Citrus Sinensis ID: 021640

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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-------31
Protein Sequence
MSSGRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEERDQRLGLMEAFSAFVRHRMADRHSHDIRGRYDSTPEHGQGFGPLLIFGGQIPLRLSGNSGFEAIFGGAPGLGFARGNTGDYFIGPGLEELFEQLSANGRRGPPPAARSAIDAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSSRIHQSSSGQSRSTSFGSNGSGRENQGRRNLFSGFWPFRSSNSSSNHNGTTESSSPAMHENNPHMGYSGWPFD
Secondary Structure (PSIPRED)
cccccccEEcccccccEEcccccccccccccccEEcccccccccccccccccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccccHHHHHccccccccccccccccccccccccccccccEEEEccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccEEEEEccEEEccccccccccccccccEEEccccccccccccccccccccccccccccHHHcHHHcccccccccccccccccccccccccccccccccccccccccccccccHcccccccccccccccccccccccHHHHHHHHHHccccccccccHHHHHccccEEEEHHHccccccccccHHHccccHHHcccccccccccccEcHHHHHccccccEccEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mssgrnthwcyrcrrpvrlqgedAVCLYCsggfvqelddmvsvspldffgldndeeRDQRLGLMEAFSAFVRHRmadrhshdirgrydstpehgqgfgpllifggqiplrlsgnsgfeaifggapglgfargntgdyfigpGLEELFEQLSangrrgpppaarsaidamptvritqrhlrsdshcpvcqdkfelgsearqmpcnhiyhsdcivpwlvqhnscpvcrqelplqgssssrihqsssgqsrstsfgsngsgrenqgrrnlfsgfwpfrssnsssnhngttessspamhennphmgysgwpfd
Flexible Loop (DISEMBL)
mssgrnthwcyrcrrpvrlqGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEERDQRLGLMEAFSAFVRHRMADRHSHDIRGRYDSTPEHGQGFGPLLIFGGQIPLRLSGNSGFEAIFGGAPGLGFARGNTGDYFIGPGLEELFEQLSANGRRGPPPAARSAIDAMPTVRITQrhlrsdshcpvCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSsrihqsssgqsrstsfgsngsgrenqGRRNLFSGFWPFRSSNSSSNHNGTTessspamhennphmgysgwpfd
Low Complexity Region (SEG)
MSSGRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEERDQRLGLMEAFSAFVRHRMADRHSHDIRGRYDSTPEHGQGFGPLLIFGGQIPLRLSGNSGFEAIFGGAPGLGFARGNTGDYFIGPGLEELFEQLSANGRRGPPPAARSAIDAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLqgssssrihqsssgqsrstsfgsNGSGRENQGRRNLFSGFWPFRssnsssnhngttesssPAMHENNPHMGYSGWPFD
Disordered region (IsUnstruct)
******THWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDND****QRLGLMEAFSAFVRHRM******************GQGFGPLLIFGGQIPLRLSGNSGFEAIFGGAPGLGFARGNTGDYFIGPGLEELFE**********************************SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQ*******************************************FW*************************************
Disordered Region (DISOPRED)
***GRNT*WCYRCRRPVRLQGEDAVCLYCSGGFVQEL*********************QRLGLMEAFSAF****************************PLLIFGGQIPLRLSGNS******************TGDYFIGPGLEELF******************IDAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQ**********************************************************************************
Disordered Region (DISEMBL)
********WCYRCRRPVRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEERDQRLGLMEAFSAFVRHRMADRHSHDIRGRYDSTPEHGQGFGPLLIFGGQIPLRLSGNSGFEAIFGGAPGLGFARGNTGDYFIGPGLEELFEQLSA**********RSAIDAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP******************************NQGRRNLFSGFWPFRSS****************MHENNPHMGYSGWPFD
Disordered Region (DISPRO)
*****NTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDD*********************LGLMEAFSAF*RHRM*********************FGPLLIFGGQIPLRLSGNSGFEAIFGGAPGLGFARGNTGDYFIGPGLEELFEQLSANGRRGPPPAARSAIDAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL********************************************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSGRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEERDQRLGLMEAFSAFVRHRMADRHSHDIRGRYDSTPEHGQGFGPLLIFGGQIPLRLSGNSGFEAIFGGAPGLGFARGNTGDYFIGPGLEELFEQLSANGRRGPPPAARSAIDAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSSRIHQSSSGQSRSTSFGSNGSGRENQGRRNLFSGFWPFRSSNSSSNHNGTTESSSPAMHENNPHMGYSGWPFD
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	309	2.2.26 [Sep-21-2011]
Q8LPN7	328	E3 ubiquitin-protein liga	no	no	0.705	0.664	0.360	3e-36
P0CH30	338	E3 ubiquitin-protein liga	N/A	no	0.864	0.789	0.336	2e-35
Q6DIP3	311	RING finger protein 126 O	yes	no	0.355	0.353	0.437	2e-23
Q9D0C1	305	E3 ubiquitin-protein liga	yes	no	0.747	0.757	0.306	2e-23
Q9BV68	326	RING finger protein 126 O	yes	no	0.355	0.337	0.464	3e-23
Q7T0Q3	312	RING finger protein 126-A	N/A	no	0.355	0.352	0.437	3e-23
Q91YL2	313	RING finger protein 126 O	no	no	0.355	0.351	0.455	4e-23
Q0II22	313	RING finger protein 126 O	no	no	0.352	0.348	0.468	4e-23
Q6IRP0	312	RING finger protein 126-B	N/A	no	0.355	0.352	0.428	6e-23
Q9Y4L5	304	E3 ubiquitin-protein liga	no	no	0.407	0.414	0.424	1e-22

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

 Score =  152 bits (384), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 88/244 (36%), Positives = 128/244 (52%), Gaps = 26/244 (10%)

Query: 9   WCYRCRRPVRLQ---GEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEERDQRLGLME 65
           +CY+C + V +      D  C  C+ GF++E +D      L+F    N    D    + +
Sbjct: 22  FCYQCNQTVTISISSSADPFCPICNQGFLEEYEDPNPNQSLNF----NPNSSDSFFPMAD 77

Query: 66  AFSAFVRHRMADRHSH------------DIRGRYDSTPEHGQ--GFGPLLIFGGQIPLRL 111
            FS  +        +              ++ +  ST ++ Q   F P       +    
Sbjct: 78  PFSTLLPLIFGSSAAAPSGMDFMSLFGPSMQPQARSTQQNPQSDAFDPFTFLQNHLQTLR 137

Query: 112 SGNSGFEAIFGGAPGLGFAR--GNTGDYFIGPGLEELFEQLSAN--GRRGPPPAARSAID 167
           S  + FE +    P     R  GN GDYF GPGLE+L +QL+ N   R G PPA++SAID
Sbjct: 138 SSGTHFEFVIENHPSDPGNRMPGNFGDYFFGPGLEQLIQQLAENDPNRYGTPPASKSAID 197

Query: 168 AMPTVRITQRHLRSD-SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCR 226
           A+PTV++T+  L+S+ + C VC D+FE GS+ +QMPC H++H DC++PWL  HNSCPVCR
Sbjct: 198 ALPTVKVTKDMLKSEMNQCAVCMDEFEDGSDVKQMPCKHVFHQDCLLPWLELHNSCPVCR 257

Query: 227 QELP 230
            ELP
Sbjct: 258 FELP 261

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

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

 Score =  149 bits (377), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 100/297 (33%), Positives = 141/297 (47%), Gaps = 30/297 (10%)

Query: 9   WCYRCRRPVRLQ----GEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEE--RDQRLG 62
           +CY+C R V +       D  C  C+ GF++E D+        F   + +     D  L 
Sbjct: 24  FCYQCNRTVNVTISPPSSDPTCPICNEGFLEEYDNPNPNQGSGFLNPNPNSIPFHDLFLT 83

Query: 63  LMEAFSAFV-------------RHRMADRHSHDIRGRYDSTPEHGQGFGPLLIFGGQIPL 109
           L + F++ +                  D ++  + G   S       F P       +  
Sbjct: 84  LSDPFASLLPLLFPSSSSTTTSSSASIDPNNPSLSGPTRSGRGDPFAFDPFTFIQNHLND 143

Query: 110 RLSGNSGFEAIFGGAPG-LGF-ARGNTGDYFIGPGLEELFEQLSAN--GRRGPPPAARSA 165
             S  +  E +    P   GF    N GDYFIGPGLE+L +QL+ N   R G PPA++SA
Sbjct: 144 LRSSGAQIEFVIQNNPSDQGFRLPANIGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSA 203

Query: 166 IDAMPTVRITQRHLRSD-SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPV 224
           I+A+P V IT+ +L S+ + C VC D FE G+EA+QMPC H+YH DC++PWL  HNSCPV
Sbjct: 204 IEALPLVNITKSNLNSEFNQCAVCMDDFEEGTEAKQMPCKHLYHKDCLLPWLELHNSCPV 263

Query: 225 CRQELPLQGSSSSRIHQSSSGQSRSTSFGSNGSGRENQGRRNLFSGF-----WPFRS 276
           CR ELP       R  + + G S     G N   R +   R +   F     WPF++
Sbjct: 264 CRHELPTDDPDYERRVRGAQGTSGGND-GDNSGQRSDGDNRTVERSFRISLPWPFQA 319

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

Gossypium hirsutum (taxid: 3635)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score =  110 bits (274), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 73/112 (65%), Gaps = 2/112 (1%)

Query: 128 GFARGNTGDYFIGP-GLEELFEQL-SANGRRGPPPAARSAIDAMPTVRITQRHLRSDSHC 185
           G    N  DY  G  GL+ +  QL +     GPPPA    I A+PT++IT+ H+ S   C
Sbjct: 168 GVLHSNPMDYAWGANGLDTIITQLLNQFENTGPPPADTEKIQALPTIQITEEHVGSGLEC 227

Query: 186 PVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSS 237
           PVC++ + +G   RQ+PCNH++H+DCI+PWL QH++CPVCR+ L  Q ++++
Sbjct: 228 PVCKEDYTVGESVRQLPCNHLFHNDCIIPWLEQHDTCPVCRKSLSGQNTATN 279

Xenopus tropicalis (taxid: 8364)

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

 Score =  109 bits (273), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 123/277 (44%), Gaps = 46/277 (16%)

Query: 9   WCYRCRRPVRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFG-----LDND--------- 54
           +C+ C+  V  +  + +C  C  GF++E+ D  S     F G      DN          
Sbjct: 21  FCHFCKGEVNPKLPEYICPRCDSGFIEEVTDDSS-----FLGGGGSRTDNSTATHFAELW 75

