-S-------SSEEE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred             cChhhhhcC-----CCeeeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence            455565442     224557 49999999999999999999999999864

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.

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

Probab=91.14  E-value=0.12  Score=50.33  Aligned_cols=44  Identities=27%  Similarity=0.714  Sum_probs=35.3

Q ss_pred             CCCccccccccccccCCceEccc--CceecccchHHHhhcCCCCCccCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPC--KHIYHPDCIMPWLELHNSCPVCRYELPT  243 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC--~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~  243 (352)
                      +-.+|+||.+.+..    -.+.|  ||+-|..|-.   +..+.||.||.++..
T Consensus        47 ~lleCPvC~~~l~~----Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g~   92 (299)
T KOG3002|consen   47 DLLDCPVCFNPLSP----PIFQCDNGHLACSSCRT---KVSNKCPTCRLPIGN   92 (299)
T ss_pred             hhccCchhhccCcc----cceecCCCcEehhhhhh---hhcccCCcccccccc
Confidence            35799999999876    34556  7999999965   457889999999973

>TIGR00100 hypA hydrogenase nickel insertion protein HypA

Probab=89.87  E-value=0.25  Score=41.35  Aligned_cols=37  Identities=24%  Similarity=0.547  Sum_probs=27.5

Q ss_pred             CCCCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEcc
Q 018689           18 QQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELE   57 (352)
Q Consensus        18 ~~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~   57 (352)
                      ...+...||..|...+.+..   ....||.|++..++-+.
T Consensus        65 ~~~p~~~~C~~Cg~~~~~~~---~~~~CP~Cgs~~~~i~~  101 (115)
T TIGR00100        65 EDEPVECECEDCSEEVSPEI---DLYRCPKCHGIMLQVRA  101 (115)
T ss_pred             EeeCcEEEcccCCCEEecCC---cCccCcCCcCCCcEEec
Confidence            34567899999998875432   46789999998766543

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

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=89.68  E-value=0.11  Score=50.78  Aligned_cols=50  Identities=20%  Similarity=0.548  Sum_probs=36.2

Q ss_pred             CCccccccccccccCC-ceEcccCceecccchHHHhh-cCCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEE-ARQMPCKHIYHPDCIMPWLE-LHNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~-~~~lpC~H~FH~~Ci~~Wl~-~~~sCP~CR~~l~~  243 (352)
                      +..|+.|++.+...++ -.-.|||...|.-|...--+ .+..||.||.....
T Consensus        14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~d   65 (480)
T COG5175          14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDD   65 (480)
T ss_pred             cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccc
Confidence            4569999999987654 44456998888888554332 35689999987643

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

Probab=89.41  E-value=0.36  Score=33.48  Aligned_cols=34  Identities=24%  Similarity=0.554  Sum_probs=27.0

Q ss_pred             CceeeecCCcccccCCCCCCCCcCCCCCCCceEEc
Q 018689           22 QMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEEL   56 (352)
Q Consensus        22 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi   56 (352)
                      ..|-|-.|...+.+.... ..+.||+|++.|+...
T Consensus         2 ~~y~C~~CG~~~~~~~~~-~~~~Cp~CG~~~~~~~   35 (46)
T PRK00398          2 AEYKCARCGREVELDEYG-TGVRCPYCGYRILFKE   35 (46)
T ss_pred             CEEECCCCCCEEEECCCC-CceECCCCCCeEEEcc
Confidence            469999999998876532 3799999999888543

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

Probab=88.85  E-value=0.31  Score=48.56  Aligned_cols=29  Identities=24%  Similarity=0.857  Sum_probs=21.8

Q ss_pred             cCceecccchHHHhhcC-------------CCCCccCCCCCC
Q 018689          215 CKHIYHPDCIMPWLELH-------------NSCPVCRYELPT  243 (352)
Q Consensus       215 C~H~FH~~Ci~~Wl~~~-------------~sCP~CR~~l~~  243 (352)
                      |.-++|.+|+-+|+..+             -.||+||+.+..
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi  352 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI  352 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence            45567789999998432             269999998764

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

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=88.79  E-value=0.35  Score=40.37  Aligned_cols=38  Identities=18%  Similarity=0.601  Sum_probs=27.0

Q ss_pred             CCCCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEcc
Q 018689           18 QQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELE   57 (352)
Q Consensus        18 ~~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~   57 (352)
                      ...+..+||..|...+.+..  .....||.|++.-++-+.
T Consensus        65 ~~~p~~~~C~~Cg~~~~~~~--~~~~~CP~Cgs~~~~i~~  102 (114)
T PRK03681         65 EEQEAECWCETCQQYVTLLT--QRVRRCPQCHGDMLRIVA  102 (114)
T ss_pred             EeeCcEEEcccCCCeeecCC--ccCCcCcCcCCCCcEEcc
Confidence            44568899999998875432  123669999988766543

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

Probab=88.64  E-value=0.26  Score=49.25  Aligned_cols=46  Identities=20%  Similarity=0.353  Sum_probs=39.3

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcC---CCCCccCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH---NSCPVCRY  239 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~---~sCP~CR~  239 (352)
                      ...|||=.+.-.+...+..|.|||+..++-|.+..+..   ..||.|=.
T Consensus       334 vF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~  382 (394)
T KOG2817|consen  334 VFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPV  382 (394)
T ss_pred             eeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence            57999999998888899999999999999999876543   36999944

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

Probab=87.94  E-value=0.13  Score=55.36  Aligned_cols=45  Identities=24%  Similarity=0.614  Sum_probs=36.6

Q ss_pred             CccccccccccccCCceEcccCceecccchHHHhhc--CCCCCccCCCCCC
Q 018689          195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL--HNSCPVCRYELPT  243 (352)
Q Consensus       195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~--~~sCP~CR~~l~~  243 (352)
                      ..|.||++    .+.....+|+|.||..|+.+-+..  ...||+||..+..
T Consensus       455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~  501 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKE  501 (674)
T ss_pred             cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHH
Confidence            79999999    345778889999999999988754  2369999987753

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=87.37  E-value=0.36  Score=29.76  Aligned_cols=23  Identities=35%  Similarity=0.797  Sum_probs=19.2

Q ss_pred             eecCCcccccCCCCCCCCcCCCCCCCce
Q 018689           26 CHQCNRTVRVTPSPSSDLVCPSCNGGFI   53 (352)
Q Consensus        26 Ch~C~r~V~~~~~~~~~~~CP~C~~gFv   53 (352)
                      |-.|...|.+     ....||+|+-.|.
T Consensus         3 CP~C~~~V~~-----~~~~Cp~CG~~F~   25 (26)
T PF10571_consen    3 CPECGAEVPE-----SAKFCPHCGYDFE   25 (26)
T ss_pred             CCCCcCCchh-----hcCcCCCCCCCCc
Confidence            7889999864     5689999998884

Several members are annotated as putative helicases.

>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional

Probab=87.19  E-value=0.53  Score=39.26  Aligned_cols=36  Identities=25%  Similarity=0.661  Sum_probs=26.3

Q ss_pred             CCCCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEc
Q 018689           18 QQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEEL   56 (352)
Q Consensus        18 ~~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi   56 (352)
                      ...+..+||..|.....+.   .....||.|++.-++-+
T Consensus        65 ~~vp~~~~C~~Cg~~~~~~---~~~~~CP~Cgs~~~~i~  100 (113)
T PRK12380         65 VYKPAQAWCWDCSQVVEIH---QHDAQCPHCHGERLRVD  100 (113)
T ss_pred             EeeCcEEEcccCCCEEecC---CcCccCcCCCCCCcEEc
Confidence            3456889999999876543   24567999998766544

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

Probab=86.90  E-value=0.2  Score=54.60  Aligned_cols=34  Identities=24%  Similarity=0.726  Sum_probs=27.8

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHh
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWL  228 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl  228 (352)
                      .+.|.+|...+.. ..-.+.||||.||+.||.+-.
T Consensus       817 ~d~C~~C~~~ll~-~pF~vf~CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  817 QDSCDHCGRPLLI-KPFYVFPCGHCFHRDCLIRHV  850 (911)
T ss_pred             ccchHHhcchhhc-CcceeeeccchHHHHHHHHHH
Confidence            5799999887755 356678999999999998764

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

Probab=86.69  E-value=0.26  Score=52.76  Aligned_cols=40  Identities=30%  Similarity=0.783  Sum_probs=28.9

Q ss_pred             ccccccccccccCCceEcccCceecccchHHHhhcCCCCCc
Q 018689          196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPV  236 (352)
Q Consensus       196 ~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~  236 (352)
                      .|.||.-.+. +.......|+|+.|..|...|++....||.
T Consensus      1030 ~C~~C~l~V~-gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1030 QCAICHLAVR-GSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             eeeeEeeEee-ccchhhccccccccHHHHHHHHhcCCcCCC
Confidence            3455443332 233455679999999999999999999984

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

Probab=86.68  E-value=0.32  Score=49.03  Aligned_cols=37  Identities=22%  Similarity=0.624  Sum_probs=28.2

Q ss_pred             CCcccccc-ccccccCCceEcccCceecccchHHHhhc
Q 018689          194 SSQCAVCK-DSFELNEEARQMPCKHIYHPDCIMPWLEL  230 (352)
Q Consensus       194 ~~~C~IC~-e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~  230 (352)
                      ..+|.||+ +.....+....+.|+|.||..|+++.++.
T Consensus       146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev  183 (384)
T KOG1812|consen  146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEV  183 (384)
T ss_pred             cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhh
Confidence            57899999 44444344446669999999999998864

>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional

Probab=86.53  E-value=0.54  Score=39.42  Aligned_cols=38  Identities=16%  Similarity=0.313  Sum_probs=26.5

Q ss_pred             CCCCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEcc
Q 018689           18 QQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELE   57 (352)
Q Consensus        18 ~~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~   57 (352)
                      ...+..+||..|.....+..  .....||.|++..++-+.
T Consensus        66 e~vp~~~~C~~Cg~~~~~~~--~~~~~CP~Cgs~~~~i~~  103 (117)
T PRK00564         66 VDEKVELECKDCSHVFKPNA--LDYGVCEKCHSKNVIITQ  103 (117)
T ss_pred             EecCCEEEhhhCCCccccCC--ccCCcCcCCCCCceEEec
Confidence            44678899999997764321  123459999998877543

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.25  E-value=0.17  Score=47.74  Aligned_cols=48  Identities=31%  Similarity=0.677  Sum_probs=35.0

Q ss_pred             CCccccccccccccCCc-eEccc-----CceecccchHHHhhcC--------CCCCccCCCC
Q 018689          194 SSQCAVCKDSFELNEEA-RQMPC-----KHIYHPDCIMPWLELH--------NSCPVCRYEL  241 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~-~~lpC-----~H~FH~~Ci~~Wl~~~--------~sCP~CR~~l  241 (352)
                      +..|-||+..=++.... -+-||     .|..|..|+..|+..+        -+||.|+.+.
T Consensus        20 eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY   81 (293)
T KOG3053|consen   20 ERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY   81 (293)
T ss_pred             ceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence            57899998875543322 34466     4899999999999432        2699999875

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=86.13  E-value=0.54  Score=40.44  Aligned_cols=38  Identities=24%  Similarity=0.532  Sum_probs=26.0

Q ss_pred             CCCCceeeecCCcccccCC---------------CC---CCCCcCCCCCCCceEEc
Q 018689           19 QEPQMYFCHQCNRTVRVTP---------------SP---SSDLVCPSCNGGFIEEL   56 (352)
Q Consensus        19 ~~~~~ywCh~C~r~V~~~~---------------~~---~~~~~CP~C~~gFvEEi   56 (352)
                      ..+..|||..|.....+..               .+   .....||.|++.-++-+
T Consensus        66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~  121 (135)
T PRK03824         66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIV  121 (135)
T ss_pred             ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEe
Confidence            3458899999998776530               00   23467999998766543

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

Probab=85.74  E-value=0.35  Score=40.23  Aligned_cols=35  Identities=23%  Similarity=0.544  Sum_probs=23.2

Q ss_pred             CCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEcc
Q 018689           20 EPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELE   57 (352)
Q Consensus        20 ~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~   57 (352)
                      .+..+||..|.....+..   ....||+|++..++-+.
T Consensus        67 ~p~~~~C~~Cg~~~~~~~---~~~~CP~Cgs~~~~i~~  101 (113)
T PF01155_consen   67 VPARARCRDCGHEFEPDE---FDFSCPRCGSPDVEIIS  101 (113)
T ss_dssp             E--EEEETTTS-EEECHH---CCHH-SSSSSS-EEEEE
T ss_pred             cCCcEECCCCCCEEecCC---CCCCCcCCcCCCcEEcc
Confidence            457899999999976543   45889999999776543

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

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

Probab=84.43  E-value=1  Score=29.16  Aligned_cols=28  Identities=29%  Similarity=0.936  Sum_probs=21.8

Q ss_pred             eeeecCCcccccCCCCCCCCcCCCCCCCce
Q 018689           24 YFCHQCNRTVRVTPSPSSDLVCPSCNGGFI   53 (352)
Q Consensus        24 ywCh~C~r~V~~~~~~~~~~~CP~C~~gFv   53 (352)
                      |-|-.|...|.+..  ...+.||+|+...|
T Consensus         1 Y~C~~Cg~~~~~~~--~~~irC~~CG~RIl   28 (32)
T PF03604_consen    1 YICGECGAEVELKP--GDPIRCPECGHRIL   28 (32)
T ss_dssp             EBESSSSSSE-BST--SSTSSBSSSS-SEE
T ss_pred             CCCCcCCCeeEcCC--CCcEECCcCCCeEE
Confidence            78999999998765  46799999998765

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

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

Probab=83.65  E-value=0.32  Score=46.73  Aligned_cols=50  Identities=20%  Similarity=0.579  Sum_probs=37.6

Q ss_pred             CCccccccccccccCC-ceEcccC-----ceecccchHHHhh--cCCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEE-ARQMPCK-----HIYHPDCIMPWLE--LHNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~-~~~lpC~-----H~FH~~Ci~~Wl~--~~~sCP~CR~~l~~  243 (352)
                      ...|-||.++...... ..+.||.     +..|+.|+..|+.  ....|.+|......
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~  135 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFIN  135 (323)
T ss_pred             CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeeccccccee
Confidence            4689999998765322 5567763     6679999999996  45689999886644

>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional

Probab=82.90  E-value=1  Score=38.18  Aligned_cols=39  Identities=21%  Similarity=0.333  Sum_probs=25.6

Q ss_pred             CCCCCceeeecCCcccccCCCCC--C--CCcCCCCCCCceEEcc
Q 018689           18 QQEPQMYFCHQCNRTVRVTPSPS--S--DLVCPSCNGGFIEELE   57 (352)
Q Consensus        18 ~~~~~~ywCh~C~r~V~~~~~~~--~--~~~CP~C~~gFvEEi~   57 (352)
                      ...+..+|| .|.....+.....  -  ...||.|++..++-+.
T Consensus        65 ~~vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~  107 (124)
T PRK00762         65 EMIPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILG  107 (124)
T ss_pred             EecCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEec
Confidence            346688999 9998754431110  1  2569999988876543

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

Probab=82.65  E-value=0.45  Score=51.45  Aligned_cols=52  Identities=29%  Similarity=0.805  Sum_probs=38.0

Q ss_pred             cCCCCccccccccccccCCceEcccC-----ceecccchHHHhhc--CCCCCccCCCCCC
Q 018689          191 SSDSSQCAVCKDSFELNEEARQMPCK-----HIYHPDCIMPWLEL--HNSCPVCRYELPT  243 (352)
Q Consensus       191 ~~~~~~C~IC~e~~~~~~~~~~lpC~-----H~FH~~Ci~~Wl~~--~~sCP~CR~~l~~  243 (352)
                      ..++..|.||..+=..++ +..-||+     ...|..|+..|+.-  ...|-+|+.++.-
T Consensus         9 N~d~~~CRICr~e~~~d~-pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~F   67 (1175)
T COG5183           9 NEDKRSCRICRTEDIRDD-PLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKF   67 (1175)
T ss_pred             CccchhceeecCCCCCCC-cCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeee
Confidence            345689999998754433 4455775     34899999999964  4579999987743

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

Probab=82.60  E-value=0.61  Score=34.72  Aligned_cols=29  Identities=28%  Similarity=0.673  Sum_probs=21.5