Query: 55  EERDQRLGLMEAFSAFVRHRMADRHSH-DIRGRYDSTPEHGQGFGPLLIF-------GGQ 106
           +  D  +  ++ F  F+     D+ +  + RG    T   G    P L         G  
Sbjct: 76  DHLDHTM-FLQDFRPFLSSNPLDQDNRANERGHQTHTDFWGPSRPPRLPMTRRYRSRGST 134

Query: 107 IPLRLSGNSGF-EAIFGG------APGL-------GFARGNTGDYFIG-PGLEELFEQLS 151
            P R     G  + IF G       PG        G    N GDY  G  GL+ +  QL 
Sbjct: 135 RPDRSPAIEGIIQQIFAGFFANSAIPGSPHPFSWSGMLHSNPGDYAWGQTGLDAIVTQLL 194

Query: 152 AN-GRRGPPPAARSAIDAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSD 210
                 GPPPA +  I ++PTV +TQ  + +   CPVC++ + +  + RQ+PCNH +HS 
Sbjct: 195 GQLENTGPPPADKEKITSLPTVTVTQEQVNTGLECPVCKEDYTVEEKVRQLPCNHFFHSS 254

Query: 211 CIVPWLVQHNSCPVCRQELPLQGSSSSRIHQSSSGQS 247
           CIVPWL  H++CPVCR+   L G  S+R  QSS   +
Sbjct: 255 CIVPWLELHDTCPVCRKS--LNGEDSTRQTQSSEASA 289

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

 Score =  109 bits (272), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 52/112 (46%), Positives = 71/112 (63%), Gaps = 2/112 (1%)

Query: 128 GFARGNTGDYFIGP-GLEELFEQL-SANGRRGPPPAARSAIDAMPTVRITQRHLRSDSHC 185
           G    N  DY  G  GL+ +  QL +     GPPPA +  I A+PTV +T+ H+ S   C
Sbjct: 170 GVLHSNPMDYAWGANGLDAIITQLLNQFENTGPPPADKEKIQALPTVPVTEEHVGSGLEC 229

Query: 186 PVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSS 237
           PVC+D + LG   RQ+PCNH++H  CIVPWL QH+SCPVCR+ L  Q ++++
Sbjct: 230 PVCKDDYALGERVRQLPCNHLFHDGCIVPWLEQHDSCPVCRKSLTGQNTATN 281

Homo sapiens (taxid: 9606)

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

 Score =  109 bits (272), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 73/112 (65%), Gaps = 2/112 (1%)

Query: 128 GFARGNTGDYFIGP-GLEELFEQL-SANGRRGPPPAARSAIDAMPTVRITQRHLRSDSHC 185
           G    N  DY  G  GL+ +  QL +     GPPPA    I A+PT++IT+ H+ S   C
Sbjct: 169 GVLHSNPMDYAWGANGLDTIITQLLNQFENTGPPPADNEKIQALPTIQITEEHVGSGLEC 228

Query: 186 PVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSS 237
           PVC++ + +G   RQ+PCNH++H+DCI+PWL QH++CPVCR+ L  Q ++++
Sbjct: 229 PVCKEDYTVGECVRQLPCNHLFHNDCIIPWLEQHDTCPVCRKSLSGQNTATN 280

Xenopus laevis (taxid: 8355)

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

 Score =  108 bits (271), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 51/112 (45%), Positives = 71/112 (63%), Gaps = 2/112 (1%)

Query: 128 GFARGNTGDYFIGP-GLEELFEQL-SANGRRGPPPAARSAIDAMPTVRITQRHLRSDSHC 185
           G    N  DY  G  GL+ +  QL +     GPPPA +  I A+PTV +T+ H+ S   C
Sbjct: 172 GVLHSNPMDYAWGANGLDTIITQLLNQFENTGPPPADKEKIQALPTVPVTEEHVGSGLEC 231

Query: 186 PVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSS 237
           PVC++ + LG   RQ+PCNH++H  CIVPWL QH+SCPVCR+ L  Q ++++
Sbjct: 232 PVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATN 283

Mus musculus (taxid: 10090)

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

 Score =  108 bits (271), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 52/111 (46%), Positives = 70/111 (63%), Gaps = 2/111 (1%)

Query: 128 GFARGNTGDYFIGP-GLEELFEQL-SANGRRGPPPAARSAIDAMPTVRITQRHLRSDSHC 185
           G    N  DY  G  GL+ +  QL +     GPPPA +  I A+PTV +T+ H+ S   C
Sbjct: 173 GVLHSNPMDYAWGANGLDAIITQLLNQFENTGPPPADKEKIQALPTVPVTEEHVGSGLEC 232

Query: 186 PVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSS 236
           PVC+D + LG   RQ+PCNH++H  CIVPWL QH+SCPVCR+ L  Q +++
Sbjct: 233 PVCKDDYGLGEHVRQLPCNHLFHDGCIVPWLEQHDSCPVCRKSLTGQNTAT 283

Bos taurus (taxid: 9913)

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

 Score =  108 bits (269), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 48/112 (42%), Positives = 72/112 (64%), Gaps = 2/112 (1%)

Query: 128 GFARGNTGDYFIGP-GLEELFEQL-SANGRRGPPPAARSAIDAMPTVRITQRHLRSDSHC 185
           G    N  DY  G  GL+ +  QL +     GPPPA    I A+PT++IT+ H+     C
Sbjct: 169 GVLHSNPMDYAWGANGLDTIITQLLNQFENTGPPPADTDKIQALPTIQITEEHVGFGLEC 228

Query: 186 PVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSS 237
           PVC++ + +G   RQ+PCNH++H+DCI+PWL QH++CPVCR+ L  Q ++++
Sbjct: 229 PVCKEDYTVGESVRQLPCNHLFHNDCIIPWLEQHDTCPVCRKSLSGQNTATN 280

Xenopus laevis (taxid: 8355)

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

 Score =  107 bits (267), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 56/132 (42%), Positives = 78/132 (59%), Gaps = 6/132 (4%)

Query: 128 GFARGNTGDYFIG-PGLEELFEQLSAN-GRRGPPPAARSAIDAMPTVRITQRHLRSDSHC 185
           G    N GDY  G  GL+ +  QL       GPPPA +  I ++PTV +TQ  +     C
Sbjct: 169 GMLHSNPGDYAWGQTGLDAIVTQLLGQLENTGPPPADKEKITSLPTVTVTQEQVDMGLEC 228

Query: 186 PVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSSRIHQSSSG 245
           PVC++ + +  E RQ+PCNH +HS CIVPWL  H++CPVCR+   L G  S+R  QS S 
Sbjct: 229 PVCKEDYTVEEEVRQLPCNHFFHSSCIVPWLELHDTCPVCRKS--LNGEDSTR--QSQST 284

Query: 246 QSRSTSFGSNGS 257
           ++ +++  SN S
Sbjct: 285 EASASNRFSNDS 296

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: -

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	309
224139648	308	predicted protein [Populus trichocarpa]	0.987	0.990	0.778	1e-132
224089895	311	predicted protein [Populus trichocarpa]	0.987	0.980	0.753	1e-123
356500343	309	PREDICTED: E3 ubiquitin-protein ligase R	0.987	0.987	0.715	1e-119
356577672	309	PREDICTED: E3 ubiquitin-protein ligase R	0.987	0.987	0.696	1e-116
255647446	309	unknown [Glycine max]	0.987	0.987	0.683	1e-114
449437755	305	PREDICTED: E3 ubiquitin-protein ligase R	0.980	0.993	0.691	1e-113
388511895	293	unknown [Lotus japonicus]	0.925	0.976	0.671	1e-110
449453133	299	PREDICTED: E3 ubiquitin-protein ligase R	0.954	0.986	0.681	1e-110
190898156	260	thioredoxin-related protein [Populus tre	0.831	0.988	0.75	1e-98
190898190	260	thioredoxin-related protein [Populus tre	0.831	0.988	0.746	1e-98

>gi|224139648|ref|XP_002323210.1| predicted protein [Populus trichocarpa] gi|222867840|gb|EEF04971.1| predicted protein [Populus trichocarpa]

 Score =  478 bits (1229), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 243/312 (77%), Positives = 269/312 (86%), Gaps = 7/312 (2%)

Query: 1   MSSGRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEERDQR 60
           MSS RNTHWCY CRRPVRL+G D+ C YCSGGFVQELDDM  +SPLDFFG+D+D++RDQR
Sbjct: 1   MSSSRNTHWCYSCRRPVRLRGRDSACPYCSGGFVQELDDMHRISPLDFFGMDSDDDRDQR 60

Query: 61  LGLMEAFSAFVRHRMADR-HSHDIRGRYDSTPEHGQGFGPLLIFGGQIPLRLSGNSGFEA 119
            GLMEAFS F+R RMADR H+HDIR R DS P H  GFGPLLIFGGQ+P RLSGN GFEA
Sbjct: 61  FGLMEAFSDFMRQRMADRSHNHDIRSRSDSVPGHNPGFGPLLIFGGQVPFRLSGNGGFEA 120

Query: 120 IFGGAPGLGFARGNTGDYFIGPGLEELFEQLSANGRRGPPPAARSAIDAMPTVRITQRHL 179
           +F GAPG+ FARGN GDYFIGPGLEELFEQLSAN +RGPPPA RS+IDAMPT++ITQ+HL
Sbjct: 121 LFSGAPGVAFARGNAGDYFIGPGLEELFEQLSANDQRGPPPATRSSIDAMPTIKITQKHL 180

Query: 180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSSRI 239
           RSDSHCPVC+DKFELGSEARQMPC+H+YHSDCIVPWLVQHNSCPVCRQELP QGSSS   
Sbjct: 181 RSDSHCPVCKDKFELGSEARQMPCDHLYHSDCIVPWLVQHNSCPVCRQELPPQGSSSRHS 240

Query: 240 HQSSSGQSRSTSFGSNGSGRENQ--GRRNLFSGFWPFRSSNSSSNHNGTTESSSPAMHEN 297
           +QSSS +SRS++     SGREN   GRRN  S  WPFRSSNSSSNH+ T ESSSPAMHEN
Sbjct: 241 YQSSSSRSRSSN----YSGRENSRGGRRNPLSYLWPFRSSNSSSNHDETPESSSPAMHEN 296

Query: 298 NPHMGYSGWPFD 309
           NPHMGYSGWPF+
Sbjct: 297 NPHMGYSGWPFN 308

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224089895|ref|XP_002308856.1| predicted protein [Populus trichocarpa] gi|222854832|gb|EEE92379.1| predicted protein [Populus trichocarpa]

 Score =  448 bits (1152), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 235/312 (75%), Positives = 258/312 (82%), Gaps = 7/312 (2%)

Query: 1   MSSGRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEERDQR 60
           MSS RNTHWCY CRRPVRL+G DA C YCSGGFVQELDDM  ++PLDFFG+D D++ D  
Sbjct: 4   MSSSRNTHWCYSCRRPVRLRGRDAACPYCSGGFVQELDDMHRINPLDFFGMDGDDDHDNM 63

Query: 61  LGLMEAFSAFVRHRMADR-HSHDIRGRYDSTPEHGQGFGPLLIFGGQIPLRLSGNSGFEA 119
            GLMEAFSAF+R RMADR H+HDIR R DS PEH  GFGPLLIFGGQIP RLSGN G EA
Sbjct: 64  FGLMEAFSAFMRQRMADRSHNHDIRSRSDSIPEHNPGFGPLLIFGGQIPFRLSGNGGLEA 123

Query: 120 IFGGAPGLGFARGNTGDYFIGPGLEELFEQLSANGRRGPPPAARSAIDAMPTVRITQRHL 179
           +F G+PG+ FARGN GDYF+GPGLEELFEQLSAN RRGPPPA RS+IDAMPT++ITQ+HL
Sbjct: 124 LFSGSPGVAFARGNAGDYFVGPGLEELFEQLSANDRRGPPPATRSSIDAMPTIKITQKHL 183

Query: 180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSSRI 239
           RSDSHCPVC+DKFELGSEARQMPC+H+YHSDCIVPWLVQHNSCPVCRQELP QGS+S   
Sbjct: 184 RSDSHCPVCKDKFELGSEARQMPCDHLYHSDCIVPWLVQHNSCPVCRQELPPQGSNSG-- 241

Query: 240 HQSSSGQSRSTSFGSNGSGREN--QGRRNLFSGFWPFRSSNSSSNHNGTTESSSPAMHEN 297
              S   S S S  SN SGREN  +GRRN  S  WPFRSSNSSSNH+ T  SSSP MHEN
Sbjct: 242 --HSYQSSSSRSRSSNYSGRENSREGRRNPLSYLWPFRSSNSSSNHDETPGSSSPTMHEN 299

Query: 298 NPHMGYSGWPFD 309
           N  MGYSGWPF+
Sbjct: 300 NHQMGYSGWPFN 311

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356500343|ref|XP_003518992.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like [Glycine max]

 Score =  435 bits (1118), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 224/313 (71%), Positives = 252/313 (80%), Gaps = 8/313 (2%)

Query: 1   MSSGRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEERDQR 60
           MS+ RNTHWCY CRRPV L   DAVC  C+ GFV EL+DMV V+P D F +DN+EERDQR
Sbjct: 1   MSNSRNTHWCYSCRRPVWLGRRDAVCPSCNEGFVHELNDMVHVNPFDLFEMDNNEERDQR 60

Query: 61  LGLMEAFSAFVRHRMADR-HSHDIRGRYDSTPEHGQGFGPLLIFGGQIPLRLSGNSGFEA 119
           LGLME FSAF+RH+MADR  SHDIR + DS PEH  GF PLLIFGGQIP RLSG+ GFEA
Sbjct: 61  LGLMETFSAFMRHQMADRGRSHDIRAQTDSNPEHSAGFAPLLIFGGQIPFRLSGHGGFEA 120

Query: 120 IFGGAPGLGFARGNTGDYFIGPGLEELFEQLSANGRRGPPPAARSAIDAMPTVRITQRHL 179
           +F GAPG+G  RGNTGDYFIGPGLEELFEQLSAN R+GPPPA+RS+IDAMPT++ITQRHL
Sbjct: 121 LFNGAPGIGLTRGNTGDYFIGPGLEELFEQLSANNRQGPPPASRSSIDAMPTIKITQRHL 180

Query: 180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSSRI 239
           RSDSHCPVC+DKFE+GSEARQMPCNH+YHSDCIVPWLVQHNSCPVCRQEL  QG SSS  
Sbjct: 181 RSDSHCPVCKDKFEVGSEARQMPCNHLYHSDCIVPWLVQHNSCPVCRQELLPQGLSSS-- 238

Query: 240 HQSSSGQSRSTSFGSNGSGRENQGRRNLFSGFWPFRSSNSSSNHNGTTESS-SPAMHEN- 297
             + S   RS S   + SGRE+ GRRN FS  WPFRSS+SSSN   T  SS +P + EN 
Sbjct: 239 --NRSTNGRSRSASLSSSGRESHGRRNPFSFLWPFRSSHSSSNDEATGSSSPTPTIPENS 296

Query: 298 -NPHMGYSGWPFD 309
            + H GYSGWPF+
Sbjct: 297 HHHHAGYSGWPFE 309

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356577672|ref|XP_003556948.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like isoform 1 [Glycine max] gi|356577674|ref|XP_003556949.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like isoform 2 [Glycine max]

 Score =  425 bits (1092), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 218/313 (69%), Positives = 248/313 (79%), Gaps = 8/313 (2%)

Query: 1   MSSGRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEERDQR 60
           MS+ RNTHWCY CRRPVRL   D VC  C+ GFV EL+D+V V+P D FG+DN+EERDQR
Sbjct: 1   MSNSRNTHWCYSCRRPVRLGRRDVVCPSCNLGFVHELNDIVHVNPFDLFGMDNNEERDQR 60

Query: 61  LGLMEAFSAFVRHRMADR-HSHDIRGRYDSTPEHGQGFGPLLIFGGQIPLRLSGNSGFEA 119
           LGLME FSAF+RH+MADR  SHDIR R DS PEH   F PLLIFGG IP RLS + GFEA
Sbjct: 61  LGLMETFSAFMRHQMADRGRSHDIRVRTDSNPEHSASFAPLLIFGGHIPFRLSRHGGFEA 120

Query: 120 IFGGAPGLGFARGNTGDYFIGPGLEELFEQLSANGRRGPPPAARSAIDAMPTVRITQRHL 179
           +F GAPG+G  +GNTGDYFIGPGLEELFEQLSAN R+GP PA+RS+IDAMPT++I QRHL
Sbjct: 121 LFNGAPGIGLTQGNTGDYFIGPGLEELFEQLSANNRQGPLPASRSSIDAMPTIKIVQRHL 180

Query: 180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSSRI 239
           RSDSHCPVC+DKFELGS+ARQMPCNH+YHSDCIVPWLVQHNSCPVCRQELP QG SSS  
Sbjct: 181 RSDSHCPVCKDKFELGSKARQMPCNHLYHSDCIVPWLVQHNSCPVCRQELPPQGLSSS-- 238

Query: 240 HQSSSGQSRSTSFGSNGSGRENQGRRNLFSGFWPFRSSNSSSNHNGTTESS-SPAMHEN- 297
             +     RS S   + SGRE+ GRRN FS  WPFRSS+SSSN   T  S+ +P + EN 
Sbjct: 239 --NGGANGRSRSARVSSSGRESHGRRNPFSFLWPFRSSHSSSNDEATGSSTPTPTIPENS 296

Query: 298 -NPHMGYSGWPFD 309
            + H GYSGWPF+
Sbjct: 297 HHHHAGYSGWPFE 309

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255647446|gb|ACU24187.1| unknown [Glycine max]

 Score =  416 bits (1068), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 214/313 (68%), Positives = 244/313 (77%), Gaps = 8/313 (2%)

Query: 1   MSSGRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEERDQR 60
           MS+ RNTHWCY CRRPVRL   D VC  C+ GFV EL+D+V V+P D FG+DN+EERDQR
Sbjct: 1   MSNSRNTHWCYSCRRPVRLGRRDVVCPSCNLGFVHELNDIVHVNPFDLFGMDNNEERDQR 60

Query: 61  LGLMEAFSAFVRHRMADR-HSHDIRGRYDSTPEHGQGFGPLLIFGGQIPLRLSGNSGFEA 119
           LGLME FSAF+RH+MADR  SHDIR R DS PEH   F PLLIFGG IP RLS + GFEA
Sbjct: 61  LGLMETFSAFMRHQMADRGRSHDIRVRTDSNPEHSASFAPLLIFGGHIPFRLSRHGGFEA 120

Query: 120 IFGGAPGLGFARGNTGDYFIGPGLEELFEQLSANGRRGPPPAARSAIDAMPTVRITQRHL 179
           +F GAPG+G  +GNTGDYFIGPGLEELFEQLSAN R+GP PA+RS+IDAMPT++I QRHL
Sbjct: 121 LFNGAPGIGLTQGNTGDYFIGPGLEELFEQLSANNRQGPLPASRSSIDAMPTIKIVQRHL 180

Query: 180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSSRI 239
           RSDSHCPVC+DKFELGS+ARQMPCNH+YHSDCIVPWLVQHNSCPVCRQELP QG SSS  
Sbjct: 181 RSDSHCPVCKDKFELGSKARQMPCNHLYHSDCIVPWLVQHNSCPVCRQELPPQGLSSS-- 238

Query: 240 HQSSSGQSRSTSFGSNGSGRENQGRRNLFSGFWPFRSSNSSSNHNGTTESS-SPAMHEN- 297
             +     RS S   + SGRE+ GRRN FS  WPFR  + SSN   T  S+ +P + EN 
Sbjct: 239 --NGGANGRSRSARVSSSGRESHGRRNPFSFLWPFRFFHFSSNDEATGSSTPTPTIPENS 296

Query: 298 -NPHMGYSGWPFD 309
            + H GY GWPF+
Sbjct: 297 LHHHAGYFGWPFE 309

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449437755|ref|XP_004136656.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like [Cucumis sativus] gi|449529445|ref|XP_004171710.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like [Cucumis sativus]

 Score =  413 bits (1062), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 213/308 (69%), Positives = 248/308 (80%), Gaps = 5/308 (1%)

Query: 3   SGRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEERDQRLG 62
           S  NTHWCYRC +PVRL+G D  CL C+GGFVQELD+M+  SPLD FG   +E +++RLG
Sbjct: 2   STANTHWCYRCEQPVRLRGRDMTCLSCNGGFVQELDEMMERSPLDLFGASGNEYQNRRLG 61