Q ss_pred             eeecCCcccccCCCCCCCCcCCCCCCC-ceEEccC
Q 018689           25 FCHQCNRTVRVTPSPSSDLVCPSCNGG-FIEELET   58 (352)
Q Consensus        25 wCh~C~r~V~~~~~~~~~~~CP~C~~g-FvEEi~~   58 (352)
                      =|++|.|.+.     ...-+||.|++. |.||-..
T Consensus         6 AC~~Ck~l~~-----~d~e~CP~Cgs~~~te~W~G   35 (64)
T COG2093           6 ACKNCKRLTP-----EDTEICPVCGSTDLTEEWFG   35 (64)
T ss_pred             HHhhccccCC-----CCCccCCCCCCcccchhhcc
Confidence            3999998763     245679999986 8887543

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

Probab=82.21  E-value=0.62  Score=49.00  Aligned_cols=46  Identities=35%  Similarity=0.905  Sum_probs=38.7

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD  245 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~  245 (352)
                      ....|.||+..+    ..+..+|.   |..|+.+|+..+..||+|+..+..++
T Consensus       478 ~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~  523 (543)
T KOG0802|consen  478 PNDVCAICYQEM----SARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDD  523 (543)
T ss_pred             ccCcchHHHHHH----Hhcccccc---chhHHHhhhhhccccCCCchhhhccc
Confidence            357899999998    46677788   99999999999999999988876543

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=81.87  E-value=0.71  Score=27.54  Aligned_cols=23  Identities=22%  Similarity=0.881  Sum_probs=18.2

Q ss_pred             eeecCCcccccCCCCCCCCcCCCCCCCc
Q 018689           25 FCHQCNRTVRVTPSPSSDLVCPSCNGGF   52 (352)
Q Consensus        25 wCh~C~r~V~~~~~~~~~~~CP~C~~gF   52 (352)
                      ||.+|-..|.     +...+||+|+..|
T Consensus         1 ~Cp~CG~~~~-----~~~~fC~~CG~~l   23 (23)
T PF13240_consen    1 YCPNCGAEIE-----DDAKFCPNCGTPL   23 (23)
T ss_pred             CCcccCCCCC-----CcCcchhhhCCcC
Confidence            6899999874     3678999998754

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

Probab=81.65  E-value=0.81  Score=42.23  Aligned_cols=40  Identities=25%  Similarity=0.658  Sum_probs=29.3

Q ss_pred             ccccccccccccCCceEcccCc-eecccchHHHhhcCCCCCccCCCCC
Q 018689          196 QCAVCKDSFELNEEARQMPCKH-IYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       196 ~C~IC~e~~~~~~~~~~lpC~H-~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      .|-+|.+.   ...+..+||.| .+|..|-..    -..||+|+....
T Consensus       160 ~Cr~C~~~---~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~  200 (207)
T KOG1100|consen  160 SCRKCGER---EATVLLLPCRHLCLCGICDES----LRICPICRSPKT  200 (207)
T ss_pred             cceecCcC---CceEEeecccceEeccccccc----CccCCCCcChhh
Confidence            38888776   45589999976 577888654    345999987654

>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]

Probab=81.08  E-value=0.78  Score=44.13  Aligned_cols=46  Identities=30%  Similarity=0.629  Sum_probs=34.0

Q ss_pred             ccccccccccccCCceEc--ccCceecccchHHHhhc-CCCCCccCCCC
Q 018689          196 QCAVCKDSFELNEEARQM--PCKHIYHPDCIMPWLEL-HNSCPVCRYEL  241 (352)
Q Consensus       196 ~C~IC~e~~~~~~~~~~l--pC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l  241 (352)
                      .|++|....-..-.++.+  +|+|..|..|++.-+.. ...||.|-..+
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iL   50 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVIL   50 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchh
Confidence            599998764433333333  69999999999998755 55899997765

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=80.48  E-value=1.2  Score=30.89  Aligned_cols=33  Identities=18%  Similarity=0.578  Sum_probs=26.9

Q ss_pred             ceeeecCCcccccCCCCCCCCcCCCCCCCceEEcc
Q 018689           23 MYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELE   57 (352)
Q Consensus        23 ~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~   57 (352)
                      .|-|-.|...|.+..  ...+.||+|++..|--.-
T Consensus         2 ~Y~C~~Cg~~~~~~~--~~~irC~~CG~rIlyK~R   34 (44)
T smart00659        2 IYICGECGRENEIKS--KDVVRCRECGYRILYKKR   34 (44)
T ss_pred             EEECCCCCCEeecCC--CCceECCCCCceEEEEeC
Confidence            489999999998763  578999999998875543

present in RNA polymerase I, II and III

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

Probab=80.38  E-value=0.98  Score=40.83  Aligned_cols=31  Identities=29%  Similarity=0.708  Sum_probs=23.1

Q ss_pred             CCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEccC
Q 018689           20 EPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELET   58 (352)
Q Consensus        20 ~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~~   58 (352)
                      ...-|||..|+-.+       ..-.|+-|+++| +++.-
T Consensus        11 k~~iyWCe~cNlPl-------~~~~c~~cg~~~-~~l~L   41 (202)
T COG5270          11 KFPIYWCEKCNLPL-------LGRRCSVCGSKV-EELRL   41 (202)
T ss_pred             ccceeehhhCCCcc-------ccccccccCCcc-eEEEe
Confidence            44679999999876       346899999665 55544

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

Probab=80.10  E-value=0.98  Score=32.13  Aligned_cols=37  Identities=22%  Similarity=0.582  Sum_probs=27.8

Q ss_pred             CCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEcc
Q 018689           20 EPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELE   57 (352)
Q Consensus        20 ~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~   57 (352)
                      ....|-|-.|.+.|.+. .....+.||+|++..+-..-
T Consensus         3 ~~~~Y~C~~Cg~~~~~~-~~~~~irCp~Cg~rIl~K~R   39 (49)
T COG1996           3 AMMEYKCARCGREVELD-QETRGIRCPYCGSRILVKER   39 (49)
T ss_pred             ceEEEEhhhcCCeeehh-hccCceeCCCCCcEEEEecc
Confidence            34679999999999632 23578999999997765443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	352
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		1e-12
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		4e-09
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		2e-07
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		3e-07
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		8e-07
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		2e-06

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 26/46 (56%), Positives = 34/46 (73%)
Query: 196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYEL 241
           +C VCK+ + L E  RQ+PC H++H  CI+PWLE H+SCPVCR  L
Sbjct: 17  ECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSL 62

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 168 GTPPASKSAIEALPSIKINEAMMSSDSSQCA-VCKDSFELNEEARQMPCKHIYHPDCIMP 226
             PPASK +I+ALP I + E   +     C  +C   +   + A ++PC H +H  C+  
Sbjct: 13  ANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSI 72
Query: 227 WLELHNSCPVCRYELP 242
           WL+   +CPVCR   P
Sbjct: 73  WLQKSGTCPVCRCMFP 88

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 34/61 (55%)
Query: 180 LPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRY 239
           LPS + N     S+ + C VC   FE  +  R +PC H +H  C+  WL+ + +CP+CR 
Sbjct: 9   LPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRA 68
Query: 240 E 240
           +
Sbjct: 69  D 69

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 22/47 (46%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 193 DSSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHNSCPVCR 238
           D  +CAVC    E  EEAR +P C H +H +C+  WL  H++CP+CR
Sbjct: 4   DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 17/51 (33%), Positives = 29/51 (56%)
Query: 196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDP 246
           +C +C    E  E+ R++PC H++H  C+  WL  +  CP+CR ++    P
Sbjct: 16  KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQLP 66

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 18/41 (43%), Positives = 26/41 (63%)
Query: 197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVC 237
           CAVC + F+  +E    PCKH +H  C++ WLE+   CP+C
Sbjct: 18  CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLC 58

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	352
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	4e-50
2ect_A	78	Ring finger protein 126; metal binding protein, st	1e-31
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	2e-31
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	3e-26
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	8e-25
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	5e-19
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	6e-19
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	9e-19
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	6e-18
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	7e-14
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	8e-14
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	7e-13
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	2e-12
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	4e-10
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	8e-10
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	2e-09
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-09
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	2e-09
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	3e-09
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	5e-07
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	3e-08
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	3e-08
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	1e-07
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	3e-07
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	4e-07
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	7e-07
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	8e-07
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	1e-06
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	1e-06
3nw0_A	238	Non-structural maintenance of chromosomes element	3e-06
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	4e-06
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	8e-06
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	2e-05
1z6u_A	150	NP95-like ring finger protein isoform B; structura	3e-05
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	5e-05
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	9e-05
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	1e-04
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	1e-04
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	3e-04
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	3e-04
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	3e-04
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	5e-04
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	6e-04

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

 Score =  161 bits (410), Expect = 4e-50
 Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 1/89 (1%)

Query: 156 IQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDS-SQCAVCKDSFELNEEARQMP 214
           +     +  +    PPASK +I+ALP I + E   +      C +C   +   + A ++P
Sbjct: 1   MGHHHHHHSHMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP 60

Query: 215 CKHIYHPDCIMPWLELHNSCPVCRYELPT 243
           C H +H  C+  WL+   +CPVCR   P 
Sbjct: 61  CHHYFHKPCVSIWLQKSGTCPVCRCMFPP 89

>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 =  113 bits (284), Expect = 1e-31
 Identities = 26/60 (43%), Positives = 35/60 (58%)

Query: 190 MSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYE 249
                 +C VCK+ + L E  RQ+PC H++H  CI+PWLE H+SCPVCR  L   +    
Sbjct: 11  HVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATN 70

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

 Score =  112 bits (282), Expect = 2e-31
 Identities = 23/73 (31%), Positives = 36/73 (49%)

Query: 172 ASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH 231
            S  +   LPS + N     S+ + C VC   FE  +  R +PC H +H  C+  WL+ +
Sbjct: 1   GSSGSSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKAN 60

Query: 232 NSCPVCRYELPTD 244
            +CP+CR +    
Sbjct: 61  RTCPICRADSGPS 73

>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 = 98.6 bits (246), Expect = 3e-26
 Identities = 18/60 (30%), Positives = 30/60 (50%)

Query: 187 EAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDP 246
           E        +C +C    E  E+ R++PC H++H  C+  WL  +  CP+CR ++    P
Sbjct: 7   EGTEEDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQLP 66

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

 Score = 94.8 bits (236), Expect = 8e-25
 Identities = 18/55 (32%), Positives = 28/55 (50%)

Query: 191 SSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD 245
            +    CAVC + F+  +E    PCKH +H  C++ WLE+   CP+C   +    
Sbjct: 12  LNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLA 66

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

 Score = 78.8 bits (195), Expect = 5e-19
 Identities = 22/52 (42%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 191 SSDSSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHNSCPVCRYEL 241
             D  +CAVC    E  EEAR +P C H +H +C+  WL  H++CP+CR  +
Sbjct: 2   MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

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

 Score = 79.0 bits (195), Expect = 6e-19
 Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 4/54 (7%)

Query: 192 SDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD 245
           +D  +C +C D          +PC H +   CI  W + H +CP+CR ++   +
Sbjct: 13  TDEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGAN 62

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

 Score = 78.1 bits (193), Expect = 9e-19
 Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 191 SSDSSQCAVCKDSFELNEE-ARQMPCKHIYHPDCIMPWLELHNSCPVCR 238
           SS SS C +C +    +   A  +PC H+ H  C    L+    CP+C 
Sbjct: 2   SSGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCS 50

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

 Score = 75.9 bits (187), Expect = 6e-18
 Identities = 13/68 (19%), Positives = 32/68 (47%), Gaps = 8/68 (11%)

Query: 190 MSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPT------ 243
           M++ + +C +C +       +  +PC H +   CI  W+  + +CP+C+  + +      
Sbjct: 1   MATVAERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVESVVHTIE 58

Query: 244 DDPDYEQR 251
            D ++  +
Sbjct: 59  SDSEFGDQ 66

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

 Score = 65.3 bits (159), Expect = 7e-14
 Identities = 11/46 (23%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 197 CAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHNSCPVCRYEL 241
           C  C+   +  +       C H +H  C+  W++ +N CP+C+ + 
Sbjct: 29  CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDW 74

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

 Score = 64.9 bits (158), Expect = 8e-14
 Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 4/60 (6%)

Query: 186 NEAMMSSDSSQCAVCKDSFE----LNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYEL 241
              +  S +  C +C D +              C H++   C+   L+  N+CP CR ++
Sbjct: 7   GTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66

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

 Score = 62.2 bits (151), Expect = 7e-13
 Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 4/59 (6%)

Query: 191 SSDSSQCAVCKDSFE----LNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD 245
            S +  C +C D +              C H++   C+   L+  N+CP CR ++    
Sbjct: 7   PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR 65

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

 Score = 60.9 bits (148), Expect = 2e-12
 Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 4/54 (7%)

Query: 196 QCAVCKDSFE----LNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD 245
            C +C D +              C H++   C+   L+  N+CP CR ++    
Sbjct: 5   SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR 58

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

 Score = 54.8 bits (132), Expect = 4e-10
 Identities = 12/51 (23%), Positives = 18/51 (35%), Gaps = 2/51 (3%)

Query: 196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDP 246
            C++CK      +      C H +   CI+      N CP C   +    P
Sbjct: 17  LCSICKGYL--IDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQP 65

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

 Score = 53.7 bits (129), Expect = 8e-10
 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 3/54 (5%)

Query: 191 SSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTD 244
           S    +CA+C  +         +PCKH++   C+     L   C +CR E+P D
Sbjct: 12  SLTVPECAICLQTCV---HPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPED 62

>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 = 54.1 bits (129), Expect = 2e-09
 Identities = 17/92 (18%), Positives = 31/92 (33%), Gaps = 21/92 (22%)

Query: 170 PPASKSAIEALPSIKINE----AMMSSDSSQ--CAVCKDSFELNEEARQMP--------- 214
            P+  ++       ++ +    A+ + D     CA+C++         Q           
Sbjct: 7   TPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEEC 66

Query: 215 ------CKHIYHPDCIMPWLELHNSCPVCRYE 240
                 C H +H  CI  WL+    CP+   E
Sbjct: 67  TVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 98

>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 = 53.7 bits (129), Expect = 2e-09
 Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 2/58 (3%)

Query: 196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYEQRRN 253
            C +C   F   +    + C H +   CI+ +LE    CP+C  ++    P    R +
Sbjct: 17  MCVLCGGYF--IDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSD 72

>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 = 54.1 bits (129), Expect = 2e-09
 Identities = 16/105 (15%), Positives = 32/105 (30%), Gaps = 21/105 (20%)

Query: 157 QQLAENDPNRYGTPPASKSAIEALPSIKINE----AMMSSDSSQ--CAVCKDSFELNEEA 210
               + +   +       ++       ++ +    A+ + D     CA+C++        
Sbjct: 5   HHHVDEENLYFQGGGRGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIE 64

Query: 211 RQMP---------------CKHIYHPDCIMPWLELHNSCPVCRYE 240
            Q                 C H +H  CI  WL+    CP+   E
Sbjct: 65  CQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 109

>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 = 53.0 bits (127), Expect = 3e-09
 Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 5/56 (8%)

Query: 192 SDSSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHN-SCPVCRYELPTDD 245
           ++  +C +C +      +AR  P C  +    CI  WL      CP CR  L   +
Sbjct: 20  AEVFRCFICMEKLR---DARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRE 72

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

 Score = 51.7 bits (123), Expect = 2e-08
 Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 4/70 (5%)

Query: 188 AMMSSDSSQCAVCKDSFELNEEARQ----MPCKHIYHPDCIMPWLELHNSCPVCRYELPT 243
             M S +  C +C D +    +  +      C H++   C+   L+  N+CP CR ++  
Sbjct: 1   GAMGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH 60

Query: 244 DDPDYEQRRN 253
                    +
Sbjct: 61  KRYHPIYIGS 70

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

 Score = 47.5 bits (112), Expect = 5e-07
 Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 4/66 (6%)

Query: 180 LPSIKINEAMMSSDSSQCAVCKDSF----ELNEEARQMPCKHIYHPDCIMPWLELHNSCP 235
           +   + +   + S +  C +C D +    +         C H++   C+   L+  N+CP
Sbjct: 58  INHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCP 117

Query: 236 VCRYEL 241
            CR ++
Sbjct: 118 TCRKKI 123

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

 Score = 54.0 bits (129), Expect = 3e-08
 Identities = 30/145 (20%), Positives = 47/145 (32%), Gaps = 19/145 (13%)