Query: 63  LMEAFSAFVRHRMADRHSHDIRGRYDSTPEHGQGFGPLLIFGGQIPLRLSGNSGFEAIFG 122
           L+E FS F+R R+ DR+  DIRGR DS P+HG GFGP LIFGGQIP+RLSG+ GFEA F 
Sbjct: 62  LLELFSNFMRQRLVDRN--DIRGRLDSIPDHGPGFGPWLIFGGQIPVRLSGHGGFEAFFN 119

Query: 123 GAPGLGFARGNTGDYFIGPGLEELFEQLSANGRRGPPPAARSAIDAMPTVRITQRHLRSD 182
           G PG+G +R N GDYFIGPGLEELFEQLSAN RRGPPPA+RS+IDAMP V+ITQRH+RS+
Sbjct: 120 GVPGIGVSRSNGGDYFIGPGLEELFEQLSANDRRGPPPASRSSIDAMPVVKITQRHIRSN 179

Query: 183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSSRIHQS 242
           SHCPVCQDKFELGSEARQMPC+H+YHSDCIVPWLVQHNSCPVCRQELP QGS SS     
Sbjct: 180 SHCPVCQDKFELGSEARQMPCDHMYHSDCIVPWLVQHNSCPVCRQELPAQGSGSSHSSSG 239

Query: 243 SSGQSRSTSFGSNGSGRENQGRRNLFSGFWPFRSSNSSSNHNGTTESSSPAMHENNPH-M 301
           S+  SR++    N  GR  QGRRN F+  WPFR+S+S+SNH+ TT S+SPA+HE N H  
Sbjct: 240 SNNSSRNSRDREN--GRTTQGRRNPFTSLWPFRASSSNSNHSATTGSNSPALHETNQHET 297

Query: 302 GYSGWPFD 309
           GY GWPFD
Sbjct: 298 GYYGWPFD 305

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388511895|gb|AFK44009.1| unknown [Lotus japonicus]

 Score =  405 bits (1042), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 196/292 (67%), Positives = 230/292 (78%), Gaps = 6/292 (2%)

Query: 1   MSSGRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEERDQR 60
           MS+ RNTHWC+ CRRPVRL   D++C  C+ GFVQELDDMV V+PLD  GLDN+EE  QR
Sbjct: 1   MSNSRNTHWCHSCRRPVRLGWRDSICRSCNEGFVQELDDMVPVNPLDLVGLDNNEEHGQR 60

Query: 61  LGLMEAFSAFVRHRMADR-HSHDIRGRYDSTPEHGQGFGPLLIFGGQIPLRLSGNSGFEA 119
            GLME FS F+RH+M +R H HDIR + DS PE G GF PLLIFGGQIP RLSG+ G EA
Sbjct: 61  FGLMETFSGFMRHQMGNRSHRHDIRAQPDSIPEQGAGFAPLLIFGGQIPFRLSGHGGIEA 120

Query: 120 IFGGAPGLGFARGNTGDYFIGPGLEELFEQLSANGRRGPPPAARSAIDAMPTVRITQRHL 179
           +F GAPG+G  RGNTGDYFIGPGLEE+FEQLS N ++GPPPA+RS+IDA+PT+RI +RHL
Sbjct: 121 LFNGAPGIGMTRGNTGDYFIGPGLEEMFEQLSINNQQGPPPASRSSIDALPTIRIVKRHL 180

Query: 180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSSRI 239
           RSDSHCP+C++KFELGSEARQMPC H+YH DCIVPWLV+HNSCPVCRQELP Q  S    
Sbjct: 181 RSDSHCPICKEKFELGSEARQMPCKHMYHPDCIVPWLVRHNSCPVCRQELPPQVLSG--- 237

Query: 240 HQSSSGQSRSTSFGSNGSGRENQGRRNLFSGFWPFRSSNSSSNHNGTTESSS 291
             S+  +SRS++     S RENQGRRN FS  WPFRSS S SN+  T  +S+
Sbjct: 238 --SNGRRSRSSNANERVSSRENQGRRNPFSFLWPFRSSISGSNNRATGRTST 287

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449453133|ref|XP_004144313.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like isoform 1 [Cucumis sativus] gi|449453135|ref|XP_004144314.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like isoform 2 [Cucumis sativus] gi|449488265|ref|XP_004157985.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like isoform 1 [Cucumis sativus] gi|449488269|ref|XP_004157986.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like isoform 2 [Cucumis sativus]

 Score =  403 bits (1036), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 210/308 (68%), Positives = 245/308 (79%), Gaps = 13/308 (4%)

Query: 1   MSSGRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEERDQR 60
           MS+GRNTHWCYRCRR VRL+G DAVC  C+GGF+QELDDMV  +P DFFGLD+DE+RD  
Sbjct: 1   MSAGRNTHWCYRCRRSVRLRGRDAVCPNCNGGFIQELDDMVPGNPFDFFGLDHDEDRDHG 60

Query: 61  LGLMEAFSAFVRHRMADRHSHDIRGRYDSTPEHGQGFGPLLIFGGQIPLRLSGNSGFEAI 120
           LG   AFSAF+R R+A+R+  D+RGR +S  EH  GFGPLLIFGGQIPLR   NS  EA+
Sbjct: 61  LG---AFSAFMRQRLAERN--DMRGRSESLFEHSPGFGPLLIFGGQIPLR---NSRLEAL 112

Query: 121 FGGAPGLGFARGNTGDYFIGPGLEELFEQLSANGRRGPPPAARSAIDAMPTVRITQRHLR 180
           F GAPG+G  RG++GDYFIGPGLEELFEQLS NG RGPPPA+RS+IDAMPTV+ITQRHLR
Sbjct: 113 FNGAPGIGITRGDSGDYFIGPGLEELFEQLSENGHRGPPPASRSSIDAMPTVKITQRHLR 172

Query: 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSSRIH 240
           SDSHCPVC++KFELGSEARQM CNH+YHSDCIVPWL+QHNSCPVCRQELP QG       
Sbjct: 173 SDSHCPVCKEKFELGSEARQMACNHMYHSDCIVPWLIQHNSCPVCRQELPPQGIGGGGGG 232

Query: 241 QSSSGQSRSTSFGSNGSGRENQGRRNLFSGFWPFRSSNSSSNHNGTTESSSPAMHENNPH 300
            S++ Q+RS S+ +    R N GRRN FS  WPFRSS+S+SNH G   SS P+ H+    
Sbjct: 233 HSTNDQNRSNSYNNGSGSRVNPGRRNPFSYLWPFRSSSSNSNHGGAG-SSEPSNHQ---- 287

Query: 301 MGYSGWPF 308
           MGYSG+ +
Sbjct: 288 MGYSGYRY 295

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|190898156|gb|ACE97591.1| thioredoxin-related protein [Populus tremula] gi|190898162|gb|ACE97594.1| thioredoxin-related protein [Populus tremula] gi|190898166|gb|ACE97596.1| thioredoxin-related protein [Populus tremula] gi|190898168|gb|ACE97597.1| thioredoxin-related protein [Populus tremula] gi|190898176|gb|ACE97601.1| thioredoxin-related protein [Populus tremula] gi|190898178|gb|ACE97602.1| thioredoxin-related protein [Populus tremula] gi|190898180|gb|ACE97603.1| thioredoxin-related protein [Populus tremula] gi|190898182|gb|ACE97604.1| thioredoxin-related protein [Populus tremula] gi|190898184|gb|ACE97605.1| thioredoxin-related protein [Populus tremula] gi|190898186|gb|ACE97606.1| thioredoxin-related protein [Populus tremula] gi|190898188|gb|ACE97607.1| thioredoxin-related protein [Populus tremula] gi|190898194|gb|ACE97610.1| thioredoxin-related protein [Populus tremula] gi|190898196|gb|ACE97611.1| thioredoxin-related protein [Populus tremula] gi|190898198|gb|ACE97612.1| thioredoxin-related protein [Populus tremula] gi|190898202|gb|ACE97614.1| thioredoxin-related protein [Populus tremula] gi|190898204|gb|ACE97615.1| thioredoxin-related protein [Populus tremula] gi|190898206|gb|ACE97616.1| thioredoxin-related protein [Populus tremula] gi|190898210|gb|ACE97618.1| thioredoxin-related protein [Populus tremula] gi|190898216|gb|ACE97621.1| thioredoxin-related protein [Populus tremula] gi|190898220|gb|ACE97623.1| thioredoxin-related protein [Populus tremula] gi|190898228|gb|ACE97627.1| thioredoxin-related protein [Populus tremula]

 Score =  365 bits (938), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 198/264 (75%), Positives = 218/264 (82%), Gaps = 7/264 (2%)

Query: 17  VRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEERDQRLGLMEAFSAFVRHRMA 76
           +RL+G DA C YCSGGFVQELDDM  ++PLDFFG+D D++ D   GLMEAFSAF+R RMA
Sbjct: 1   IRLRGRDAACPYCSGGFVQELDDMHRINPLDFFGMDGDDDHDNMFGLMEAFSAFMRQRMA 60

Query: 77  DR-HSHDIRGRYDSTPEHGQGFGPLLIFGGQIPLRLSGNSGFEAIFGGAPGLGFARGNTG 135
           DR H+HD+R R DS PEH  GFGPLLIFGGQIP RLSGN GFEA+F G+PG+ FARGN G
Sbjct: 61  DRSHNHDVRSRSDSIPEHNPGFGPLLIFGGQIPFRLSGNGGFEALFSGSPGVAFARGNAG 120

Query: 136 DYFIGPGLEELFEQLSANGRRGPPPAARSAIDAMPTVRITQRHLRSDSHCPVCQDKFELG 195
           DYF+GPGLEELFEQLSAN RRGP PA RS+IDAMPTV+ITQRHLR+DSHCPVC+DKFELG
Sbjct: 121 DYFVGPGLEELFEQLSANDRRGPAPATRSSIDAMPTVKITQRHLRTDSHCPVCKDKFELG 180

Query: 196 SEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSSRIHQSSSGQSRSTSFGSN 255
           SEARQMPCNH+YHSDCIVPWLVQHNSCPVCRQELP QGSSS      S   S S S  SN
Sbjct: 181 SEARQMPCNHLYHSDCIVPWLVQHNSCPVCRQELPPQGSSSG----HSYQSSSSRSRNSN 236

Query: 256 GSGREN--QGRRNLFSGFWPFRSS 277
            SGREN  +GRRN  S  WPFRSS
Sbjct: 237 YSGRENSREGRRNPLSYLWPFRSS 260

Source: Populus tremula

Species: Populus tremula

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|190898190|gb|ACE97608.1| thioredoxin-related protein [Populus tremula]

 Score =  365 bits (938), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 197/264 (74%), Positives = 223/264 (84%), Gaps = 7/264 (2%)

Query: 17  VRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEERDQRLGLMEAFSAFVRHRMA 76
           +RL+G DA C YCSGGFVQELDDM  ++PLDFFG+D D++ D   GLMEAFSAF+R RMA
Sbjct: 1   IRLRGRDAACPYCSGGFVQELDDMHRINPLDFFGMDGDDDHDNMFGLMEAFSAFMRQRMA 60

Query: 77  DR-HSHDIRGRYDSTPEHGQGFGPLLIFGGQIPLRLSGNSGFEAIFGGAPGLGFARGNTG 135
           DR H+HD+R R DS PEH  GFGPLLIF GQIP RLSGN GFEA+F G+PG+ FARGN G
Sbjct: 61  DRSHNHDVRSRSDSIPEHNPGFGPLLIFCGQIPFRLSGNGGFEALFSGSPGVAFARGNAG 120

Query: 136 DYFIGPGLEELFEQLSANGRRGPPPAARSAIDAMPTVRITQRHLRSDSHCPVCQDKFELG 195
           DYF+GPGLEELFEQLSAN RRGP PA RS+IDAMPTV+ITQRHLR+DSHCPVC+DKFELG
Sbjct: 121 DYFVGPGLEELFEQLSANDRRGPAPATRSSIDAMPTVKITQRHLRTDSHCPVCKDKFELG 180

Query: 196 SEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSSRIHQSSSGQSRSTSFGSN 255
           SEARQMPCNH+YHSDCIVPWLVQHNSCPVCRQELP QGSSS   +QSS  +SR++++   
Sbjct: 181 SEARQMPCNHLYHSDCIVPWLVQHNSCPVCRQELPPQGSSSGHSYQSSGSRSRNSNY--- 237

Query: 256 GSGREN--QGRRNLFSGFWPFRSS 277
            SGREN  +GRRN FS  WPFRSS
Sbjct: 238 -SGRENSREGRRNPFSYLWPFRSS 260

Source: Populus tremula

Species: Populus tremula

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	309
TAIR|locus:2058465	328	RHC1A "RING-H2 finger C1A" [Ar	0.996	0.939	0.579	8.7e-95
TAIR|locus:2102569	320	RZF1 "AT3G56580" [Arabidopsis	0.944	0.912	0.514	1.1e-80
TAIR|locus:2092231	328	AT3G19950 [Arabidopsis thalian	0.673	0.634	0.385	4.6e-34
TAIR|locus:2075175	395	RDUF1 "RING and Domain of Unkn	0.352	0.275	0.482	7.1e-34
TAIR|locus:1006230278	199	AT3G10815 [Arabidopsis thalian	0.440	0.683	0.503	3e-33
TAIR|locus:2195573	327	AT1G60360 [Arabidopsis thalian	0.320	0.302	0.534	6.2e-33
TAIR|locus:2193874	351	AT1G55530 [Arabidopsis thalian	0.417	0.367	0.416	2.1e-32
TAIR|locus:2092895	315	AT3G13430 [Arabidopsis thalian	0.307	0.301	0.509	4.3e-32
TAIR|locus:2148318	407	RDUF2 "RING and Domain of Unkn	0.352	0.267	0.482	5.5e-32
TAIR|locus:2063912	401	RHC2A "RING-H2 finger C2A" [Ar	0.307	0.236	0.514	6.9e-32

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

 Score = 943 (337.0 bits), Expect = 8.7e-95, P = 8.7e-95
 Identities = 190/328 (57%), Positives = 217/328 (66%)

Query:     1 MSSGRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDE-ERDQ 59
             MSS RNTHWC+RC+R VRL G++ VC YC GGFV+ELD M   SP D F       ERDQ
Sbjct:     1 MSSSRNTHWCHRCQRAVRLHGQEPVCFYCGGGFVEELD-MAQASPFDMFRSHRGVVERDQ 59

Query:    60 RLGLMEAFSAFVRHRMADR-HSHDIRGR-YDSTPEHGQGFGPLLIFGGQIPLRLSGNSGF 117
                LM+AFS F+R+R+A+R H  +IRGR   S PE+  G  PLLIFGGQ+P RL+G++  
Sbjct:    60 TFDLMDAFSVFMRNRLAERSHDREIRGRTISSGPENFPGLAPLLIFGGQVPYRLTGDNAV 119

Query:   118 EAIF-GGAPGLGFARGNTGDYFIGPGLEELFEQLSANG-RRGPPPAARSAIDAMPTVRIT 175
             EA+F GG+PG+G  RGNTGDYF GPGLEELFEQLSA   RRGPPPA RSAIDA+PT++I 
Sbjct:   120 EALFNGGSPGIGITRGNTGDYFFGPGLEELFEQLSAGTTRRGPPPAPRSAIDALPTIKIA 179

Query:   176 QRHLRS-DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLXXX 234
             QRHLRS DS+CPVC+D+FELGSEA+QMPCNHIYHSDCIVPWLVQHNSCPVCRQELP    
Sbjct:   180 QRHLRSSDSNCPVCKDEFELGSEAKQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPSASG 239

Query:   235 XXXXXXXXXXXXXXXXXXXXNGSG-RENQG-RRNLFSGFWPFRXXXXXXXXXXXXXXX-- 290
                                 + S  REN   RRN FS FWPFR                 
Sbjct:   240 PSSSQNRTTPTRNYRSSSSSSSSNSRENGNERRNPFSSFWPFRSSGSSSSSTQNRGGTRN 299

Query:   291 XPAMHEN-NPH--------MGYSGWPFD 309
                  EN N H        MGYSGWPFD
Sbjct:   300 SDTSDENHNYHQQQHQQSYMGYSGWPFD 327

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

GO:0005618 "cell wall" evidence=IDA

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

 Score = 810 (290.2 bits), Expect = 1.1e-80, P = 1.1e-80
 Identities = 173/336 (51%), Positives = 204/336 (60%)

Query:     1 MSSGRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDMVSVSPLDFFGLDNDEERDQR 60
             MSS RNTHWC+RC+R V L+  DAVC YC GGFV+E+D    + P        D ERD  
Sbjct:     1 MSSIRNTHWCHRCQRAVWLRARDAVCSYCGGGFVEEID----IGPSR---AHRDVERDPT 53

Query:    61 LGLMEAFSAFVRHRMADR-HSHDIRGRYDST-PEHGQGFGPLLIFGGQIPLRLSG--NSG 116
               LMEAFSAF+R R+A+R +  +I GR  S   E      PLLIFGGQ P RL+G  NS 
Sbjct:    54 FDLMEAFSAFMRSRLAERSYDREISGRLGSAGSESFSNLAPLLIFGGQAPFRLAGGDNSS 113

Query:   117 FEA-IFGGAPGLGFARG-NTGDYFIGPGLEELFEQLSANGR-RGPPPAARSAIDAMPTVR 173
              EA + G APG+G ARG N GDYF GPGLEEL EQLS+    RGPPPA +S+IDA+PT++
Sbjct:   114 VEAFVNGAAPGIGIARGTNAGDYFFGPGLEELIEQLSSGTHHRGPPPAPKSSIDALPTIK 173

Query:   174 ITQRHLRS-DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLX 232
             ITQ+HL+S DSHCPVC+D+FEL SEA+QMPC+HIYHSDCIVPWLVQHNSCPVCR+ELP  
Sbjct:   174 ITQKHLKSSDSHCPVCKDEFELKSEAKQMPCHHIYHSDCIVPWLVQHNSCPVCRKELP-- 231

Query:   233 XXXXXXXXXXXXXXXXXXXXXXNGSGRENQGRRNLFSGFWPFRXXXXXXXXXXXXXXXXP 292
                                   + +GREN  RRN+FS  WPFR                 
Sbjct:   232 --------SRGSSSSTQSSQNRSTNGRENSRRRNIFSNLWPFRSSSSSSTQNRRDTNNTA 283

Query:   293 AMHENN-------------------PHMGYSGWPFD 309
                E +                    HMGYSGWPFD
Sbjct:   284 TAEEGHYHHHQQQQQQHQHQHQQQQSHMGYSGWPFD 319

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:2092231 AT3G19950 [Arabidopsis thaliana (taxid:3702)]

 Score = 370 (135.3 bits), Expect = 4.6e-34, P = 4.6e-34
 Identities = 86/223 (38%), Positives = 121/223 (54%)

Query:    23 DAVCLYCSGGFVQELDDMVSVSPLDFFGLDND------EERDQRLGLMEAFSAFVRHRM- 75
             D  C  C+ GF++E +D      L+F    +D      +     L L+   SA     M 
Sbjct:    39 DPFCPICNQGFLEEYEDPNPNQSLNFNPNSSDSFFPMADPFSTLLPLIFGSSAAAPSGMD 98

Query:    76 -ADRHSHDIRGRYDSTPEHGQG--FGPLLIFGGQIPLRLSGNSGFEAIFGGAPGLGFAR- 131
                     ++ +  ST ++ Q   F P       +    S  + FE +    P     R 
Sbjct:    99 FMSLFGPSMQPQARSTQQNPQSDAFDPFTFLQNHLQTLRSSGTHFEFVIENHPSDPGNRM 158

Query:   132 -GNTGDYFIGPGLEELFEQLSAN--GRRGPPPAARSAIDAMPTVRITQRHLRSD-SHCPV 187
              GN GDYF GPGLE+L +QL+ N   R G PPA++SAIDA+PTV++T+  L+S+ + C V
Sbjct:   159 PGNFGDYFFGPGLEQLIQQLAENDPNRYGTPPASKSAIDALPTVKVTKDMLKSEMNQCAV 218

Query:   188 CQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP 230
             C D+FE GS+ +QMPC H++H DC++PWL  HNSCPVCR ELP
Sbjct:   219 CMDEFEDGSDVKQMPCKHVFHQDCLLPWLELHNSCPVCRFELP 261

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

GO:0010200 "response to chitin" evidence=RCA

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

 Score = 289 (106.8 bits), Expect = 7.1e-34, Sum P(2) = 7.1e-34
 Identities = 56/116 (48%), Positives = 73/116 (62%)