Query: 103 QNYLQNLRANGASIQFVVENNSNVDPAAGGAGAAFRLPANLGDYFIGPGLEQLIQQLAEN 162
           Q  +  + A+G  +Q +  N         G    F L      +  G      +  L E 
Sbjct: 256 QWAIGYVTADGNILQTIPHNKPLFQALIDGFREGFYL------FPDGRNQNPDLTGLCEP 309

Query: 163 DPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPD 222
            P            I+           M S    C +C    E +++ +  PC H+    
Sbjct: 310 TPQ---------DHIKVTQEQYELYCEMGSTFQLCKIC---AENDKDVKIEPCGHLMCTS 357

Query: 223 CIMPWLELHN-SCPVCRYELPTDDP 246
           C+  W E     CP CR E+   +P
Sbjct: 358 CLTSWQESEGQGCPFCRCEIKGTEP 382

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

 Score = 49.2 bits (117), Expect = 3e-08
 Identities = 11/62 (17%), Positives = 18/62 (29%), Gaps = 4/62 (6%)

Query: 188 AMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNS--CPVCRYELPTDD 245
                    C +C     L +      C    H  C+  + + +    CP C    P + 
Sbjct: 9   ETYPDAVKICNICHS--LLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEI 66

Query: 246 PD 247
           P 
Sbjct: 67  PK 68

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

 Score = 47.9 bits (114), Expect = 1e-07
 Identities = 8/43 (18%), Positives = 17/43 (39%), Gaps = 3/43 (6%)

Query: 196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCR 238
           +C +C+ +F+         C+H +   C +        C +C 
Sbjct: 17  RCFICRQAFQ---NPVVTKCRHYFCESCALEHFRATPRCYICD 56

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

 Score = 48.9 bits (116), Expect = 3e-07
 Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 4/55 (7%)

Query: 192 SDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNS-CPVCRYELPTDD 245
               +C +C  +     EA Q PC H +   CI+  +      CPV    L  + 
Sbjct: 16  ESKYECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQ 67

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

 Score = 48.1 bits (114), Expect = 4e-07
 Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 3/53 (5%)

Query: 196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDY 248
           QC +C + F    EA  + C H +   CI  W++    CP+CR ++ +     
Sbjct: 66  QCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSL 115

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

 Score = 46.8 bits (111), Expect = 7e-07
 Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 4/50 (8%)

Query: 197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNS-CPVCRYELPTDD 245
           C +C+       +  +  CKH++   CI+  L++  S CP CRY     D
Sbjct: 26  CQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTD 72

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

 Score = 44.8 bits (106), Expect = 8e-07
 Identities = 10/51 (19%), Positives = 17/51 (33%), Gaps = 4/51 (7%)

Query: 196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHN-SCPVCRYELPTDD 245
           +C  C          +Q  C H +   C+   L   +  C  C+  +  D 
Sbjct: 17  KCEKCHLVLC---SPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDK 64

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

 Score = 46.0 bits (109), Expect = 1e-06
 Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 4/55 (7%)

Query: 192 SDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNS-CPVCRYELPTDD 245
               +C +C  +     EA Q PC H +   CI+  +      CPV    L  + 
Sbjct: 16  ESKYECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQ 67

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

 Score = 44.7 bits (105), Expect = 1e-06
 Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 191 SSDSSQCAVCKDSFELNEEA-RQMPCKHIYHPDCIMPWL-ELHNSCPVCRYELPTDDPDY 248
             D  +C +C +  E+++       C +     C      + +  CP CR   P D   Y
Sbjct: 8   KEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAVY 67

Query: 249 EQ 250
           + 
Sbjct: 68  KP 69

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

 Score = 46.7 bits (110), Expect = 3e-06
 Identities = 10/67 (14%), Positives = 18/67 (26%), Gaps = 4/67 (5%)

Query: 183 IKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNS--CPVCRYE 240
            +            C +C       +      C    H  C+  + + +    CP C   
Sbjct: 169 EQYIRETYPDAVKICNICHSLLIQGQSCET--CGIRMHLPCVAKYFQSNAEPRCPHCNDY 226

Query: 241 LPTDDPD 247
            P + P 
Sbjct: 227 WPHEIPK 233

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

 Score = 44.0 bits (104), Expect = 4e-06
 Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 4/51 (7%)

Query: 196 QCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHNSCPVCRYELPTDD 245
           +C +C + F     A  +P C H Y   CI  +L     CP C   +   D
Sbjct: 24  RCGICFEYFN---IAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPD 71

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

 Score = 44.3 bits (104), Expect = 8e-06
 Identities = 16/86 (18%), Positives = 29/86 (33%), Gaps = 5/86 (5%)

Query: 169 TPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWL 228
           TPP S   ++   S  +    + +    C+ C++         Q  C H Y   C+   L
Sbjct: 7   TPPGSLELLQPGFSKTLLGTKLEAKY-LCSACRNVLR---RPFQAQCGHRYCSFCLASIL 62

Query: 229 ELHNS-CPVCRYELPTDDPDYEQRRN 253
                 C  C +E   ++       +
Sbjct: 63  SSGPQNCAACVHEGIYEEGISILESS 88

>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 = 42.5 bits (99), Expect = 2e-05
 Identities = 15/88 (17%), Positives = 25/88 (28%), Gaps = 21/88 (23%)

Query: 171 PASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEA---------------RQMPC 215
             S    E +   K  E +  +    C +C +   +                   R   C
Sbjct: 3   SGSSGEPEQVIR-KYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKC 61

Query: 216 KHIYHPDCIMPWLELHN-----SCPVCR 238
            H +H  C++      N      CP C+
Sbjct: 62  SHAFHLLCLLAMYCNGNKDGSLQCPSCK 89

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

 Score = 42.7 bits (100), Expect = 3e-05
 Identities = 24/136 (17%), Positives = 42/136 (30%), Gaps = 15/136 (11%)

Query: 121 ENNSNVDPAAGGAGAAFRLPANLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAIEAL 180
            ++S + P    + +     ++  +      L    Q L   D          K   E L
Sbjct: 9   HHSSGLVPRGSPSASKVYKASDSAEAIEAFQLTPQQQHLIREDC------QNQKLWDEVL 62

Query: 181 PSIKINEAMMSS--DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHN-SCPVC 237
             +      +     S  C  C++      +     C H    DC+    +    SCP C
Sbjct: 63  SHLVEGPNFLKKLEQSFMCVCCQELVY---QPVTTECFHNVCKDCLQRSFKAQVFSCPAC 119

Query: 238 RYELPTDDPDYEQRRN 253
           R++L     +Y    N
Sbjct: 120 RHDLG---QNYIMIPN 132

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

 Score = 44.1 bits (103), Expect = 5e-05
 Identities = 11/67 (16%), Positives = 20/67 (29%), Gaps = 16/67 (23%)

Query: 191 SSDSSQCAVCKDSFELNEEARQM-----PCKHIYHPDCIMPWLE-----------LHNSC 234
            ++  +C +C        E   +      C    H  C+  W +               C
Sbjct: 305 DNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQC 364

Query: 235 PVCRYEL 241
           P C+ +L
Sbjct: 365 PFCKAKL 371

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

 Score = 40.7 bits (95), Expect = 9e-05
 Identities = 22/104 (21%), Positives = 35/104 (33%), Gaps = 9/104 (8%)

Query: 153 EQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSS--DSSQCAVCKDSFELNEEA 210
            Q    + E+  N         S  +   S    +  +S   ++ QC  C++        
Sbjct: 9   AQQSSLIREDKSNAKLWNEVLASLKDRPASGSPFQLFLSKVEETFQCICCQELVF---RP 65

Query: 211 RQMPCKHIYHPDCIMPWLELH-NSCPVCRYELPTDDPDYEQRRN 253
               C+H    DC+         SCP CRY+L      Y  + N
Sbjct: 66  ITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLG---RSYAMQVN 106

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

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 19/78 (24%), Positives = 27/78 (34%), Gaps = 12/78 (15%)

Query: 188 AMMSSDSS-------QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHN-SCPVCRY 239
           +M     +       QC +C +      E   +PC H     C    +E  +  CP CR 
Sbjct: 2   SMALPKDAIPSLSECQCGICMEILV---EPVTLPCNHTLCKPCFQSTVEKASLCCPFCRR 58

Query: 240 ELPTDDPDYEQRRNGNGN 257
            +      Y  RRN   N
Sbjct: 59  RVS-SWTRYHTRRNSLVN 75

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

 Score = 38.8 bits (90), Expect = 1e-04
 Identities = 13/52 (25%), Positives = 17/52 (32%), Gaps = 3/52 (5%)

Query: 193 DSSQCAVCKDSFELNEEARQM--PCKHIYHPDCIMPWLELH-NSCPVCRYEL 241
           D   C  CK +   N   + M   C H     C+         +CP C   L
Sbjct: 2   DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 53

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

 Score = 37.3 bits (87), Expect = 3e-04
 Identities = 10/47 (21%), Positives = 18/47 (38%), Gaps = 6/47 (12%)

Query: 196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP 242
           +C  C+   +     + +PC H     C+         CP+C+   P
Sbjct: 8   RCQQCQAEAK---CPKLLPCLHTLCSGCLE---ASGMQCPICQAPWP 48

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

 Score = 37.8 bits (88), Expect = 3e-04
 Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 6/54 (11%)

Query: 196 QCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHN--SCPVCRYELPTDDP 246
            C +CKD      +A  +P C + Y  +CI   L   +  +CP C     + D 
Sbjct: 17  LCLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA 67

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A Length = 61

 Score = 37.3 bits (87), Expect = 3e-04
 Identities = 6/48 (12%), Positives = 19/48 (39%), Gaps = 1/48 (2%)

Query: 199 VCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHNSCPVCRYELPTDD 245
           +C  S ++       P  + I+    +  +++   + P+    L  ++
Sbjct: 5   LCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEE 52

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

 Score = 38.3 bits (89), Expect = 5e-04
 Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 15/83 (18%)

Query: 163 DPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPD 222
           +P+  G    S++A++ L               +C+ C +     E      C+HI+  +
Sbjct: 2   EPDGRGAWAHSRAALDRL-----------EKLLRCSRCTNIL--REPVCLGGCEHIFCSN 48

Query: 223 CIMPWLELHNSCPVCRYELPTDD 245
           C+   +     CPVC       D
Sbjct: 49  CVSDCIG--TGCPVCYTPAWIQD 69

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus} Length = 101

 Score = 37.9 bits (87), Expect = 6e-04
 Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 7/61 (11%)

Query: 197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWL-ELHNSCPVCRYELPTDDPDYEQRRNGN 255
           C  C    ++    R +PCKH++  DC +    +    CP C   +       EQ   G+
Sbjct: 4   CDKCGLPIKVY--GRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPV----QRIEQCTRGS 57

Query: 256 G 256
            
Sbjct: 58  L 58

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	352
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.69
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.66
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.51
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.49
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.48
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.46
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.43
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.39
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.37
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.37
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.35
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.34
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.33
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.31
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.3
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.3
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.28
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.27
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.26
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.24
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.24
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.23
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.22
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.2
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.19
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.18
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.15
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.14
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.14
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.13
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.12
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.11
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.1
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.08
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.07
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.07
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.07
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.07
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.05
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.05
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.04
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.01
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.0
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	98.98
1z6u_A	150	NP95-like ring finger protein isoform B; structura	98.97
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.97
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.96
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.95
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.94
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.93
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.92
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.88
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.86
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.83
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	98.82
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.8
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.72
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.71
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.71
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.68
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.64
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.59
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.57
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.56
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.51
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.44
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.43
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.43
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.35
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.23
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	97.96
3nw0_A	238	Non-structural maintenance of chromosomes element	97.85
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	95.52
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	94.53
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	93.74
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	93.12
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	91.66
1we9_A	64	PHD finger family protein; structural genomics, PH	90.71
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	90.71
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	89.62
1wfp_A	74	Zinc finger (AN1-like) family protein; ZF-AN1 doma	88.15
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	86.44
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	85.84
1wg2_A	64	Zinc finger (AN1-like) family protein; riken struc	85.75
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	85.74
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	85.14
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	84.89
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	83.99
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	83.62
4ayb_P	48	DNA-directed RNA polymerase; transferase, multi-su	83.58
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	81.95
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	81.32
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	80.77
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	80.04

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

Probab=99.69  E-value=1.7e-17  Score=131.56  Aligned_cols=79  Identities=34%  Similarity=0.799  Sum_probs=69.2

Q ss_pred             CCCCCCCCCHHHHhhCCcceeccccc-cCCCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCC
Q 018689          165 NRYGTPPASKSAIEALPSIKINEAMM-SSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPT  243 (352)
Q Consensus       165 ~~~g~~pas~~~i~~lp~~~~~~~~~-~~~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~  243 (352)
                      ......+++++.|+.||.+++..... ..+...|+||++.|..++.++.|+|+|.||..||.+||+.+.+||+||+.+..
T Consensus        10 ~~~~~~~~s~~~i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           10 HMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFPP   89 (91)
T ss_dssp             CSSCCCCCCHHHHHTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTCBCTTTCCBSSC
T ss_pred             CCcCCCCCCHHHHHhCCCeeecccccccCCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCCcCcCcCccCCC
Confidence            45567889999999999998876543 33467899999999998889999999999999999999999999999999864

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

Probab=99.66  E-value=2.8e-17  Score=125.35  Aligned_cols=72  Identities=32%  Similarity=0.743  Sum_probs=62.5

Q ss_pred             CHHHHhhCCcceeccccccCCCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689          173 SKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       173 s~~~i~~lp~~~~~~~~~~~~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      +.+.++.||.+++.......+...|+||++.|..++.++.|+|+|+||..||.+||+.+.+||+||+.+...
T Consensus         2 s~~~i~~lp~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A            2 SSGSSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             CCCCCSSCCCEEBCSSSCSSSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             cHhhHhhCCcEEecCccccCCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            345678899988877665556789999999999988889999999999999999999999999999998753

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

Probab=99.51  E-value=9e-15  Score=104.39  Aligned_cols=50  Identities=44%  Similarity=1.015  Sum_probs=46.3

Q ss_pred             CCCccccccccccccCCceEcc-cCceecccchHHHhhcCCCCCccCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      +...|+||++.|..++.+..++ |+|+||..||.+|++.+.+||+||+.+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            3579999999999988899998 9999999999999999999999999874

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

Probab=99.49  E-value=2.4e-14  Score=109.56  Aligned_cols=52  Identities=50%  Similarity=1.234  Sum_probs=47.5

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      +...|+||++.|.....++.|+|+|+||..||.+|++.+.+||+||+.+...
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (78)
T 2ect_A           14 SGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQ   65 (78)
T ss_dssp             SSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCCCS
T ss_pred             CCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccCCc
Confidence            3579999999999888888999999999999999999999999999998753

>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=99.48  E-value=2.1e-14  Score=107.26  Aligned_cols=52  Identities=31%  Similarity=0.959  Sum_probs=47.5

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      +...|+||++.|..+..++.++|+|+||..||.+|++.+.+||+||..+...
T Consensus        13 ~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           13 TEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             CCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             CCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            3578999999998888899999999999999999999999999999998653

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

Probab=99.46  E-value=2.7e-14  Score=108.13  Aligned_cols=50  Identities=36%  Similarity=0.970  Sum_probs=46.6

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~  243 (352)
                      ...|+||++.|.....++.|+|+|+||..||.+|++.+.+||+||+.+..
T Consensus        15 ~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2ep4_A           15 HELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQ   64 (74)
T ss_dssp             SCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCSBCTTTCCBCSS
T ss_pred             CCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCCcCCCcCccccc
Confidence            57999999999988888899999999999999999999999999999864

>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=99.43  E-value=9.6e-14  Score=98.87  Aligned_cols=50  Identities=28%  Similarity=0.648  Sum_probs=43.8

Q ss_pred             CCCcccccccccccc-CCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689          193 DSSQCAVCKDSFELN-EEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~-~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      +...|+||++.|... ..++.++|+|+||..||.+|++.+.+||+||+.+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            357899999999654 45778899999999999999999999999999875

>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=99.39  E-value=1.9e-13  Score=111.64  Aligned_cols=50  Identities=26%  Similarity=0.576  Sum_probs=43.0

Q ss_pred             CCCcccccccccccc---------------CCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689          193 DSSQCAVCKDSFELN---------------EEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~---------------~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      +...|+||++.|...               ..++.++|+|.||..||.+||+.+.+||+||+++.
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  100 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcCCcCcCCCCcce
Confidence            468999999999753               12567889999999999999999999999999864