Query:   122 GGAPGLGFARGNTGDYFIGPGLEELFEQLS-----ANG--RRGPPPAARSAIDAMPTVRI 174
             G   GL     +  +  +G G E L EQLS      NG  R G PPA++SAI+++P V I
Sbjct:   145 GSGSGLRPLPDSVSEILMGSGFERLLEQLSQIEASGNGIGRSGNPPASKSAIESLPRVEI 204

Query:   175 TQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP 230
             +  H +++++C VC + FE G E R+MPC HI+H DCIVPWL   NSCPVCR ELP
Sbjct:   205 SDCHTKAEANCAVCTEVFEAGIEGREMPCKHIFHGDCIVPWLSIRNSCPVCRFELP 260

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:1006230278 AT3G10815 [Arabidopsis thaliana (taxid:3702)]

 Score = 338 (124.0 bits), Expect = 3.0e-33, Sum P(2) = 3.0e-33
 Identities = 72/143 (50%), Positives = 94/143 (65%)

Query:    94 GQGFGPLLIFGGQIPLRLSGN---SGFEAIFGGAPGLGFARGNTGDYFIGPGL--EELFE 148
             G+  G  +  G     RL  N   S F+ +FG A      R N     IG  L  EELF 
Sbjct:    25 GRREGACIYCGNTFLERLYENVELSPFD-LFGLAYEEARNRRNNRRSVIGEQLSFEELFN 83

Query:   149 QLSA-NGRRGPPPAARSAIDAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIY 207
             +L A   RRGPPPA+ +AI+++  ++I Q+HL  D +CPVCQD+FE+GS+AR+MPC HIY
Sbjct:    84 RLPALQDRRGPPPASLAAINSLQKIKIRQKHLGLDPYCPVCQDQFEIGSDARKMPCKHIY 143

Query:   208 HSDCIVPWLVQHNSCPVCRQELP 230
             HS+CI+PWLVQ N+CPVCR+ELP
Sbjct:   144 HSECILPWLVQRNTCPVCRKELP 166

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 314 (115.6 bits), Expect = 6.2e-33, Sum P(2) = 6.2e-33
 Identities = 54/101 (53%), Positives = 76/101 (75%)

Query:   133 NTGDYFIGPG-LEELFEQLSANGRRGPPPAARSAIDAMPTVRITQRHLRSD-SHCPVCQD 190
             N+ DYF G   LE+L EQL+ + R GPPPA+   I+++P+V+IT +HL +D S C VC +
Sbjct:   170 NSHDYFTGASSLEQLIEQLTQDDRPGPPPASEPTINSLPSVKITPQHLTNDMSQCTVCME 229

Query:   191 KFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPL 231
             +F +G +A ++PC HIYH DCIVPWL  +NSCP+CR++LPL
Sbjct:   230 EFIVGGDATELPCKHIYHKDCIVPWLRLNNSCPICRRDLPL 270

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

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

 Score = 296 (109.3 bits), Expect = 2.1e-32, Sum P(2) = 2.1e-32
 Identities = 57/137 (41%), Positives = 75/137 (54%)

Query:   132 GNTGDYFIGPGLEELFEQLSAN--GRRGPPPAARSAIDAMPTVRITQRHLRSDSHCPVCQ 189
             G+ GDYFIGPG E L ++L+ N   R G PPA + A++A+ TV+I +        C VC 
Sbjct:   173 GSLGDYFIGPGFEMLLQRLAENDPNRYGTPPAKKEAVEALATVKIEET-----LQCSVCL 227

Query:   190 DKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLXXXXXXXXXXXXXXXXXX 249
             D FE+G+EA+ MPC H +HSDC++PWL  H+SCPVCR +LP                   
Sbjct:   228 DDFEIGTEAKLMPCTHKFHSDCLLPWLELHSSCPVCRYQLPADEAKTDSVTTTSDNNGSS 287

Query:   250 XXXXXNGSGRENQ-GRR 265
                     G EN  G R
Sbjct:   288 SASATTSHGAENSDGNR 304

GO:0005737 "cytoplasm" evidence=ISM

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

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

 Score = 284 (105.0 bits), Expect = 4.3e-32, Sum P(2) = 4.3e-32
 Identities = 52/102 (50%), Positives = 69/102 (67%)

Query:   132 GNTGDYFIGPGLEELFEQLSAN---GRRGPPPAARSAIDAMPTVRITQRHLRSDSHCPVC 188
             G+ GDYFIGPG E L ++L+ N    R G PPA + A++A+  V+I    L+    C VC
Sbjct:   173 GSLGDYFIGPGFETLLQRLAENDLNNRYGTPPATKEAVEALAMVKIEDSLLQ----CSVC 228

Query:   189 QDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP 230
              D FE+G EA++MPC H +HSDC++PWL  H+SCPVCR  LP
Sbjct:   229 LDDFEIGMEAKEMPCKHKFHSDCLLPWLELHSSCPVCRYLLP 270

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

 Score = 286 (105.7 bits), Expect = 5.5e-32, Sum P(2) = 5.5e-32
 Identities = 56/116 (48%), Positives = 75/116 (64%)

Query:   122 GGAPGLGFARGNTGDYFIGPGLEELFEQLS---AN----GRRGPPPAARSAIDAMPTVRI 174
             G   GL     +  +  +G G E L EQLS   A+    GR G PPA++SAI+++P V I
Sbjct:   129 GSGSGLRPLPDSVSEILMGSGFERLLEQLSQIEASATGIGRSGNPPASKSAIESLPRVEI 188

Query:   175 TQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP 230
             +  H+ S+++C VC + FE  +EAR+MPC H++H DCIVPWL   NSCPVCR ELP
Sbjct:   189 SDCHIGSEANCAVCTEIFETETEAREMPCKHLFHDDCIVPWLSIRNSCPVCRFELP 244

GO:0005634 "nucleus" evidence=ISM

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

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

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

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

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

GO:0051865 "protein autoubiquitination" evidence=IDA

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

GO:0009693 "ethylene biosynthetic process" evidence=RCA

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

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

GO:0035556 "intracellular signal transduction" evidence=RCA

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

 Score = 282 (104.3 bits), Expect = 6.9e-32, Sum P(2) = 6.9e-32
 Identities = 54/105 (51%), Positives = 69/105 (65%)

Query:   136 DYFIGPGLEELFEQLSA---NGRRG-----PPPAARSAIDAMPTVRITQRHLRSDS--HC 185
             ++ +G G + L +Q+S    N  R       PPA++SAI+A+P + I   HL SDS  HC
Sbjct:   142 EFLLGSGFDRLLDQISQIELNTNRNLRSCEHPPASKSAIEALPLIEIDPTHLLSDSQSHC 201

Query:   186 PVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP 230
              VC++ F L S AR+MPCNHIYH DCI+PWL   NSCPVCR ELP
Sbjct:   202 AVCKENFVLKSSAREMPCNHIYHPDCILPWLAIRNSCPVCRHELP 246

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

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: estExt_Genewise1_v1.C_LG_XVI1068 hypothetical protein (309 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

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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	309
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	9e-17
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	2e-11
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	1e-09
pfam14369	34	pfam14369, zf-RING_3, zinc-finger	6e-09
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	9e-09
smart00184	40	smart00184, RING, Ring finger	1e-08
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	1e-07
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	4e-07
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	1e-06
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	2e-06
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	9e-05
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	2e-04
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	3e-04
pfam13920	49	pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RI	0.002

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

 Score = 72.4 bits (178), Expect = 9e-17
 Identities = 20/44 (45%), Positives = 29/44 (65%)

Query: 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQE 228
           CP+C D+FE G E   +PC H++H +C+  WL   N+CP+CR  
Sbjct: 3   CPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

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

 Score = 57.8 bits (140), Expect = 2e-11
 Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 3/46 (6%)

Query: 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQEL 229
           CP+C ++F        +PC H++   CI  WL    N+CP+CR  +
Sbjct: 2   CPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 52.5 bits (126), Expect = 1e-09
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQ 227
            +  CP+C D           PC H++  +CI+ +L + + CP+CR 
Sbjct: 1   EELECPICLDLLR--DPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 50.6 bits (122), Expect = 6e-09
 Identities = 16/34 (47%), Positives = 23/34 (67%), Gaps = 2/34 (5%)

Query: 6  NTHWCYRCRRPVRLQ--GEDAVCLYCSGGFVQEL 37
          + +WCY+C R VR+   G+  VC  C GGFV+E+
Sbjct: 1  SRYWCYQCDRFVRIAPSGDSDVCPRCGGGFVEEI 34

Length = 34

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

 Score = 55.4 bits (133), Expect = 9e-09
 Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH-NSCPVCRQELP 230
           C +C   F      R +PC+H +H  C+  WL+ + N CPVCR  +P
Sbjct: 326 CAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372

Length = 374

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

 Score = 49.8 bits (119), Expect = 1e-08
 Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 3/42 (7%)

Query: 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN-SCPVC 225
           CP+C +++    +   +PC H +   CI  WL   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|221705 pfam12678, zf-rbx1, RING-H2 zinc finger

 Score = 47.8 bits (114), Expect = 1e-07
 Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCR 226
           D  CP C+   +         C H +H  CI  WL   N+CP+CR
Sbjct: 30  DGTCPECKSPGD-DCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 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|227521 COG5194, APC11, Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]

 Score = 47.1 bits (112), Expect = 4e-07
 Identities = 19/50 (38%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 185 CPVCQDKFELGSEARQM--PCNHIYHSDCIVPWLVQHNSCPVCRQELPLQ 232
           CP CQ     G E   +   CNH +H  CI  WL     CP+ RQ   L 
Sbjct: 34  CPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLA 83

Length = 88

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

 Score = 49.2 bits (117), Expect = 1e-06
 Identities = 38/157 (24%), Positives = 56/157 (35%), Gaps = 25/157 (15%)

Query: 167 DAMPTVRITQRHLRSDSHCPVCQDK-FELGSEA---------RQMPCNHIYHSDCIVPWL 216
              PT    Q    SD  C +C D+ F    E          +++PC HI H  C+  WL
Sbjct: 273 AMYPTATEEQLT-NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWL 331

Query: 217 VQHNSCPVCRQELPLQGSSSSRIHQSS-------SGQSRSTSFGSNGSGRENQGRRNLFS 269
            +  +CP+CR   P+    SS    S        + Q  +    +  +     G  N  S
Sbjct: 332 ERQQTCPICR--RPVIFDQSSPTPASPNVRNTQIATQVPNPD--NTPTTTAVPGITNS-S 386