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

Probab=99.37  E-value=1.2e-13  Score=107.00  Aligned_cols=50  Identities=24%  Similarity=0.696  Sum_probs=41.3

Q ss_pred             CCccccccccccc-----------cCCceEcc-cCceecccchHHHhhcCCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFEL-----------NEEARQMP-CKHIYHPDCIMPWLELHNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~-----------~~~~~~lp-C~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~  243 (352)
                      +..|+||++.|..           ++.++.++ |+|+||..||.+||+.+.+||+||+++..
T Consensus        15 ~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   76 (81)
T 2ecl_A           15 CDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVV   76 (81)
T ss_dssp             CSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCE
T ss_pred             CCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcch
Confidence            4678888877753           45566776 99999999999999999999999998863

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

Probab=99.37  E-value=1.9e-13  Score=102.24  Aligned_cols=52  Identities=23%  Similarity=0.647  Sum_probs=45.2

Q ss_pred             CCCcccccccccccc----CCceEcccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689          193 DSSQCAVCKDSFELN----EEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~----~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      +...|+||++.|...    ..++.++|||.||..||.+|++.+.+||+||..+...
T Consensus         9 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (71)
T 3ng2_A            9 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK   64 (71)
T ss_dssp             TCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCCC
T ss_pred             CCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccChh
Confidence            358999999998763    4458889999999999999999999999999998754

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

Probab=99.35  E-value=3e-13  Score=100.36  Aligned_cols=51  Identities=24%  Similarity=0.656  Sum_probs=44.1

Q ss_pred             CCCcccccccccccc----CCceEcccCceecccchHHHhhcCCCCCccCCCCCC
Q 018689          193 DSSQCAVCKDSFELN----EEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPT  243 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~----~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~  243 (352)
                      +...|+||++.|...    ..++.++|+|+||..||.+|++.+.+||+||..|..
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           14 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             CCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            357999999999763    334788999999999999999999999999998853

>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=99.34  E-value=3.4e-13  Score=110.41  Aligned_cols=50  Identities=20%  Similarity=0.610  Sum_probs=41.4

Q ss_pred             CCccccccccccccC---------------CceEcccCceecccchHHHh-----hcCCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNE---------------EARQMPCKHIYHPDCIMPWL-----ELHNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~---------------~~~~lpC~H~FH~~Ci~~Wl-----~~~~sCP~CR~~l~~  243 (352)
                      +..|+||++.|....               .++.++|+|+||..||..||     ..+.+||+||..+..
T Consensus        25 ~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~   94 (114)
T 1v87_A           25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGE   94 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSS
T ss_pred             CCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCC
Confidence            468999999996643               34478899999999999999     457799999998854

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

Probab=99.33  E-value=3.9e-13  Score=98.29  Aligned_cols=51  Identities=24%  Similarity=0.640  Sum_probs=44.5

Q ss_pred             CCcccccccccccc----CCceEcccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELN----EEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~----~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      ...|+||++.|...    ..++.++|||.||..||.+|++.+.+||+||..+...
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   57 (64)
T 2xeu_A            3 MVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK   57 (64)
T ss_dssp             CCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTTT
T ss_pred             CCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCcc
Confidence            57899999998763    3457889999999999999999999999999998754

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

Probab=99.31  E-value=7.7e-13  Score=99.54  Aligned_cols=47  Identities=30%  Similarity=0.721  Sum_probs=42.8

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      +...|+||++.+..   .+.++|+|+||..||..|+..+.+||+||..+.
T Consensus        14 ~~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (71)
T 2d8t_A           14 TVPECAICLQTCVH---PVSLPCKHVFCYLCVKGASWLGKRCALCRQEIP   60 (71)
T ss_dssp             SCCBCSSSSSBCSS---EEEETTTEEEEHHHHHHCTTCSSBCSSSCCBCC
T ss_pred             CCCCCccCCcccCC---CEEccCCCHHHHHHHHHHHHCCCcCcCcCchhC
Confidence            35789999999866   688899999999999999999999999999986

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

Probab=99.30  E-value=1.6e-12  Score=96.64  Aligned_cols=48  Identities=23%  Similarity=0.770  Sum_probs=42.8

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~  243 (352)
                      ...|+||++.+..  ..+.++|+|.||..||.+|++.+.+||+||..+..
T Consensus         5 ~~~C~IC~~~~~~--~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            5 AERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCSSCCSCCCS--CEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCeeCCccccC--CcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            5789999999864  35889999999999999999999999999998853

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

Probab=99.30  E-value=3.3e-13  Score=101.03  Aligned_cols=49  Identities=31%  Similarity=0.891  Sum_probs=43.8

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD  245 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~  245 (352)
                      +...|+||++.+..    +.++|+|.||..||.+|+..+.+||+||+.+...+
T Consensus        14 ~~~~C~IC~~~~~~----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (70)
T 2ecn_A           14 DEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGAN   62 (70)
T ss_dssp             CCCCCSSSCCSCCS----EEETTTEEECHHHHHHSSCCCSSCHHHHHCTTCCC
T ss_pred             CCCCCeeCCcCccC----cccCCCCcccHHHHHHHHHCcCcCCCcCCcccCCC
Confidence            35799999999876    78999999999999999999999999999987544

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

Probab=99.28  E-value=1.8e-12  Score=97.78  Aligned_cols=49  Identities=24%  Similarity=0.596  Sum_probs=43.1

Q ss_pred             CCccccccccccccCCceEc-ccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQM-PCKHIYHPDCIMPWLELHNSCPVCRYELPTDD  245 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~  245 (352)
                      ...|+||++.|..   ++.+ +|+|.||..||..|++.+.+||+||+.+...+
T Consensus        15 ~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   64 (72)
T 2djb_A           15 YILCSICKGYLID---ATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQ   64 (72)
T ss_dssp             GGSCTTTSSCCSS---CEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSC
T ss_pred             CCCCCCCChHHHC---cCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCccc
Confidence            5799999999876   5565 89999999999999999999999999987543

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

Probab=99.27  E-value=2.2e-12  Score=100.06  Aligned_cols=51  Identities=24%  Similarity=0.740  Sum_probs=43.4

Q ss_pred             CCCccccccccccccCCceEcccC-----ceecccchHHHhhcC--CCCCccCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCK-----HIYHPDCIMPWLELH--NSCPVCRYELPTD  244 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~-----H~FH~~Ci~~Wl~~~--~sCP~CR~~l~~~  244 (352)
                      +...|.||+++|..++.+ ++||+     |.||..||++||..+  .+||+||+.+...
T Consensus        14 ~~~~C~IC~~~~~~~~~l-~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~   71 (80)
T 2d8s_A           14 SQDICRICHCEGDDESPL-ITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIME   71 (80)
T ss_dssp             TSCCCSSSCCCCCSSSCE-ECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCC
T ss_pred             CCCCCeEcCccccCCCee-EeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecC
Confidence            457999999999876655 68996     999999999999775  4899999998754

>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=99.26  E-value=7.4e-13  Score=109.93  Aligned_cols=50  Identities=28%  Similarity=0.620  Sum_probs=1.0

Q ss_pred             CCCcccccccccccc-------------C--CceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689          193 DSSQCAVCKDSFELN-------------E--EARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~-------------~--~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      +...|+||++.|...             +  .+..++|+|.||..||.+||+.+.+||+||+++.
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~  111 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  111 (117)
T ss_dssp             CC---------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeee
Confidence            457999999999752             2  2333579999999999999999999999999864

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

Probab=99.24  E-value=4e-12  Score=98.84  Aligned_cols=52  Identities=21%  Similarity=0.547  Sum_probs=45.1

Q ss_pred             CCCccccccccccccCC-ceEcccCceecccchHHHhhcC---CCCCccCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEE-ARQMPCKHIYHPDCIMPWLELH---NSCPVCRYELPTD  244 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~-~~~lpC~H~FH~~Ci~~Wl~~~---~sCP~CR~~l~~~  244 (352)
                      +...|+||++.|...+. ++.++|||.||..||..|++.+   .+||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           14 EVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             SCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             CCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            35789999999987654 7888999999999999999876   7899999988653

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

Probab=99.24  E-value=4.6e-12  Score=96.14  Aligned_cols=48  Identities=29%  Similarity=0.618  Sum_probs=42.0

Q ss_pred             CCccccccccccccCCceEcc-cCceecccchHHHhhcC--CCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELH--NSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~--~sCP~CR~~l~~~  244 (352)
                      ...|+||++.|..   ++.++ |+|.||..||..|++.+  .+||+||+.+...
T Consensus        15 ~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~   65 (74)
T 2yur_A           15 ELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSP   65 (74)
T ss_dssp             GGSCSSSCCCCTT---CEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCT
T ss_pred             CCCCcCCChHHhC---CeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCc
Confidence            5799999999876   77899 99999999999999865  6899999986543

>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=4.7e-12  Score=97.52  Aligned_cols=46  Identities=17%  Similarity=0.593  Sum_probs=42.3

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      ...|+||++.|..   +++++|+|.||..||..|++...+||+||..+.
T Consensus        15 ~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           15 PFRCFICRQAFQN---PVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CSBCSSSCSBCCS---EEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCcCCCchhcC---eeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            5789999999866   678999999999999999999999999999985

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

Probab=99.22  E-value=5.3e-12  Score=94.93  Aligned_cols=49  Identities=22%  Similarity=0.584  Sum_probs=42.5

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhh---cCCCCCccCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLE---LHNSCPVCRYELPTD  244 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~---~~~sCP~CR~~l~~~  244 (352)
                      +...|+||++.|..   ++.++|||.||..||..|++   .+..||+||..+..+
T Consensus        19 ~~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   70 (73)
T 2ysl_A           19 EEVICPICLDILQK---PVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKN   70 (73)
T ss_dssp             CCCBCTTTCSBCSS---EEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCC
T ss_pred             cCCEeccCCcccCC---eEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcc
Confidence            35799999999875   77889999999999999996   456899999998754

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

Probab=99.20  E-value=5.3e-12  Score=107.21  Aligned_cols=48  Identities=29%  Similarity=0.816  Sum_probs=43.6

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      ...|+||++.|..   ++.++|||.||..||..|+..+.+||+||..+...
T Consensus        53 ~~~C~iC~~~~~~---~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           53 ELQCIICSEYFIE---AVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             HSBCTTTCSBCSS---EEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             cCCCcccCcccCC---ceECCCCCCccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            4689999999876   78899999999999999999999999999998654

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

Probab=99.19  E-value=5.1e-12  Score=93.53  Aligned_cols=48  Identities=21%  Similarity=0.542  Sum_probs=41.5

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhh-cCCCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLE-LHNSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~-~~~sCP~CR~~l~~~  244 (352)
                      ...|+||++.+..   ++.++|||.||..||.+|+. ...+||+||..+..+
T Consensus        15 ~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           15 KYKCEKCHLVLCS---PKQTECGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             CEECTTTCCEESS---CCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             CCCCCCCChHhcC---eeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            5789999999876   55689999999999999994 567899999998754

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

Probab=99.18  E-value=1e-11  Score=94.68  Aligned_cols=49  Identities=18%  Similarity=0.442  Sum_probs=43.4

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhc-CCCCCccCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYELPTD  244 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~~~  244 (352)
                      +...|+||++.|..   ++.++|||.||+.||..|+.. +.+||+||..+...
T Consensus         7 ~~~~C~IC~~~~~~---Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~   56 (78)
T 1t1h_A            7 EYFRCPISLELMKD---PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             SSSSCTTTSCCCSS---EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             ccCCCCCccccccC---CEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChh
Confidence            35899999999876   778899999999999999987 78999999998654

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

Probab=99.15  E-value=1.2e-11  Score=94.47  Aligned_cols=50  Identities=18%  Similarity=0.515  Sum_probs=42.4

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcC--CCCCccCCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH--NSCPVCRYELPTDD  245 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~--~sCP~CR~~l~~~~  245 (352)
                      ...|+||++.|..+...  ..|+|.||..||.+||+.+  .+||+||.++....
T Consensus        15 i~~C~IC~~~i~~g~~C--~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~   66 (74)
T 2ct0_A           15 VKICNICHSLLIQGQSC--ETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEI   66 (74)
T ss_dssp             SCBCSSSCCBCSSSEEC--SSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCC
T ss_pred             CCcCcchhhHcccCCcc--CCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCC
Confidence            57999999999875433  3799999999999999887  89999999987543

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

Probab=99.14  E-value=2e-11  Score=93.81  Aligned_cols=48  Identities=27%  Similarity=0.665  Sum_probs=42.4

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhc------CCCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL------HNSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~------~~sCP~CR~~l~~~  244 (352)
                      ...|+||++.|..   .+.++|+|.||..||..|+..      ...||+||..+...
T Consensus        19 ~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecw_A           19 EVTCPICLELLKE---PVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG   72 (85)
T ss_dssp             TTSCTTTCSCCSS---CEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTT
T ss_pred             CCCCcCCChhhCc---ceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHH
Confidence            5799999999876   568999999999999999987      67899999998643

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

Probab=99.14  E-value=2.2e-11  Score=93.64  Aligned_cols=47  Identities=23%  Similarity=0.652  Sum_probs=42.0

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhc------CCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL------HNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~------~~sCP~CR~~l~~  243 (352)
                      ...|+||++.|..   ++.++|+|.||..||..|+..      ...||+||..+..
T Consensus        19 ~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecv_A           19 EVTCPICLELLTQ---PLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQP   71 (85)
T ss_dssp             CCCCTTTCSCCSS---CBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCS
T ss_pred             CCCCCCCCcccCC---ceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCH
Confidence            5799999999866   667899999999999999987      7899999999864

>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=99.13  E-value=1.4e-11  Score=99.00  Aligned_cols=48  Identities=29%  Similarity=0.662  Sum_probs=42.5

Q ss_pred             CCccccccccccccCCceE-cccCceecccchHHHhhcC-CCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQ-MPCKHIYHPDCIMPWLELH-NSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~-lpC~H~FH~~Ci~~Wl~~~-~sCP~CR~~l~~~  244 (352)
                      ...|+||++.|..   ++. ++|||.||..||..|+..+ .+||+||..+...
T Consensus        22 ~~~C~IC~~~~~~---p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (100)
T 3lrq_A           22 VFRCFICMEKLRD---ARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLR   71 (100)
T ss_dssp             HTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CCCCccCCccccC---ccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHH
Confidence            5789999999975   667 8999999999999999887 6999999998643

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

Probab=99.12  E-value=2e-11  Score=101.44  Aligned_cols=53  Identities=23%  Similarity=0.633  Sum_probs=45.7

Q ss_pred             CCCcccccccccccc----CCceEcccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689          193 DSSQCAVCKDSFELN----EEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD  245 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~----~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~  245 (352)
                      +...|+||++.|...    ..++.++|||.||..||.+||+.+.+||+||+.+...+
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (133)
T 4ap4_A            6 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR   62 (133)
T ss_dssp             CSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTC
T ss_pred             CCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCcccc
Confidence            458999999999763    34588999999999999999999999999999986543

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

Probab=99.11  E-value=8.2e-12  Score=95.21  Aligned_cols=48  Identities=23%  Similarity=0.542  Sum_probs=42.1

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhc-------CCCCCccCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-------HNSCPVCRYELPT  243 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-------~~sCP~CR~~l~~  243 (352)
                      +...|+||++.|..   ++.++|||.||..||..|+..       ...||+||..+..
T Consensus        11 ~~~~C~IC~~~~~~---p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~   65 (79)
T 2egp_A           11 EEVTCPICLELLTE---PLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSF   65 (79)
T ss_dssp             CCCEETTTTEECSS---CCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCS
T ss_pred             cCCCCcCCCcccCC---eeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCH
Confidence            35799999999876   667899999999999999976       6689999999875

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

Probab=99.10  E-value=3.5e-11  Score=88.07  Aligned_cols=42  Identities=26%  Similarity=0.647  Sum_probs=37.0

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhh---cCCCCCcc
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLE---LHNSCPVC  237 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~---~~~sCP~C  237 (352)
                      +...|+||++.|..   ++.++|||.||..||.+|++   ...+||+|
T Consensus        19 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           19 EEVICPICLDILQK---PVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCBCTTTCSBCSS---CEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             cCCCCCcCCchhCC---eEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            35799999999876   77889999999999999997   45689998

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

Probab=99.08  E-value=4.4e-11  Score=95.52  Aligned_cols=47  Identities=28%  Similarity=0.725  Sum_probs=42.1