Query: 270 GFWPFRSSNSSSNHNGTTESSSPAMHENNPHMGYSGW 306
                ++  S+ N      SS  A H  +      GW
Sbjct: 387 NQGDPQA--STFNGVPNANSSGFAAHTQDLSSVIPGW 421

Length = 491

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

 Score = 43.6 bits (103), Expect = 2e-06
 Identities = 14/42 (33%), Positives = 25/42 (59%), Gaps = 3/42 (7%)

Query: 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWL-VQHNSCPVC 225
           CP+C ++ +       +PC H++ S CI+ WL   + +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|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional

 Score = 42.8 bits (101), Expect = 9e-05
 Identities = 12/26 (46%), Positives = 17/26 (65%)

Query: 203 CNHIYHSDCIVPWLVQHNSCPVCRQE 228
           CNH++  +CI  W  + N+CPVCR  
Sbjct: 200 CNHVFCIECIDIWKKEKNTCPVCRTP 225

Length = 238

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

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 19/68 (27%), Positives = 26/68 (38%), Gaps = 13/68 (19%)

Query: 178 HLRSDSHCPVCQDKFELGSEARQMP----------CNHIYHSDCIVPWLVQHNS---CPV 224
              SD  C +C+  F+      + P          C H +H  CI+ WL    S   CP+
Sbjct: 17  DTPSDDVCGICRVSFDGTCPQCKFPGDDCPLVWGKCKHNFHMHCILKWLATETSKGLCPM 76

Query: 225 CRQELPLQ 232
           CRQ     
Sbjct: 77  CRQTFVFA 84

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

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

 Score = 42.0 bits (98), Expect = 3e-04
 Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 10/54 (18%)

Query: 185  CPVCQDKFELGSEARQMP------CNHIYHSDCIVPWLVQHNS--CPVCRQELP 230
            C +C     L    R +P      C + +H+ C+  W        CP+CR E+ 
Sbjct: 1472 CAICY--SVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523

Length = 1525

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

 Score = 35.0 bits (81), Expect = 0.002
 Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 5/45 (11%)

Query: 185 CPVCQDKFELGSEARQMPCNH-IYHSDCIVPWLVQHNSCPVCRQE 228
           C +C ++         +PC H     +C    L     CP+CRQ 
Sbjct: 5   CVICLERP---RNVVFLPCGHLCLCEECAK-RLRSKKKCPICRQP 45

Length = 49

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	309
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.62
PF14369	35	zf-RING_3: zinc-finger	99.51
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.48
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.31
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.22
PHA02929	238	N1R/p28-like protein; Provisional	99.22
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.16
KOG1002	791	consensus Nucleotide excision repair protein RAD16	99.14
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.88
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	98.87
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	98.83
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.81
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.8
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.79
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.78
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.72
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.57
PF14634	44	zf-RING_5: zinc-RING finger domain	98.56
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.53
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.53
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.53
PHA02926	242	zinc finger-like protein; Provisional	98.49
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.46
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.43
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.39
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.3
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.26
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.16
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.1
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.08
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.04
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.01
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	97.95
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	97.89
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	97.89
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.88
COG5219	1525	Uncharacterized conserved protein, contains RING Z	97.84
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	97.77
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	97.76
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.75
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.74
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	97.71
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.57
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.45
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.44
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.42
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.38
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.36
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.28
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.16
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.09
KOG0297	391	consensus TNF receptor-associated factor [Signal t	96.75
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	96.73
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	96.68
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	96.61
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	96.58
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	96.52
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.45
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	96.35
COG5152	259	Uncharacterized conserved protein, contains RING a	96.12
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	96.05
KOG2660	331	consensus Locus-specific chromosome binding protei	96.04
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	95.91
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	95.78
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	95.38
PHA02862	156	5L protein; Provisional	95.27
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	95.24
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	95.17
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	94.94
PHA02825	162	LAP/PHD finger-like protein; Provisional	94.85
KOG3039	303	consensus Uncharacterized conserved protein [Funct	94.62
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	94.55
PF04641	260	Rtf2: Rtf2 RING-finger	94.48
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	94.36
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	94.34
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	94.26
COG0375	115	HybF Zn finger protein HypA/HybF (possibly regulat	94.19
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	94.02
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	93.77
KOG4739	233	consensus Uncharacterized protein involved in syna	93.74
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	93.49
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	93.19
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	92.86
KOG1940	276	consensus Zn-finger protein [General function pred	92.59
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	92.27
TIGR00100	115	hypA hydrogenase nickel insertion protein HypA. In	91.56
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	91.4
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	91.07
PF01155	113	HypA: Hydrogenase expression/synthesis hypA family	90.48
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	90.33
PRK12380	113	hydrogenase nickel incorporation protein HybF; Pro	90.3
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	90.2
COG5236	493	Uncharacterized conserved protein, contains RING Z	90.13
PHA03096	284	p28-like protein; Provisional	90.09
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	90.02
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	89.53
PRK00564	117	hypA hydrogenase nickel incorporation protein; Pro	89.31
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	89.12
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	89.07
KOG3002	299	consensus Zn finger protein [General function pred	88.97
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	88.84
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	88.72
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	87.88
KOG1001	674	consensus Helicase-like transcription factor HLTF/	87.6
COG5222	427	Uncharacterized conserved protein, contains RING Z	86.59
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	86.23
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	86.04
PRK00762	124	hypA hydrogenase nickel incorporation protein; Pro	85.54
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	85.16
PRK06266	178	transcription initiation factor E subunit alpha; V	85.12
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	84.98
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	84.61
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	84.57
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	84.14
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	83.96
KOG0298	1394	consensus DEAD box-containing helicase-like transc	83.75
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	83.14
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	82.64
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	81.72
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	81.69
KOG1609	323	consensus Protein involved in mRNA turnover and st	81.46
COG2093	64	DNA-directed RNA polymerase, subunit E'' [Transcri	80.94

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

Probab=99.62  E-value=7.3e-16  Score=145.51  Aligned_cols=82  Identities=27%  Similarity=0.724  Sum_probs=69.6

Q ss_pred             CCCCcchhhhhcCCceeeeccccccc-ccccccccccccCCceEEccccceeccccchhhhccCCC-cCcccccccCCCC
Q 021640          157 GPPPAARSAIDAMPTVRITQRHLRSD-SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNS-CPVCRQELPLQGS  234 (309)
Q Consensus       157 ~~ppa~~~~i~~lp~~~~~~~~~~~~-~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~s-CP~CR~~l~~~~~  234 (309)
                      ....+.+..++++|..+++....+.. ..|+||+|+|+.|++++.|||+|.||..||++||.++.+ ||+||+++.....
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            44568899999999999987664433 499999999999999999999999999999999998865 9999998876665


Q ss_pred             CCCc
Q 021640          235 SSSR  238 (309)
Q Consensus       235 ~~~~  238 (309)
                      ....
T Consensus       283 ~~~~  286 (348)
T KOG4628|consen  283 SEPV  286 (348)
T ss_pred             CCCc
Confidence            5433

>PF14369 zf-RING_3: zinc-finger

Probab=99.51  E-value=6.8e-15  Score=94.39  Aligned_cols=32  Identities=44%  Similarity=1.047  Sum_probs=27.6

Q ss_pred             CceecccCCCceeecC---CCccCCCCCCCceEEe
Q 021640            6 NTHWCYRCRRPVRLQG---EDAVCLYCSGGFVQEL   37 (309)
Q Consensus         6 ~~ywCh~C~r~v~~~~---~~~~CP~C~~gFvEE~   37 (309)
                      ++||||+|++.|++..   .+++||+|++||||||
T Consensus         1 ~~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFvEei   35 (35)
T PF14369_consen    1 QRYWCHQCNRFVRIAPSPDSDVACPRCHGGFVEEI   35 (35)
T ss_pred             CCEeCccCCCEeEeCcCCCCCcCCcCCCCcEeEeC
Confidence            4899999999999863   3445999999999997

>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=99.48  E-value=7.7e-15  Score=99.18  Aligned_cols=44  Identities=48%  Similarity=1.294  Sum_probs=40.6

Q ss_pred             ccccccccccccCCceEEccccceeccccchhhhccCCCcCccc
Q 021640          183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCR  226 (309)
Q Consensus       183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR  226 (309)
                      ++|+||+++|..++.++.++|+|+||.+||..|++.+++||+||
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            36999999999889999999999999999999999999999997

...

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

Probab=99.31  E-value=2.1e-12  Score=121.28  Aligned_cols=54  Identities=31%  Similarity=0.929  Sum_probs=45.3

Q ss_pred             ccccccccccccc-ccC---------CceEEccccceeccccchhhhccCCCcCcccccccCCC
Q 021640          180 RSDSHCPVCQDKF-ELG---------SEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG  233 (309)
Q Consensus       180 ~~~~~C~IC~~~~-~~~---------~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~  233 (309)
                      .++..|.||++++ ..+         .+.++|||||++|.+|++-|++++++||+||.++.-+.
T Consensus       285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~ifd~  348 (491)
T COG5243         285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVIFDQ  348 (491)
T ss_pred             CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCcccccc
Confidence            4567999999994 333         25789999999999999999999999999999964443

>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=99.22  E-value=3.9e-12  Score=95.38  Aligned_cols=45  Identities=42%  Similarity=1.059  Sum_probs=36.2

Q ss_pred             ccccccccccccc----------CCceEEccccceeccccchhhhccCCCcCccc
Q 021640          182 DSHCPVCQDKFEL----------GSEARQMPCNHIYHSDCIVPWLVQHNSCPVCR  226 (309)
Q Consensus       182 ~~~C~IC~~~~~~----------~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR  226 (309)
                      ++.|+||++.|..          .-.+...+|+|.||..||.+||+.+++||+||
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            4569999999932          12455667999999999999999999999997

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

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.22  E-value=4.9e-12  Score=114.73  Aligned_cols=69  Identities=28%  Similarity=0.636  Sum_probs=55.3

Q ss_pred             chhhhhcCCceeeecccc---cccccccccccccccCCc-----eEEccccceeccccchhhhccCCCcCccccccc
Q 021640          162 ARSAIDAMPTVRITQRHL---RSDSHCPVCQDKFELGSE-----ARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       162 ~~~~i~~lp~~~~~~~~~---~~~~~C~IC~~~~~~~~~-----~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      .+..++.+|.+...-+.+   ..+.+|+||++.+..++.     ++.++|+|.||..||.+|+..+.+||+||..+.
T Consensus       151 ~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~  227 (238)
T PHA02929        151 YKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI  227 (238)
T ss_pred             hHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence            889999999887654332   346789999999765431     245579999999999999999999999998774