Q ss_pred             CCccccccccccccCCceEc-ccCceecccchHHHhhcCCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQM-PCKHIYHPDCIMPWLELHNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~  243 (352)
                      ...|+||++.|..   ++.+ +|||.||..||..|+..+.+||+||..+..
T Consensus        22 ~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           22 LLRCGICFEYFNI---AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             HTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCCcccCChhhCC---cCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            4789999999876   5666 899999999999999999999999999864

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

Probab=99.07  E-value=6.9e-11  Score=92.93  Aligned_cols=47  Identities=32%  Similarity=0.658  Sum_probs=41.2

Q ss_pred             CCCccccccccccccCCceEcc-cCceecccchHHHhhcC--CCCCccCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELH--NSCPVCRYELP  242 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~--~sCP~CR~~l~  242 (352)
                      +...|+||++.|..   ++.++ |||.||..||..|+..+  .+||+||..+.
T Consensus        12 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           12 DELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             TTTEETTTTEECSS---CEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             cCCCCCCCChhhcC---ceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            35899999999876   78899 99999999999999754  58999999973

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

Probab=99.07  E-value=3.5e-11  Score=118.40  Aligned_cols=47  Identities=28%  Similarity=0.773  Sum_probs=42.1

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhh-cCCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLE-LHNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~-~~~sCP~CR~~l~~  243 (352)
                      ...|+||++.+..   ++.+||||.||..||..|+. .+.+||+||..+..
T Consensus       332 ~~~C~ICle~~~~---pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~  379 (389)
T 2y1n_A          332 FQLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKG  379 (389)
T ss_dssp             SSBCTTTSSSBCC---EEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCE
T ss_pred             CCCCCccCcCCCC---eEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCC
Confidence            3689999999865   78899999999999999998 68899999998864

>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=99.07  E-value=4.6e-11  Score=96.96  Aligned_cols=48  Identities=27%  Similarity=0.695  Sum_probs=42.9

Q ss_pred             CCccccccccccccCCceEc-ccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQM-PCKHIYHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      ...|+||++.|..   ++.+ +|||.||..||..|+..+.+||+||..+...
T Consensus        15 ~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           15 HLMCVLCGGYFID---ATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GTBCTTTSSBCSS---EEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             cCCCccCChHHhC---cCEeCCCCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            5899999999876   5666 9999999999999999999999999998754

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

Probab=99.07  E-value=4.6e-11  Score=99.24  Aligned_cols=53  Identities=25%  Similarity=0.649  Sum_probs=45.2

Q ss_pred             CCCCcccccccccccc----CCceEcccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689          192 SDSSQCAVCKDSFELN----EEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       192 ~~~~~C~IC~e~~~~~----~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      .+...|+||++.|...    ...+.++|||.||..||.+||+.+.+||+||..+..+
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  126 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK  126 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChh
Confidence            3468899999998762    3347889999999999999999999999999998753

>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=99.05  E-value=6.4e-11  Score=98.46  Aligned_cols=47  Identities=30%  Similarity=0.643  Sum_probs=41.7

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCC-CCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHN-SCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~-sCP~CR~~l~~  243 (352)
                      ...|+||++.|..   ++.++|||.||..||..|+..+. +||+||..+..
T Consensus        52 ~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           52 TFQCICCQELVFR---PITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HTBCTTTSSBCSS---EEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             CCCCCcCChHHcC---cEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            4789999999986   78899999999999999998544 99999999865

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

Probab=99.05  E-value=7.4e-11  Score=86.94  Aligned_cols=51  Identities=20%  Similarity=0.428  Sum_probs=40.9

Q ss_pred             CCccccccc-cccccCC-ceEcccCceecccchHHHhhc-CCCCCccCCCCCCC
Q 018689          194 SSQCAVCKD-SFELNEE-ARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e-~~~~~~~-~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~~~  244 (352)
                      +..|+||++ .|..... ...++|||.||..||.+|+.. ..+||+||+.+...
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   56 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccc
Confidence            478999999 7765433 256789999999999999754 56899999998654

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

Probab=99.04  E-value=5.8e-11  Score=85.08  Aligned_cols=42  Identities=31%  Similarity=0.799  Sum_probs=36.2

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHh---hcCCCCCcc
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWL---ELHNSCPVC  237 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl---~~~~sCP~C  237 (352)
                      +...|+||++.|..   .+.++|+|.||..||.+|+   ..+.+||+|
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           14 VEASCSVCLEYLKE---PVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCBCSSSCCBCSS---CCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cCCCCccCCcccCc---cEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            35799999999876   5678999999999999995   456789998

>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=99.01  E-value=1.1e-10  Score=94.78  Aligned_cols=48  Identities=21%  Similarity=0.692  Sum_probs=41.3

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCC---CCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHN---SCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~---sCP~CR~~l~~~  244 (352)
                      ...|+||++.|..   ++.++|||.||..||..|+..+.   +||+||..+...
T Consensus        21 ~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (112)
T 1jm7_A           21 ILECPICLELIKE---PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (112)
T ss_dssp             HTSCSSSCCCCSS---CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             CCCCcccChhhcC---eEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHh
Confidence            4689999999865   56789999999999999998654   899999988653

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

Probab=99.00  E-value=1.1e-10  Score=96.34  Aligned_cols=49  Identities=27%  Similarity=0.547  Sum_probs=42.8

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhcCC-CCCccCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHN-SCPVCRYELPTD  244 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~-sCP~CR~~l~~~  244 (352)
                      +...|+||++.|..   ++.++|||.||..||..|+.... +||+||..+...
T Consensus        17 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           17 SKYECPICLMALRE---AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             GGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCcCChhhcC---eEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            35799999999876   67889999999999999998765 999999998754

>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=98.98  E-value=1.5e-10  Score=100.79  Aligned_cols=47  Identities=30%  Similarity=0.721  Sum_probs=41.1

Q ss_pred             CCccccccccccccCCceEc-ccCceecccchHHHhhc-CCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQM-PCKHIYHPDCIMPWLEL-HNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~~  243 (352)
                      ...|+||++.|..   ++.+ +|||.||..||..|+.. +.+||+||..+..
T Consensus        54 ~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           54 ELMCPICLDMLKN---TMTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHBCTTTSSBCSS---EEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCcccChHhhC---cCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            4689999999976   5555 89999999999999987 7889999999854

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

Probab=98.97  E-value=2.1e-10  Score=98.92  Aligned_cols=48  Identities=27%  Similarity=0.573  Sum_probs=42.5

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCC-CCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHN-SCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~-sCP~CR~~l~~~  244 (352)
                      ...|+||++.|..   ++.++|||.||..||..|+.... +||+||..+...
T Consensus        78 ~~~C~IC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           78 SFMCVCCQELVYQ---PVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HTBCTTTSSBCSS---EEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CCEeecCChhhcC---CEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            4789999999876   77899999999999999998754 899999998754

>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=98.97  E-value=1.1e-10  Score=95.71  Aligned_cols=46  Identities=26%  Similarity=0.689  Sum_probs=41.3

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhc-CCCCCccCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYELP  242 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~  242 (352)
                      ...|+||++.|..   ++.++|||.||..||..|+.. +.+||+||..+.
T Consensus        15 ~~~C~iC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   61 (115)
T 3l11_A           15 ECQCGICMEILVE---PVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVS   61 (115)
T ss_dssp             HHBCTTTCSBCSS---CEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCH
T ss_pred             CCCCccCCcccCc---eeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccC
Confidence            4789999999875   788899999999999999976 678999999885

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

Probab=98.96  E-value=2.2e-10  Score=89.53  Aligned_cols=49  Identities=14%  Similarity=0.139  Sum_probs=44.7

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      +...|+||++.|.+   +++++|||.|++.||..||..+.+||+||..+...
T Consensus        13 ~~~~CpI~~~~m~d---PV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~   61 (85)
T 2kr4_A           13 DEFRDPLMDTLMTD---PVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTES   61 (85)
T ss_dssp             TTTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             hheECcccCchhcC---CeECCCCCEECHHHHHHHHhcCCCCCCCcCCCChH
Confidence            35899999999988   88999999999999999999899999999988654

>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=98.95  E-value=3.3e-10  Score=91.32  Aligned_cols=50  Identities=16%  Similarity=0.135  Sum_probs=45.5

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD  245 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~  245 (352)
                      +...|+||++.|.+   +++++|||.|++.||..||..+.+||+||..+...+
T Consensus        28 ~~~~CpI~~~~m~d---PV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~   77 (100)
T 2kre_A           28 DEFRDPLMDTLMTD---PVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTESM   77 (100)
T ss_dssp             TTTBCTTTCSBCSS---EEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCTTS
T ss_pred             HhhCCcCccCcccC---CeECCCCCEEchHHHHHHHHcCCCCCCCCCCCChhh
Confidence            36899999999988   889999999999999999998899999999987654

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

Probab=98.94  E-value=4.1e-10  Score=90.44  Aligned_cols=49  Identities=14%  Similarity=0.059  Sum_probs=45.0

Q ss_pred             CCccccccccccccCCceEcccC-ceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCK-HIYHPDCIMPWLELHNSCPVCRYELPTDD  245 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~-H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~  245 (352)
                      ...|+||++.|++   +++++|| |.|++.||.+||..+.+||+||..+...+
T Consensus        22 ~~~CpI~~~~m~d---PV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~   71 (98)
T 1wgm_A           22 EFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQ   71 (98)
T ss_dssp             TTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTT
T ss_pred             hcCCcCccccccC---CeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCChhh
Confidence            5899999999988   8899999 99999999999998899999999997654

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

Probab=98.93  E-value=3e-10  Score=81.65  Aligned_cols=45  Identities=22%  Similarity=0.648  Sum_probs=39.2

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPT  243 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~  243 (352)
                      +...|+||++.|..   ++.|+|+|.||..||..|   ...||+||+.+..
T Consensus         5 ~~~~C~IC~~~~~~---p~~l~CgH~fC~~Ci~~~---~~~CP~Cr~~~~~   49 (56)
T 1bor_A            5 QFLRCQQCQAEAKC---PKLLPCLHTLCSGCLEAS---GMQCPICQAPWPL   49 (56)
T ss_dssp             CCSSCSSSCSSCBC---CSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSC
T ss_pred             cCCCceEeCCccCC---eEEcCCCCcccHHHHccC---CCCCCcCCcEeec
Confidence            35789999999876   688999999999999885   6689999998864

>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=98.92  E-value=3.4e-10  Score=92.88  Aligned_cols=48  Identities=29%  Similarity=0.723  Sum_probs=42.4

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhc-CCCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~~~  244 (352)
                      ...|+||++.|..   ++.++|||.||..||..|+.. ..+||+||..+...
T Consensus        23 ~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (116)
T 1rmd_A           23 SISCQICEHILAD---PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (116)
T ss_dssp             HTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCcHhcC---cEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHh
Confidence            4789999999876   677999999999999999987 77999999998643

>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=98.88  E-value=6.4e-10  Score=82.23  Aligned_cols=47  Identities=19%  Similarity=0.452  Sum_probs=40.7

Q ss_pred             CCCccccccccccccCCceEc--ccCce-ecccchHHHhhcCCCCCccCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQM--PCKHI-YHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~l--pC~H~-FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      +...|.||++.+..   ...+  ||||. |+..|+..|++.+..||+||..+.
T Consensus         7 ~~~~C~IC~~~~~~---~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            7 AIEPCVICQGRPKN---GCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             GGSCCTTTSSSCSC---EEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CcCCCCcCCCCCCC---EEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            35789999998765   5555  99999 899999999998899999999885

>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=98.86  E-value=9.3e-10  Score=90.59  Aligned_cols=46  Identities=22%  Similarity=0.609  Sum_probs=40.6

Q ss_pred             CCccccccccccccCCceEc-ccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQM-PCKHIYHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      ...|+||++.|..   ++.+ +|||.||..||..|+.  ..||+||..+...
T Consensus        22 ~~~C~IC~~~~~~---pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~   68 (117)
T 1jm7_B           22 LLRCSRCTNILRE---PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQ   68 (117)
T ss_dssp             TTSCSSSCSCCSS---CBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCS
T ss_pred             CCCCCCCChHhhC---ccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCccc
Confidence            5799999999876   6777 8999999999999998  7899999998543

>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=98.83  E-value=6.3e-10  Score=95.03  Aligned_cols=48  Identities=23%  Similarity=0.464  Sum_probs=41.8

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhcCC-CCCccCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHN-SCPVCRYELPT  243 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~-sCP~CR~~l~~  243 (352)
                      +...|+||++.|..   ++.++|||.||..||.+|+.... +||+||.++..
T Consensus        30 ~~~~C~IC~~~~~~---pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   78 (141)
T 3knv_A           30 AKYLCSACRNVLRR---PFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIY   78 (141)
T ss_dssp             GGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHGGGSCEECHHHHHTTCC
T ss_pred             cCcCCCCCChhhcC---cEECCCCCccCHHHHHHHHhcCCCCCCCCCCcccc
Confidence            35899999999877   67789999999999999998665 89999998743

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

Probab=98.82  E-value=1.1e-09  Score=84.28  Aligned_cols=52  Identities=25%  Similarity=0.611  Sum_probs=41.0

Q ss_pred             CCCccccccccccccCCceEcc--cCceecccchHHHhh-cCCCCCccCCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMP--CKHIYHPDCIMPWLE-LHNSCPVCRYELPTDD  245 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lp--C~H~FH~~Ci~~Wl~-~~~sCP~CR~~l~~~~  245 (352)
                      +...|+||++.+...+ ...+|  |||.||..||..|+. ....||+||+.+....
T Consensus        10 ~~~~CpICle~~~~~d-~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~   64 (78)
T 1e4u_A           10 DPVECPLCMEPLEIDD-INFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDP   64 (78)
T ss_dssp             CCCBCTTTCCBCCTTT-TTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCS
T ss_pred             cCCcCCccCccCcccc-ccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCc
Confidence            4579999999886532 34444  999999999999884 3568999999987544

>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=98.80  E-value=1.8e-09  Score=79.54  Aligned_cols=46  Identities=20%  Similarity=0.473  Sum_probs=39.8

Q ss_pred             CCccccccccccccCCceEc--ccCce-ecccchHHHhhcCCCCCccCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQM--PCKHI-YHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~l--pC~H~-FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      ...|.||++.+..   ...+  ||||. |+..|+..|.+....||+||..+.
T Consensus         7 ~~~C~IC~~~~~~---~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            7 LKPCSLCEKRPRD---GNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GSBCTTTSSSBSC---EEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             CCCCcccCCcCCC---eEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            4789999998654   4455  99998 999999999988889999999885

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

Probab=98.72  E-value=2.6e-09  Score=81.07  Aligned_cols=43  Identities=23%  Similarity=0.594  Sum_probs=38.3

Q ss_pred             CCccccccccccccCCceEcccCce-ecccchHHHhhcCCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHI-YHPDCIMPWLELHNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~sCP~CR~~l~~  243 (352)
                      ...|+||++.+..   ++.+||||. ||..|+..|    ..||+||..+..
T Consensus        24 ~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           24 EKLCKICMDRNIA---IVFVPCGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HTBCTTTSSSBCC---EEEETTCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             CCCCCCCCCCCCC---EEEcCCCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            4789999998766   788999999 999999999    789999998853

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

Probab=98.71  E-value=5.4e-09  Score=97.14  Aligned_cols=49  Identities=18%  Similarity=0.129  Sum_probs=42.9

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhc-CCCCCccCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYELPTD  244 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~~~  244 (352)
                      +...|+||++.|.+   +++++|||.||+.||..||.. +.+||+||.++...
T Consensus       207 ~~~~c~i~~~~~~d---Pv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~  256 (281)
T 2c2l_A          207 DYLCGKISFELMRE---PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQE  256 (281)
T ss_dssp             STTBCTTTCSBCSS---EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGG
T ss_pred             cccCCcCcCCHhcC---CeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCchh
Confidence            35899999999987   889999999999999999986 44599999998643

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

Probab=98.71  E-value=3.1e-09  Score=84.39  Aligned_cols=48  Identities=23%  Similarity=0.556  Sum_probs=40.8

Q ss_pred             CCCccccccccccccCCceEcc-cCceecccchHHHhhcC------CCCCc--cCCC-CCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELH------NSCPV--CRYE-LPT  243 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~------~sCP~--CR~~-l~~  243 (352)
                      +...|+||++.|.+   +++++ |||.|++.||..||..+      .+||+  |+.. +..
T Consensus         6 ~~~~CPI~~~~~~d---PV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~   63 (94)
T 2yu4_A            6 SGFTCPITKEEMKK---PVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRK   63 (94)
T ss_dssp             SCCBCTTTCSBCSS---EEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCG
T ss_pred             cEeECcCcCchhcC---CEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCH
Confidence            35899999999987   88886 99999999999999764      48999  9876 543

>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=98.68  E-value=5.1e-09  Score=91.47  Aligned_cols=49  Identities=27%  Similarity=0.553  Sum_probs=42.6

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhcC-CCCCccCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH-NSCPVCRYELPTD  244 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~-~sCP~CR~~l~~~  244 (352)
                      +...|+||++.|..   ++.++|||.||..||.+|+... .+||+||..+...
T Consensus        17 ~~~~C~IC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           17 SKYECPICLMALRE---AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             GGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCChhhcC---cEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            35899999999876   6778999999999999999764 4999999998753

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

Probab=98.64  E-value=7.5e-09  Score=99.74  Aligned_cols=50  Identities=22%  Similarity=0.581  Sum_probs=39.5

Q ss_pred             CCCccccccccccccCCc-----eEcccCceecccchHHHhhcC-----------CCCCccCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEA-----RQMPCKHIYHPDCIMPWLELH-----------NSCPVCRYELP  242 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~-----~~lpC~H~FH~~Ci~~Wl~~~-----------~sCP~CR~~l~  242 (352)
                      ...+|+||++.+..+..+     ....|+|.||..||.+||+..           .+||+||++|.
T Consensus       307 ~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs  372 (381)
T 3k1l_B          307 EELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLS  372 (381)
T ss_dssp             SCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEE
T ss_pred             CCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCC
Confidence            467999999998873322     124699999999999999752           46999999875

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

Probab=98.59  E-value=1.1e-08  Score=77.60  Aligned_cols=44  Identities=23%  Similarity=0.589  Sum_probs=37.3

Q ss_pred             CCccccccccccccCCceEcccCce-ecccchHHHhhcCCCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHI-YHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      ...|+||++.+..   ++.+||||. ||..|+..    ...||+||..+...
T Consensus        25 ~~~C~IC~~~~~~---~~~~pCgH~~~C~~C~~~----~~~CP~Cr~~i~~~   69 (75)
T 2ecg_A           25 EKLCKICMDRNIA---IVFVPCGHLVTCKQCAEA----VDKCPMCYTVITFK   69 (75)
T ss_dssp             HHSCSSSCSSCCC---BCCSSSCCCCBCHHHHHH----CSBCTTTCCBCCCC
T ss_pred             CCCCCcCCCCCCC---EEEecCCCHHHHHHHhhC----CCCCccCCceecCc
Confidence            4689999999766   778999999 99999964    47899999998653

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

Probab=98.57  E-value=3.8e-08  Score=73.60  Aligned_cols=44  Identities=27%  Similarity=0.708  Sum_probs=37.8

Q ss_pred             CCCccccccccccccCCceEcccCce-ecccchHHHhhcCCCCCccCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHI-YHPDCIMPWLELHNSCPVCRYELPT  243 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~sCP~CR~~l~~  243 (352)
                      +...|.||++.+..   ++.+||+|. |+..|+..    ...||+||..+..
T Consensus        14 ~~~~C~IC~~~~~~---~v~~pCgH~~~C~~C~~~----~~~CP~CR~~i~~   58 (68)
T 2ea5_A           14 NSKDCVVCQNGTVN---WVLLPCRHTCLCDGCVKY----FQQCPMCRQFVQE   58 (68)
T ss_dssp             CSSCCSSSSSSCCC---CEETTTTBCCSCTTHHHH----CSSCTTTCCCCCC
T ss_pred             CCCCCCCcCcCCCC---EEEECCCChhhhHHHHhc----CCCCCCCCcchhc
Confidence            45799999998655   889999999 99999984    5789999998864

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

Probab=98.56  E-value=1.9e-08  Score=89.24  Aligned_cols=48  Identities=19%  Similarity=0.099  Sum_probs=42.7

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcC-CCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH-NSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~-~sCP~CR~~l~~~  244 (352)
                      ...|+||++.|.+   +++++|||.|++.||..||..+ .+||+|+..+...
T Consensus       106 ~f~CPI~~elm~D---PV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~  154 (179)
T 2f42_A          106 YLCGKISFELMRE---PCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQD  154 (179)
T ss_dssp             GGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             hhcccCccccCCC---CeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChh
Confidence            5899999999987   8899999999999999999764 5799999988654

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=98.51  E-value=3.4e-08  Score=72.17  Aligned_cols=48  Identities=27%  Similarity=0.745  Sum_probs=37.5

Q ss_pred             CCCccccccccccccCCceEcccC--c---eecccchHHHhhc--CCCCCccCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCK--H---IYHPDCIMPWLEL--HNSCPVCRYELPT  243 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~--H---~FH~~Ci~~Wl~~--~~sCP~CR~~l~~  243 (352)
                      +...|.||+++.  ++. .++||.  |   .||..||.+||..  +.+||+|++.+..
T Consensus         5 ~~~~CrIC~~~~--~~~-l~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            5 DVPVCWICNEEL--GNE-RFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             SCCEETTTTEEC--SCC-CCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCEeEEeecCC--CCc-eecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            357899999973  233 468854  4   9999999999964  6789999998753

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A

Probab=98.44  E-value=5e-08  Score=71.49  Aligned_cols=47  Identities=11%  Similarity=0.195  Sum_probs=42.2

Q ss_pred             CccccccccccccCCceEc-ccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689          195 SQCAVCKDSFELNEEARQM-PCKHIYHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       195 ~~C~IC~e~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      ..|+||++.|++   ++++ +|||+|.+.||.+||+.+.+||+++.+|..+
T Consensus         4 ~~CpIs~~~m~d---PV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~   51 (61)
T 2bay_A            4 MLCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   51 (61)
T ss_dssp             CCCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             EEecCCCCCCCC---CEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChh
Confidence            689999999986   6777 8999999999999999888999999998654

>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=98.43  E-value=4.4e-08  Score=77.34  Aligned_cols=47  Identities=28%  Similarity=0.691  Sum_probs=38.4

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhc--------CCCCCc--cCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL--------HNSCPV--CRYE  240 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~--------~~sCP~--CR~~  240 (352)
                      ..+|+||++.+.........+|+|.||..||..+++.        ...||.  |+..
T Consensus         5 ~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            5 SSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            5789999999876544444579999999999999853        237999  9998

>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=98.43  E-value=4.5e-08  Score=75.30  Aligned_cols=43  Identities=30%  Similarity=0.648  Sum_probs=37.5

Q ss_pred             CCccccccccccccCCceEcccCce-ecccchHHHhhcCCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHI-YHPDCIMPWLELHNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~sCP~CR~~l~~  243 (352)
                      ...|.||++.+..   ++.+||||. |+..|+..|    ..||+||..+..
T Consensus        18 ~~~C~IC~~~~~~---~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   61 (79)
T 2yho_A           18 AMLCMVCCEEEIN---STFCPCGHTVCCESCAAQL----QSCPVCRSRVEH   61 (79)
T ss_dssp             HTBCTTTSSSBCC---EEEETTCBCCBCHHHHTTC----SBCTTTCCBCCE
T ss_pred             CCEeEEeCcccCc---EEEECCCCHHHHHHHHHhc----CcCCCCCchhhC
Confidence            4689999998765   888999999 999999987    389999998864

>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=98.35  E-value=1.8e-07  Score=90.97  Aligned_cols=44  Identities=27%  Similarity=0.684  Sum_probs=38.9

Q ss_pred             CCCccccccccccccCCceEcccCce-ecccchHHHhhcCCCCCccCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHI-YHPDCIMPWLELHNSCPVCRYELPT  243 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~sCP~CR~~l~~  243 (352)
                      +...|+||++.+..   ++.+||||. ||..|+..|    ..||+||..+..
T Consensus       294 ~~~~C~IC~~~~~~---~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          294 EERTCKVCMDKEVS---VVFIPCGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             TTCBCTTTSSSBCC---EEEETTCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             CCCCCCccCCcCCc---eEEcCCCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            35799999999866   788999999 999999998    789999998853

>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=98.23  E-value=2.4e-07  Score=86.42  Aligned_cols=49  Identities=22%  Similarity=0.532  Sum_probs=41.1

Q ss_pred             CCccccccccccccCCceE-cccCceecccchHHHhhcC--CCCCc--cCCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQ-MPCKHIYHPDCIMPWLELH--NSCPV--CRYELPTDD  245 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~-lpC~H~FH~~Ci~~Wl~~~--~sCP~--CR~~l~~~~  245 (352)
                      ...|+||++.|..   ++. +.|||.|++.||..|++.+  .+||+  |++.+...+
T Consensus       181 el~CPIcl~~f~D---PVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~d  234 (267)
T 3htk_C          181 ELTCPITCKPYEA---PLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRD  234 (267)
T ss_dssp             CSBCTTTSSBCSS---EEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGG
T ss_pred             eeECcCccCcccC---CeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhh
Confidence            5799999999977   555 5899999999999999764  47999  999876543

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=97.96  E-value=3e-06  Score=67.59  Aligned_cols=46  Identities=26%  Similarity=0.635  Sum_probs=39.0

Q ss_pred             ccccccccccccCCceEcccCceecccchHHHhh-cCCCCCccCCCCCC
Q 018689          196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLE-LHNSCPVCRYELPT  243 (352)
Q Consensus       196 ~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~-~~~sCP~CR~~l~~  243 (352)
                      -|.+|--.+..  ..+.+||+|+||.+|+..|.+ ..++||.|+..+..
T Consensus         3 fC~~C~~Pi~i--ygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~r   49 (101)
T 3vk6_A            3 FCDKCGLPIKV--YGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQR   49 (101)
T ss_dssp             BCTTTCSBCSE--EEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCSE
T ss_pred             ecCccCCCeEE--EeeeccccccHHHHHHHHHHhccCCCCcCcCCeeee
Confidence            48888777665  688999999999999999985 46899999998864

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

Probab=97.85  E-value=4.8e-06  Score=76.91  Aligned_cols=50  Identities=18%  Similarity=0.519  Sum_probs=40.6

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCC--CCCccCCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHN--SCPVCRYELPTDD  245 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~--sCP~CR~~l~~~~  245 (352)
                      ...|.||.+.+..+...  -.|+|.||..|+.+|++.+.  .||.|+..++...
T Consensus       180 i~~C~iC~~iv~~g~~C--~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~~  231 (238)
T 3nw0_A          180 VKICNICHSLLIQGQSC--ETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEI  231 (238)
T ss_dssp             CCBCTTTCSBCSSCEEC--SSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSCC
T ss_pred             CCcCcchhhHHhCCccc--CccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCCC
Confidence            57899999998875322  23999999999999997654  8999999887543

>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=94.53  E-value=0.023  Score=41.47  Aligned_cols=48  Identities=19%  Similarity=0.542  Sum_probs=29.6

Q ss_pred             CCccccCCCCCCCCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEcc
Q 018689            8 FGGAAAAAPPQQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELE   57 (352)
Q Consensus         8 ~~~~~~~~~~~~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~   57 (352)
                      +.||.|..++.+..-.|-|-.|...|.+..  ...+.||+|+...|...-
T Consensus         6 ~~~g~~~~~~~~~~v~Y~C~~Cg~~~~l~~--~~~iRC~~CG~RILyK~R   53 (63)
T 3h0g_L            6 STGGTAFNPPRPATMIYLCADCGARNTIQA--KEVIRCRECGHRVMYKMR   53 (63)
T ss_dssp             -------------CCCCBCSSSCCBCCCCS--SSCCCCSSSCCCCCBCCC
T ss_pred             cCCccccCCCCCCCeEEECCCCCCeeecCC--CCceECCCCCcEEEEEec
Confidence            344445555555678899999999998764  467999999999887654

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=93.74  E-value=0.042  Score=40.40  Aligned_cols=44  Identities=23%  Similarity=0.599  Sum_probs=32.3

Q ss_pred             CCccccccccccccCCceEc-ccCceecccchHHHhhcCC----CCCccCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQM-PCKHIYHPDCIMPWLELHN----SCPVCRYEL  241 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~~~----sCP~CR~~l  241 (352)
                      ...|.||.+.   + +++.- .|...||..|+.+.|....    .||.|+...
T Consensus        12 ~~~C~vC~~~---~-~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           12 GARCGVCGDG---T-DVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             TCCCTTTSCC---T-TCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCcCCCCCC---C-eEEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            5789999753   3 33333 4999999999999886532    699997654

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=93.12  E-value=0.039  Score=43.19  Aligned_cols=34  Identities=15%  Similarity=0.423  Sum_probs=25.6

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHH
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPW  227 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~W  227 (352)
                      +..|.||++.+.......-+.|+|.|+..|+..|
T Consensus         3 e~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            3 KVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CCBCTTCCSSSCCBCCEEETTTTEEECHHHHHHH
T ss_pred             CCCCcCCCCCCCCCceEECCcCChHHhHHHCHHH
Confidence            4789999986533222333899999999999983

>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}

Probab=91.66  E-value=0.11  Score=42.28  Aligned_cols=35  Identities=20%  Similarity=0.461  Sum_probs=27.3

Q ss_pred             CCCceeeecCCcccccCCCCCCCC-cCCCCCCCceEEcc
Q 018689           20 EPQMYFCHQCNRTVRVTPSPSSDL-VCPSCNGGFIEELE   57 (352)
Q Consensus        20 ~~~~ywCh~C~r~V~~~~~~~~~~-~CP~C~~gFvEEi~   57 (352)
                      .+..|||..|...+.+.   .... .||.|++..++-+.
T Consensus        70 ~p~~~~C~~CG~~~e~~---~~~~~~CP~Cgs~~~~i~~  105 (119)
T 2kdx_A           70 EKVELECKDCSHVFKPN---ALDYGVCEKCHSKNVIITQ  105 (119)
T ss_dssp             ECCEEECSSSSCEECSC---CSTTCCCSSSSSCCCEEEE
T ss_pred             ccceEEcCCCCCEEeCC---CCCCCcCccccCCCcEEec
Confidence            35789999999988653   2456 89999999877554

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=90.71  E-value=0.097  Score=37.74  Aligned_cols=48  Identities=25%  Similarity=0.548  Sum_probs=33.8

Q ss_pred             CCCccccccccccccCCceEc-ccCceecccchHHHhh-----cCCCCCccCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQM-PCKHIYHPDCIMPWLE-----LHNSCPVCRYE  240 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~-----~~~sCP~CR~~  240 (352)
                      +...|+||...+..+...+.- .|...||..|+.--..     ..-.||.|+..
T Consensus         5 e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            357899999887654444444 4999999999875432     24579999764

>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=90.71  E-value=0.13  Score=39.61  Aligned_cols=33  Identities=18%  Similarity=0.546  Sum_probs=22.5

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHH
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPW  227 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~W  227 (352)
                      +..|.||- .|..++....=-|+-+||..|+.+-
T Consensus        15 D~~C~VC~-~~t~~~l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           15 DEMCDVCE-VWTAESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             SCCCTTTC-CCCSSCCSSCSSSSSCCCHHHHHHH
T ss_pred             CcccCccc-cccccceeccccccccccHhhcccc
Confidence            58999994 3444322222228999999999996

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=89.62  E-value=0.27  Score=38.20  Aligned_cols=47  Identities=26%  Similarity=0.579  Sum_probs=32.8

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhcC----CCCCccCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH----NSCPVCRYELP  242 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~----~sCP~CR~~l~  242 (352)
                      ....|.||...   ++-+..-.|.-.||..|+.+=|...    -.||.|+..-.
T Consensus        24 n~~~C~vC~~~---g~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~~   74 (88)
T 1fp0_A           24 SATICRVCQKP---GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   74 (88)
T ss_dssp             SSSCCSSSCSS---SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             CCCcCcCcCCC---CCEEECCCCCCceecccCCCCCCCCcCCCcCCccccCCCc
Confidence            35789999865   3322222489999999998876542    26999986543

>1wfp_A Zinc finger (AN1-like) family protein; ZF-AN1 domain, zinc binding, structural genomics, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: g.80.1.1

Probab=88.15  E-value=0.43  Score=35.76  Aligned_cols=32  Identities=28%  Similarity=0.620  Sum_probs=24.9

Q ss_pred             CCCCCceeeecCCcccccCCCCCCCCcCCCCCCCceEE
Q 018689           18 QQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEE   55 (352)
Q Consensus        18 ~~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEE   55 (352)
                      +.-.....|+.|.+.|-+.     .+.| +|+.-|=-.
T Consensus        20 ~~k~~~~RC~~C~kkvgL~-----~f~C-rCg~~FCs~   51 (74)
T 1wfp_A           20 PPKSTATRCLSCNKKVGVT-----GFKC-RCGSTFCGT   51 (74)
T ss_dssp             CTTCCCCBCSSSCCBCTTT-----CEEC-TTSCEECTT
T ss_pred             cCcccCccchhhcCccccc-----ceEe-ccCCEeccc
Confidence            4455678999999998765     4999 899988643

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=86.44  E-value=0.41  Score=42.04  Aligned_cols=49  Identities=20%  Similarity=0.504  Sum_probs=35.4

Q ss_pred             CccccccccccccCC---ceEcc-cCceecccchHHH------hh-----cCCCCCccCCCCCC
Q 018689          195 SQCAVCKDSFELNEE---ARQMP-CKHIYHPDCIMPW------LE-----LHNSCPVCRYELPT  243 (352)
Q Consensus       195 ~~C~IC~e~~~~~~~---~~~lp-C~H~FH~~Ci~~W------l~-----~~~sCP~CR~~l~~  243 (352)
                      ..|+||...|..++.   .+..- |...||..|+.--      +.     ..-.||.|+..-+.
T Consensus         3 ~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~~~   66 (183)
T 3lqh_A            3 NFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHPA   66 (183)
T ss_dssp             CBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSSSC
T ss_pred             CcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCCCH
Confidence            569999999987753   44444 9999999998532      11     15689999886543

>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A

Probab=85.84  E-value=0.54  Score=33.61  Aligned_cols=46  Identities=33%  Similarity=0.542  Sum_probs=31.6

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcC----CCCCccCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH----NSCPVCRYELP  242 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~----~sCP~CR~~l~  242 (352)
                      ...|.||.+.   ++-+.--.|...||..|+.+-|...    -.||.|+....
T Consensus         9 ~~~C~vC~~~---g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~   58 (61)
T 1mm2_A            9 MEFCRVCKDG---GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPAL   58 (61)
T ss_dssp             CSSCTTTCCC---SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTCC
T ss_pred             CCcCCCCCCC---CCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCchh
Confidence            5789999863   2223223489999999999766432    25999977543

>1wg2_A Zinc finger (AN1-like) family protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.80.1.1

Probab=85.75  E-value=0.44  Score=34.75  Aligned_cols=32  Identities=25%  Similarity=0.572  Sum_probs=24.3

Q ss_pred             CCCCCceeeecCCcccccCCCCCCCCcCCCCCCCceEE
Q 018689           18 QQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEE   55 (352)
Q Consensus        18 ~~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEE   55 (352)
                      ........|..|.+.|.+.     .+.| +|+.-|=-.
T Consensus        10 ~~~~~~~rC~~C~kkvgl~-----~f~C-rCg~~FC~~   41 (64)
T 1wg2_A           10 RPVRPNNRCFSCNKKVGVM-----GFKC-KCGSTFCGS   41 (64)
T ss_dssp             CCSCCSCSCTTTCCCCTTS-----CEEC-TTSCEECSS
T ss_pred             CCCCcCCcChhhCCccccc-----CeEe-ecCCEeccc
Confidence            3344567899999998764     3899 999988644

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=85.74  E-value=0.24  Score=34.76  Aligned_cols=44  Identities=32%  Similarity=0.693  Sum_probs=29.8

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhcC----CCCCccCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH----NSCPVCRY  239 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~----~sCP~CR~  239 (352)
                      .+..|.||...   ++-+.--.|...||..|+.+-|...    -.||.|+.
T Consensus         8 ~~~~C~vC~~~---g~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            8 HEDFCSVCRKS---GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SCCSCSSSCCS---SCCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCccCCCC---CeEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            35789999874   3223223499999999999766432    25888854

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

Probab=85.14  E-value=0.56  Score=35.83  Aligned_cols=39  Identities=21%  Similarity=0.547  Sum_probs=28.5

Q ss_pred             CCCCCCCceeeecCCcccccCCCCCCCCcCCCCCCCceEE
Q 018689           16 PPQQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEE   55 (352)
Q Consensus        16 ~~~~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEE   55 (352)
                      ........+||-.|...|...+ ....+.||.|+..|-=.
T Consensus        18 ~v~~~~~~~wCP~C~~~~~~~~-~~~~v~C~~C~~~FC~~   56 (86)
T 2ct7_A           18 VLMRDPKFLWCAQCSFGFIYER-EQLEATCPQCHQTFCVR   56 (86)
T ss_dssp             CCCSCCCEECCSSSCCCEECCC-SCSCEECTTTCCEECSS
T ss_pred             HHhcCCCEeECcCCCchheecC-CCCceEeCCCCCccccc
Confidence            3345678899999999875443 24568999999887643

>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=84.89  E-value=0.47  Score=41.24  Aligned_cols=44  Identities=30%  Similarity=0.622  Sum_probs=32.1

Q ss_pred             CCccccccccccccCCceEc-ccCceecccchHHHhhcC----CCCCccCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQM-PCKHIYHPDCIMPWLELH----NSCPVCRYEL  241 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~~----~sCP~CR~~l  241 (352)
                      +..|.||...   ++ +... .|...||..|+.+-|...    -.||.|+...
T Consensus         4 ~~~C~~C~~~---g~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A            4 EDWCAVCQNG---GE-LLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             CSSCTTTCCC---SS-CEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCccccCCCC---Ce-eeecCCCCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            4789999854   33 3333 399999999998877542    3699998754

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=83.99  E-value=0.48  Score=32.37  Aligned_cols=44  Identities=27%  Similarity=0.547  Sum_probs=28.7

Q ss_pred             ccccccccccccCCceEcccCceecccchHHHhhcC----CCCCccCC
Q 018689          196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH----NSCPVCRY  239 (352)
Q Consensus       196 ~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~----~sCP~CR~  239 (352)
                      .|.||...-..++-+.--.|...||..|+.+=|...    -.||.|+.
T Consensus         2 ~C~vC~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCCEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            588998753322222222499999999998655432    25999965

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=83.62  E-value=0.52  Score=33.71  Aligned_cols=43  Identities=35%  Similarity=0.725  Sum_probs=30.4

Q ss_pred             CCccccccccccccCCceEc-ccCceecccchHHHhhc----CCCCCccCCC
Q 018689          194 SSQCAVCKDSFELNEEARQM-PCKHIYHPDCIMPWLEL----HNSCPVCRYE  240 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~----~~sCP~CR~~  240 (352)
                      ...|.||...   + .+..- .|...||..|+.+-|..    .-.||.|+..
T Consensus        11 ~~~C~vC~~~---g-~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A           11 QDYCEVCQQG---G-EIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             CSSCTTTSCC---S-SEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCccCCCC---C-cEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            5789999873   2 23333 48999999999986543    2369999653

>4ayb_P DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2pmz_P 2wb1_P 2y0s_P 3hkz_P 2waq_P 4b1o_P 4b1p_X

Probab=83.58  E-value=1  Score=30.68  Aligned_cols=38  Identities=24%  Similarity=0.481  Sum_probs=27.3

Q ss_pred             CceeeecCCcccccCCC-CCCCCcCCCCCCCceEEccCC
Q 018689           22 QMYFCHQCNRTVRVTPS-PSSDLVCPSCNGGFIEELETP   59 (352)
Q Consensus        22 ~~ywCh~C~r~V~~~~~-~~~~~~CP~C~~gFvEEi~~~   59 (352)
                      ..|-|-.|-+++..... ....+.||+|+=..+..+-.+
T Consensus         2 ~iY~C~rCg~~fs~~el~~lP~IrCpyCGyrii~KvR~p   40 (48)
T 4ayb_P            2 AVYRCGKCWKTFTDEQLKVLPGVRCPYCGYKIIFMVRKP   40 (48)
T ss_dssp             ---CCCCTTTTCCCCCSCCCSSSCCTTTCCSCEECCCCC
T ss_pred             cEEEeeccCCCccHHHHhhCCCcccCccCcEEEEEecCC
Confidence            46999999999876543 257899999998877766543

>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=81.95  E-value=0.61  Score=50.57  Aligned_cols=50  Identities=16%  Similarity=0.107  Sum_probs=44.0

Q ss_pred             CCCccccccccccccCCceEcccC-ceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCK-HIYHPDCIMPWLELHNSCPVCRYELPTDD  245 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~-H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~  245 (352)
                      +...|+|-++.|.+   ++++|-| +.|-+.+|.+||..+.+||+=|.++...+
T Consensus       890 ~~F~cPIs~~lM~D---PVilpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~  940 (968)
T 3m62_A          890 DEFLDPLMYTIMKD---PVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLED  940 (968)
T ss_dssp             GGGBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGG
T ss_pred             HHhCCcchhhHHhC---CeEcCCCCEEECHHHHHHHHhcCCCCCCCCCCCCccc
Confidence            35789999999887   8999987 68999999999999999999999987543

>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=81.32  E-value=0.61  Score=41.39  Aligned_cols=44  Identities=27%  Similarity=0.582  Sum_probs=31.7

Q ss_pred             CCccccccccccccCCceEcc-cCceecccchHHHhhcC----CCCCccCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELH----NSCPVCRYEL  241 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~----~sCP~CR~~l  241 (352)
                      ...|.||...   ++ +.... |...||..|+.+.|...    -.||.|+..-
T Consensus         7 ~~~C~~C~~~---g~-ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A            7 EDWCAVCQNG---GD-LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             CSSBTTTCCC---EE-EEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCCCCCCC---Cc-eEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            5789999754   22 33333 89999999998877543    3699998754

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=80.77  E-value=0.95  Score=36.00  Aligned_cols=46  Identities=26%  Similarity=0.559  Sum_probs=30.0

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhc----CCCCCccC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL----HNSCPVCR  238 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~----~~sCP~CR  238 (352)
                      ++..|.||.+.-+..+-+.--.|...||..|+..++..    .-.||.|+
T Consensus         6 ~~~~C~~C~~~g~~~~ll~C~~C~~~~H~~Cl~~~~~~~~~~~W~C~~C~   55 (111)
T 2ysm_A            6 SGANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPECK   55 (111)
T ss_dssp             CCSCBTTTCCCCCTTTSEECSSSCCEECTTTTTCCCCTTTSTTCCCTTTC
T ss_pred             CCCCCcCCCCCCCCcCCeECCCCCCCcChHHhCCccccccccCccCCcCC
Confidence            35789999876332222333359999999999987642    22466654

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=80.04  E-value=1.2  Score=34.98  Aligned_cols=47  Identities=17%  Similarity=0.259  Sum_probs=30.3

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhc---CCCCCccCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL---HNSCPVCRYEL  241 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~---~~sCP~CR~~l  241 (352)
                      ...| ||......+.-+..-.|.-.||..|+..=+..   .-.||.|+..-
T Consensus        28 ~vrC-iC~~~~~~~~mi~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~~~   77 (98)
T 2lv9_A           28 VTRC-ICGFTHDDGYMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQPRN   77 (98)
T ss_dssp             BCCC-TTSCCSCSSCEEEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSSSC
T ss_pred             CEEe-ECCCccCCCcEEEcCCCCCcCcCcCCCCCccCCCCCEECCCCcCCC
Confidence            3567 88776544332322349999999999764332   34799997543

---

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	352
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	5e-20
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	2e-18
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	7e-15
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	3e-14
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	3e-11
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	2e-10
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	6e-10
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	8e-10
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	8e-09
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	2e-08
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	3e-07
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	6e-07
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	6e-07
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	1e-06

>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 = 80.3 bits (198), Expect = 5e-20
 Identities = 22/50 (44%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 193 DSSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHNSCPVCRYEL 241
           D  +CAVC    E  EEAR +P C H +H +C+  WL  H++CP+CR  +
Sbjct: 4   DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 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 = 76.1 bits (187), Expect = 2e-18
 Identities = 13/68 (19%), Positives = 32/68 (47%), Gaps = 8/68 (11%)

Query: 190 MSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPT------ 243
           M++ + +C +C +       +  +PC H +   CI  W+  + +CP+C+  + +      
Sbjct: 1   MATVAERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVESVVHTIE 58

Query: 244 DDPDYEQR 251
            D ++  +
Sbjct: 59  SDSEFGDQ 66

>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 = 67.1 bits (163), Expect = 7e-15
 Identities = 12/54 (22%), Positives = 17/54 (31%)

Query: 187 EAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYE 240
             +M       A    +           C H +H  CI  WL+    CP+   E
Sbjct: 29  NHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 82

>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 = 65.0 bits (158), Expect = 3e-14
 Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 4/58 (6%)

Query: 190 MSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYELPTDDP 246
           M S    C +C ++ +   + +  PC H+    C+  W E     CP CR E+   +P
Sbjct: 19  MGSTFQLCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP 73

>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 = 56.3 bits (135), Expect = 3e-11
 Identities = 13/56 (23%), Positives = 18/56 (32%), Gaps = 3/56 (5%)

Query: 193 DSSQCAVCKDSFELNEEARQM--PCKHIYHPDCIMPWLEL-HNSCPVCRYELPTDD 245
           D   C  CK +   N   + M   C H     C+         +CP C   L   +
Sbjct: 2   DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSN 57

>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 = 53.3 bits (128), Expect = 2e-10
 Identities = 10/46 (21%), Positives = 17/46 (36%), Gaps = 6/46 (13%)

Query: 197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP 242
           C  C+   +     + +PC H     C+         CP+C+   P
Sbjct: 9   CQQCQAEAK---CPKLLPCLHTLCSGCLEAS---GMQCPICQAPWP 48

>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 = 52.0 bits (124), Expect = 6e-10
 Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 2/51 (3%)

Query: 196 QCAVCKDSFELNEEA-RQMPCKHIYHPDCIMPWLELHN-SCPVCRYELPTD 244
           +C +C +  E+++       C +     C        N  CP CR   P D
Sbjct: 2   ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED 52

>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 = 52.2 bits (124), Expect = 8e-10
 Identities = 11/59 (18%), Positives = 17/59 (28%), Gaps = 4/59 (6%)

Query: 189 MMSSDSSQCAVCKDSFELNEEARQMP--CKHIYHPDCIMPWLELH--NSCPVCRYELPT 243
           M   D   C +C +                   H  C+  WL +    +C +C     T
Sbjct: 1   MEDEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT 59

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.2 bits (119), Expect = 8e-09
 Identities = 16/84 (19%), Positives = 30/84 (35%), Gaps = 15/84 (17%)

Query: 163 DPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPD 222
           +P+  G    S++A++ L               +C+ C +            C+HI+  +
Sbjct: 2   EPDGRGAWAHSRAALDRLE-----------KLLRCSRCTNILREPV--CLGGCEHIFCSN 48

Query: 223 CIMPWLELHNSCPVCRYELPTDDP 246
           C+     +   CPVC       D 
Sbjct: 49  CVSDC--IGTGCPVCYTPAWIQDL 70

>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 = 49.7 bits (118), Expect = 2e-08
 Identities = 11/53 (20%), Positives = 22/53 (41%), Gaps = 6/53 (11%)

Query: 196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHN---SCPVCRYELPTDD 245
           +C +C +  +   E     C HI+   C++  L        CP+C+ ++    
Sbjct: 23  ECPICLELIK---EPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS 72

>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 = 44.7 bits (105), Expect = 3e-07
 Identities = 5/49 (10%), Positives = 16/49 (32%), Gaps = 2/49 (4%)

Query: 197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD 245
           CA+                + I+    +  +++   + P+    L  ++
Sbjct: 3   CAISGKVPR--RPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEE 49

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 6e-07
 Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 8/67 (11%)

Query: 191 SSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHN--------SCPVCRYELP 242
           SS SS C +C   + + +      C+ I+   C+  ++EL          SCP       
Sbjct: 2   SSGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ 61

Query: 243 TDDPDYE 249
               + E
Sbjct: 62  GHLQENE 68

>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 = 44.5 bits (105), Expect = 6e-07
 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 4/54 (7%)

Query: 193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNS-CPVCRYELPTDD 245
            S  C +C+       +  +  CKH++   CI+  L++  S CP CRY     D
Sbjct: 22  KSISCQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTD 72

>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 = 44.6 bits (104), Expect = 1e-06
 Identities = 9/57 (15%), Positives = 16/57 (28%), Gaps = 5/57 (8%)

Query: 187 EAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLE-----LHNSCPVCR 238
           E +  +          +       R   C H +H  C++             CP C+
Sbjct: 33  EKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCK 89

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	352
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.63
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.45
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.36
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.35
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.33
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.32
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.3
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.21
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.15
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.11
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.11
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.0
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.94
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.94
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	98.94
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.73
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.43
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	92.55
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	92.16
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	91.14
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	87.52
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	86.06
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	80.7
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	80.59

>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=99.63  E-value=7.7e-17  Score=114.84  Aligned_cols=50  Identities=44%  Similarity=1.015  Sum_probs=46.1

Q ss_pred             CCCccccccccccccCCceEcc-cCceecccchHHHhhcCCCCCccCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      +..+|+||+++|..++.+++++ |+|.||..||.+||+.+++||+||++|.
T Consensus         4 d~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            3578999999999999998886 9999999999999999999999999874

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=99.45  E-value=2.2e-14  Score=106.05  Aligned_cols=47  Identities=23%  Similarity=0.776  Sum_probs=42.2

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      .+.|+||++.|..  .++.++|+|.||..||.+||+.+.+||+||+++.
T Consensus         5 ~d~C~IC~~~~~~--~~~~~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~   51 (68)
T d1chca_           5 AERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCSSCCSCCCS--CEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCccCCcCccC--CcEEeCCCCcCcHHHHHHHHHhCCcCCCCCcchH
Confidence            4689999999864  4677899999999999999999999999999875

>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=99.36  E-value=6.9e-14  Score=98.07  Aligned_cols=48  Identities=21%  Similarity=0.492  Sum_probs=40.8

Q ss_pred             ccccccccccccCC-ceEcccCceecccchHHHhhc-CCCCCccCCCCCC
Q 018689          196 QCAVCKDSFELNEE-ARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYELPT  243 (352)
Q Consensus       196 ~C~IC~e~~~~~~~-~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~~  243 (352)
                      +|+||+++|..++. ++.++|+|.||..||++|++. +.+||+||+++..
T Consensus         2 eCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            69999999987655 455689999999999999986 4579999998864

>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=99.35  E-value=1.5e-13  Score=106.48  Aligned_cols=49  Identities=27%  Similarity=0.607  Sum_probs=42.0

Q ss_pred             CCccccccccccccC---------------CceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689          194 SSQCAVCKDSFELNE---------------EARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP  242 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~---------------~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~  242 (352)
                      .+.|+||++.+....               .+..++|+|+||..||.+||+.+++||+||+++.
T Consensus        21 ~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~   84 (88)
T d3dplr1          21 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE   84 (88)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCCcCCCCCCccc
Confidence            567999999886532               3567889999999999999999999999999874

>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=99.33  E-value=2.1e-13  Score=110.21  Aligned_cols=50  Identities=20%  Similarity=0.560  Sum_probs=40.3

Q ss_pred             CCcccccccccccc---------------CCceEcccCceecccchHHHhhcC-----CCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELN---------------EEARQMPCKHIYHPDCIMPWLELH-----NSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~---------------~~~~~lpC~H~FH~~Ci~~Wl~~~-----~sCP~CR~~l~~  243 (352)
                      +..|+||++.|...               ..+.+++|+|+||..||..||+..     .+||+||..+..
T Consensus        25 ~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~   94 (114)
T d1v87a_          25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGE   94 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSS
T ss_pred             cccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhcc
Confidence            46899999998542               235677899999999999999753     489999998754

>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=99.32  E-value=4.1e-13  Score=102.05  Aligned_cols=48  Identities=27%  Similarity=0.762  Sum_probs=41.6

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhc-CCCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~~~  244 (352)
                      ...|+||++.+..   ++.++|||.||..||..||+. +++||+||..|...
T Consensus        23 ~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~   71 (79)
T d1fbva4          23 FQLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT   71 (79)
T ss_dssp             TTBCTTTSSSBCC---EECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCC
T ss_pred             CCCCccCCCcCCC---eEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCC
Confidence            3579999998765   889999999999999999974 57899999999653

>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=99.30  E-value=4.4e-13  Score=98.10  Aligned_cols=52  Identities=23%  Similarity=0.442  Sum_probs=41.3

Q ss_pred             CCCccccccccccccC--CceEcccCceecccchHHHhhc-CCCCCccCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNE--EARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYELPTD  244 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~--~~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~~~  244 (352)
                      ++..|+||++.+....  ...+++|+|.||..||.+||+. +.+||+||+.|...
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~   56 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCcccc
Confidence            3579999999865433  3456689999999999999965 56899999988543

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.21  E-value=1e-12  Score=93.27  Aligned_cols=47  Identities=13%  Similarity=0.282  Sum_probs=41.5

Q ss_pred             ccccccccccccCCceEcc-cCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689          196 QCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHNSCPVCRYELPTDD  245 (352)
Q Consensus       196 ~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~  245 (352)
                      .|+||++.|+.   ++.++ |||+||+.||.+||+.+.+||+||.++..++
T Consensus         2 ~C~Ic~~~~~~---Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~d   49 (56)
T d2baya1           2 LCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEE   49 (56)
T ss_dssp             CCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGG
T ss_pred             CCccCCchHHh---cCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHh
Confidence            69999999876   66775 9999999999999999999999999987543

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.15  E-value=4.2e-12  Score=90.15  Aligned_cols=45  Identities=22%  Similarity=0.642  Sum_probs=39.2

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      ...|+||++.|..   ++++||||.||..||.+|   +.+||+||.++...
T Consensus         6 ~l~C~IC~~~~~~---p~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T d1bora_           6 FLRCQQCQAEAKC---PKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CSSCSSSCSSCBC---CSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             CCCCcccCcccCC---CEEecCCCHHhHHHHHcC---CCcCcCCCCcccCC
Confidence            3689999999876   788999999999999887   66899999999743

>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=99.11  E-value=1.1e-11  Score=98.37  Aligned_cols=48  Identities=21%  Similarity=0.692  Sum_probs=41.1

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcC---CCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH---NSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~---~sCP~CR~~l~~~  244 (352)
                      ...|+||++.|..   ++.++|||.||..||..|+...   ..||+||..+...
T Consensus        21 ~l~CpIC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (103)
T d1jm7a_          21 ILECPICLELIKE---PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (103)
T ss_dssp             HTSCSSSCCCCSS---CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             CcCCCccCchhCC---eEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChh
Confidence            3689999999876   6778999999999999999764   3799999988643

>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=99.11  E-value=9.9e-12  Score=95.81  Aligned_cols=47  Identities=30%  Similarity=0.738  Sum_probs=41.2

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhc-CCCCCccCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYELPT  243 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~~  243 (352)
                      ...|+||++.|..   +++++|||.||+.||.+|++. +.+||+||.++..
T Consensus        23 ~l~C~IC~~~~~~---pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~   70 (86)
T d1rmda2          23 SISCQICEHILAD---PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFP   70 (86)
T ss_dssp             HTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CcCCccCCcchhc---ceecCCCChhhHHHHHHHHhhCCCcCcccCCCCCh
Confidence            3689999999876   789999999999999999975 4589999998864

>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=99.00  E-value=4.6e-11  Score=93.67  Aligned_cols=46  Identities=22%  Similarity=0.564  Sum_probs=38.2

Q ss_pred             CCccccccccccccCCceE-cccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQ-MPCKHIYHPDCIMPWLELHNSCPVCRYELPTD  244 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~-lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~  244 (352)
                      ...|+||++.|..   ++. .+|||.||..||.+|+.  +.||+||..+...
T Consensus        22 ~l~C~IC~~~~~~---pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~   68 (97)
T d1jm7b_          22 LLRCSRCTNILRE---PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQ   68 (97)
T ss_dssp             TTSCSSSCSCCSS---CBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCS
T ss_pred             cCCCccCCchhhc---CceeCCCCCchhHHHHHHHHh--ccccccCCcCchh
Confidence            4789999999976   444 47999999999999984  4699999987544

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.94  E-value=1.9e-10  Score=86.47  Aligned_cols=50  Identities=18%  Similarity=0.434  Sum_probs=43.6

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhc-CCCCCccCCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYELPTDD  245 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~~~~  245 (352)
                      +...|+||++.|.+   +++++|||.|++.||.+|++. ..+||+|+..+...+
T Consensus         7 ~~l~CpIc~~~m~d---PV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~   57 (78)
T d1t1ha_           7 EYFRCPISLELMKD---PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAG   57 (78)
T ss_dssp             SSSSCTTTSCCCSS---EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCC
T ss_pred             ccCCCcCcCchhhC---ceEccCCCcchHHHHHHHHHHCCCCCCcccccCCccc
Confidence            36899999999987   788999999999999999976 467999999986543

>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=98.94  E-value=1.2e-10  Score=83.43  Aligned_cols=48  Identities=23%  Similarity=0.596  Sum_probs=37.5

Q ss_pred             CCCccccccccccccCCceEcc-----cCceecccchHHHhhc--CCCCCccCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMP-----CKHIYHPDCIMPWLEL--HNSCPVCRYELPT  243 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lp-----C~H~FH~~Ci~~Wl~~--~~sCP~CR~~l~~  243 (352)
                      +...|.||++.+...   ...+     |+|.||..||.+|+..  +.+||+||+++..
T Consensus         5 d~~~C~IC~~~~~~~---~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           5 DVPVCWICNEELGNE---RFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             SCCEETTTTEECSCC---CCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCccCCccCCCc---eeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            467899999987653   2233     4699999999999954  5689999998753

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.94  E-value=2e-10  Score=86.85  Aligned_cols=49  Identities=18%  Similarity=0.129  Sum_probs=42.8

Q ss_pred             CCCccccccccccccCCceEcccCceecccchHHHhhc-CCCCCccCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYELPTD  244 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~~~  244 (352)
                      +...|+||++.|.+   +++++|||.|++.||.+||.. +.+||+||..+...
T Consensus         6 ~~l~CpIc~~l~~d---Pv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~   55 (80)
T d2c2la2           6 DYLCGKISFELMRE---PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQE   55 (80)
T ss_dssp             STTBCTTTCSBCSS---EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGG
T ss_pred             ccccCcCcCchhhh---hcccCCcCeecHHHHHHHHhcCCccCCCcccccccc
Confidence            36899999999987   788999999999999999975 56899999988644

>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=98.73  E-value=3.6e-09  Score=82.98  Aligned_cols=50  Identities=16%  Similarity=0.089  Sum_probs=44.5

Q ss_pred             CCCccccccccccccCCceEcccC-ceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689          193 DSSQCAVCKDSFELNEEARQMPCK-HIYHPDCIMPWLELHNSCPVCRYELPTDD  245 (352)
Q Consensus       193 ~~~~C~IC~e~~~~~~~~~~lpC~-H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~  245 (352)
                      +...|+||++.|.+   +++++|+ |.|++.||..||..+.+||+||..|..++
T Consensus        21 ~~f~CPI~~~lm~d---PV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~   71 (98)
T d1wgma_          21 DEFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQ   71 (98)
T ss_dssp             TTTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTT
T ss_pred             HHhCCcCchhHHHH---HHhcccccchhhHHHHHHHHHhcCCcccccccccchh
Confidence            36899999999988   8899965 58999999999999999999999987654

>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=98.43  E-value=2.8e-08  Score=76.68  Aligned_cols=45  Identities=27%  Similarity=0.637  Sum_probs=37.0

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhcC--------CCCCccC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH--------NSCPVCR  238 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~--------~sCP~CR  238 (352)
                      ...|+||++++...+.+..++|+|.||..||..|++.+        .+||.|+
T Consensus         5 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           5 SSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            57899999999876667777899999999999999531        2699864

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=92.55  E-value=0.03  Score=38.77  Aligned_cols=47  Identities=26%  Similarity=0.567  Sum_probs=33.9

Q ss_pred             CCccccccccccccCCceEcc-cCceecccchHHHhh-----cCCCCCccCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLE-----LHNSCPVCRYE  240 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~-----~~~sCP~CR~~  240 (352)
                      ...|.||......++..+.-. |+..||..|+..-..     .+-.||.|+..
T Consensus         6 ~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           6 SGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             CCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            578999998876665544444 999999999964221     23479999754

>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=92.16  E-value=0.028  Score=37.16  Aligned_cols=43  Identities=28%  Similarity=0.620  Sum_probs=29.9

Q ss_pred             ccccccccccccCCceEc-ccCceecccchHHHhhcCC----CCCccCC
Q 018689          196 QCAVCKDSFELNEEARQM-PCKHIYHPDCIMPWLELHN----SCPVCRY  239 (352)
Q Consensus       196 ~C~IC~e~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~~~----sCP~CR~  239 (352)
                      .|.||...-..+ .++.- .|...||..|+.+-+....    .||.||.
T Consensus         2 ~C~vC~~~~~~~-~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCC-CEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            588997654332 33333 3999999999998775422    5999975

>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=91.14  E-value=0.06  Score=38.00  Aligned_cols=45  Identities=27%  Similarity=0.650  Sum_probs=30.6

Q ss_pred             CCccccccccccccCCceEc-ccCceecccchHHHhhcCC----CCCccCCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQM-PCKHIYHPDCIMPWLELHN----SCPVCRYELP  242 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~~~----sCP~CR~~l~  242 (352)
                      ...|.||.+.   ++ ++.- .|...||..|+.+.|....    .||.|+....
T Consensus         7 c~~C~~C~~~---~~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   56 (70)
T d1fp0a1           7 ATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   56 (70)
T ss_dssp             SSCCSSSCSS---SC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             CCCCCCCCCc---CE-EEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCc
Confidence            3567777543   33 3333 4999999999999875432    5999976544

>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=87.52  E-value=0.11  Score=37.82  Aligned_cols=33  Identities=18%  Similarity=0.561  Sum_probs=24.3

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHH
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPW  227 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~W  227 (352)
                      +..|.|| +.|...+..-.--|+-+||..|+.+-
T Consensus        15 D~mC~vC-~v~t~~~l~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          15 DEMCDVC-EVWTAESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             SCCCTTT-CCCCSSCCSSCSSSSSCCCHHHHHHH
T ss_pred             Ccccccc-CcccccceecceeecchhhHHHHHHh
Confidence            5899999 77766443311128999999999986

>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=86.06  E-value=0.2  Score=34.08  Aligned_cols=45  Identities=33%  Similarity=0.590  Sum_probs=30.8

Q ss_pred             CCccccccccccccCCceEcccCceecccchHHHhhc----CCCCCccCCCC
Q 018689          194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL----HNSCPVCRYEL  241 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~----~~sCP~CR~~l  241 (352)
                      ...|.||.+.   ++-+.--.|.-.||..||...+..    .-.||.|+...
T Consensus         9 ~~~C~~C~~~---g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           9 MEFCRVCKDG---GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             CSSCTTTCCC---SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             cCCCcCCCCC---CeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            4579999753   332322348999999999877643    23699997654

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.70  E-value=0.23  Score=36.11  Aligned_cols=47  Identities=23%  Similarity=0.559  Sum_probs=31.0

Q ss_pred             CCccccccccccccC-CceEc-ccCceecccchHHHhh-----c---CCCCCccCCC
Q 018689          194 SSQCAVCKDSFELNE-EARQM-PCKHIYHPDCIMPWLE-----L---HNSCPVCRYE  240 (352)
Q Consensus       194 ~~~C~IC~e~~~~~~-~~~~l-pC~H~FH~~Ci~~Wl~-----~---~~sCP~CR~~  240 (352)
                      ...|.||........ .++.- .|...||..|+.+.+.     .   .-.||.|...
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~   72 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQ   72 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHH
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCch
Confidence            467999987543322 23333 3899999999886542     1   2369999653

>d1y02a2 g.50.1.1 (A:20-70) Rififylin (FYVE-RING finger protein Sakura) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Rififylin (FYVE-RING finger protein Sakura)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.59  E-value=0.17  Score=33.52  Aligned_cols=43  Identities=19%  Similarity=0.432  Sum_probs=29.6

Q ss_pred             ccccccccccccCCceEcc-cCceecccchHHHhhcCCCCCccC
Q 018689          196 QCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHNSCPVCR  238 (352)
Q Consensus       196 ~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~sCP~CR  238 (352)
                      .|.+|...|..-.....-. ||++|+..|..........|..|.
T Consensus         2 ~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~RvC~~C~   45 (51)
T d1y02a2           2 SCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQ   45 (51)
T ss_dssp             CCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHH
T ss_pred             CccccCCcccCCccCcccccCCcccCccccCCCCCCCeECHhHh
Confidence            5889999997654433443 999999999877665666787774