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

Probab=99.16  E-value=8.1e-12  Score=114.62  Aligned_cols=51  Identities=35%  Similarity=0.977  Sum_probs=47.0

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhc-cCCCcCcccccccC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV-QHNSCPVCRQELPL  231 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~-~~~sCP~CR~~l~~  231 (309)
                      ..-+|+||++.|..++.++.|||.|.||..||.+|+. -++.||+||.+||+
T Consensus       322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            4578999999999999999999999999999999999 56789999999986

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

Probab=99.14  E-value=1.2e-11  Score=120.47  Aligned_cols=200  Identities=17%  Similarity=0.324  Sum_probs=138.0

Q ss_pred             CceecccCCCceeecC--CCccCCCCCCCceEEecCCCC--CCCCCcCCCCCchhhHhhhhhHHHHHHHHhhhhcCCCCC
Q 021640            6 NTHWCYRCRRPVRLQG--EDAVCLYCSGGFVQELDDMVS--VSPLDFFGLDNDEERDQRLGLMEAFSAFVRHRMADRHSH   81 (309)
Q Consensus         6 ~~ywCh~C~r~v~~~~--~~~~CP~C~~gFvEE~~~~~~--~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (309)
                      ++|||.+|.+.+..+.  +-..|++|.+.-+.+..-.+.  .-|++-||.++.+..+.. -....+..+|.+        
T Consensus       375 syyfc~~cdc~~~~~~ftdr~~c~~c~h~~m~h~~~~n~~mlk~IqkfG~eGpGk~af~-~~h~llk~Imlr--------  445 (791)
T KOG1002|consen  375 SYYFCTKCDCASLDWKFTDRMHCDHCSHNIMQHTCFFNHFMLKPIQKFGVEGPGKEAFN-NIHTLLKNIMLR--------  445 (791)
T ss_pred             hhhhhhhccccccceeecccccCCcccchhhhhhhhhcccccccchhhcccCchHHHHH-HHHHHHHHHHHH--------
Confidence            6899999999998887  467999999999988866654  457788898888776543 223345567765        


Q ss_pred             CccCCCCCCCCCCCCCCCeEEeccCCCcccCCCCccccccCCCCC-------CCCCCCCCCCCccCcchHHHHHHHHhcC
Q 021640           82 DIRGRYDSTPEHGQGFGPLLIFGGQIPLRLSGNSGFEAIFGGAPG-------LGFARGNTGDYFIGPGLEELFEQLSANG  154 (309)
Q Consensus        82 ~~r~r~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~g-------~~~~~~~~~dy~~~~~l~~l~~~l~~~~  154 (309)
                          |++-+.+++.+++|.++.-+..-|...+.+.++.+|..+..       .|.   -+.+|.   .+..|+..|.+..
T Consensus       446 ----rTkl~RAdDLgLPPRiv~vRrD~fn~eE~D~YeSLY~dSkrkfntyieeGv---vlNNYA---nIF~LitRmRQ~a  515 (791)
T KOG1002|consen  446 ----RTKLERADDLGLPPRIVTVRRDFFNEEEKDLYESLYKDSKRKFNTYIEEGV---VLNNYA---NIFTLITRMRQAA  515 (791)
T ss_pred             ----HhhcccccccCCCccceeeehhhhhhHHHHHHHHHHHhhHHhhhhHHhhhh---hhhhHH---HHHHHHHHHHHhc
Confidence                56667778889999988777777777777888888866421       011   123443   4567777777754


Q ss_pred             CCCCCCcchhhhhcCCceeeecccccccccccccccccccCCceEEccccceeccccchhhhc-----cCCCcCcccccc
Q 021640          155 RRGPPPAARSAIDAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV-----QHNSCPVCRQEL  229 (309)
Q Consensus       155 ~~~~ppa~~~~i~~lp~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~-----~~~sCP~CR~~l  229 (309)
                      .++-.. ..++...|+.      .-.++..|.+|.+.-+   ..+...|.|.||.-||..++.     .+-+||+|...|
T Consensus       516 DHP~LV-l~S~~~n~~~------enk~~~~C~lc~d~ae---d~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~L  585 (791)
T KOG1002|consen  516 DHPDLV-LYSANANLPD------ENKGEVECGLCHDPAE---DYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGL  585 (791)
T ss_pred             cCccee-eehhhcCCCc------cccCceeecccCChhh---hhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccc
Confidence            432211 1122333321      1134578999998753   457788999999999988886     245799999888


Q ss_pred             cCCCC
Q 021640          230 PLQGS  234 (309)
Q Consensus       230 ~~~~~  234 (309)
                      ..+..
T Consensus       586 siDls  590 (791)
T KOG1002|consen  586 SIDLS  590 (791)
T ss_pred             ccccc
Confidence            76643

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

Probab=98.88  E-value=1.5e-09  Score=96.88  Aligned_cols=55  Identities=24%  Similarity=0.650  Sum_probs=43.2

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccC---CCcCcccccccCCCCCCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH---NSCPVCRQELPLQGSSSS  237 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~---~sCP~CR~~l~~~~~~~~  237 (309)
                      ...-+|.|||+.-+   ..+++.|+|.||+.||.+||..+   +.|||||..|..++...-
T Consensus        45 ~~~FdCNICLd~ak---dPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPl  102 (230)
T KOG0823|consen   45 GGFFDCNICLDLAK---DPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPL  102 (230)
T ss_pred             CCceeeeeeccccC---CCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEee
Confidence            34578999998764   34677799999999999999854   459999999876665433

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=98.87  E-value=1.1e-09  Score=95.82  Aligned_cols=52  Identities=25%  Similarity=0.645  Sum_probs=41.8

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhcc----------------CCCcCcccccccCCCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ----------------HNSCPVCRQELPLQGS  234 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~----------------~~sCP~CR~~l~~~~~  234 (309)
                      .+..+|+||++.++.   .+.++|+|.||+.||..|+..                ...||+||..+.....
T Consensus        16 ~~~~~CpICld~~~d---PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~L   83 (193)
T PLN03208         16 GGDFDCNICLDQVRD---PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATL   83 (193)
T ss_pred             CCccCCccCCCcCCC---cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcE
Confidence            356789999998854   477889999999999999852                2469999999865544

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

Probab=98.83  E-value=1.6e-09  Score=99.30  Aligned_cols=51  Identities=25%  Similarity=0.823  Sum_probs=44.1

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG  233 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~  233 (309)
                      +....|.+|++...   ....+||||+||+.||..|+..+..||+||..+.+.+
T Consensus       237 ~a~~kC~LCLe~~~---~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~psk  287 (293)
T KOG0317|consen  237 EATRKCSLCLENRS---NPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSK  287 (293)
T ss_pred             CCCCceEEEecCCC---CCCcCcCcchHHHHHHHHHHccccCCCcccccCCCcc
Confidence            34578999998764   4579999999999999999999999999999886654

>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=98.81  E-value=1.8e-09  Score=74.80  Aligned_cols=46  Identities=30%  Similarity=0.929  Sum_probs=39.3

Q ss_pred             cccccccccccccCCceEEccccce-eccccchhhhccCCCcCccccccc
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHI-YHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~-fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      +..|.||++..   ..+..+||+|. |+..|+..|++....||+||+++.
T Consensus         2 ~~~C~iC~~~~---~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENP---RDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSB---SSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccC---CceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            46899999876   45789999999 999999999999999999999874

...

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

Probab=98.80  E-value=1.7e-09  Score=71.11  Aligned_cols=39  Identities=36%  Similarity=1.002  Sum_probs=33.3

Q ss_pred             ccccccccccCCceEEccccceeccccchhhhccCCCcCcc
Q 021640          185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVC  225 (309)
Q Consensus       185 C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~C  225 (309)
                      |+||++.+..  .++.++|+|.|+..||..|++.+..||+|
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            8999998864  45789999999999999999998899998

>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=98.79  E-value=1.7e-09  Score=71.66  Aligned_cols=44  Identities=36%  Similarity=1.131  Sum_probs=36.6

Q ss_pred             cccccccccccCCceEEccccceeccccchhhhcc-CCCcCcccccc
Q 021640          184 HCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQEL  229 (309)
Q Consensus       184 ~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~-~~sCP~CR~~l  229 (309)
                      .|+||++.+.  +.+..++|+|.||..|+..|++. ...||+|+..+
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            4999999883  44556669999999999999997 66799999764

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

Probab=98.78  E-value=1.6e-09  Score=82.65  Aligned_cols=54  Identities=31%  Similarity=0.810  Sum_probs=40.9

Q ss_pred             ccccccccccccccccc--------CC--ceEEccccceeccccchhhhccC---CCcCcccccccC
Q 021640          178 HLRSDSHCPVCQDKFEL--------GS--EARQMPCNHIYHSDCIVPWLVQH---NSCPVCRQELPL  231 (309)
Q Consensus       178 ~~~~~~~C~IC~~~~~~--------~~--~~~~lpC~H~fh~~Ci~~Wl~~~---~sCP~CR~~l~~  231 (309)
                      .+..++.|.||...|..        ++  .++.-.|+|.||..||.+||...   ..||+||+++..
T Consensus        17 d~~~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~   83 (85)
T PF12861_consen   17 DVANDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF   83 (85)
T ss_pred             ecCCCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence            34457899999999852        11  23444599999999999999853   579999998753

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

Probab=98.72  E-value=2.7e-09  Score=108.22  Aligned_cols=50  Identities=34%  Similarity=1.024  Sum_probs=44.8

Q ss_pred             ccccccccccccccCCc--eEEccccceeccccchhhhccCCCcCccccccc
Q 021640          181 SDSHCPVCQDKFELGSE--ARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~--~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      .+..|+||+|++..+.+  +++|+|+|+||..|+..|+++.++||+||..+.
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            46799999999987655  799999999999999999999999999999553

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

Probab=98.57  E-value=1.9e-08  Score=67.29  Aligned_cols=38  Identities=34%  Similarity=0.977  Sum_probs=29.3

Q ss_pred             ccccccccccCCceEEccccceeccccchhhhccC----CCcCcc
Q 021640          185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH----NSCPVC  225 (309)
Q Consensus       185 C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~----~sCP~C  225 (309)
                      |+||++.|.   +.+.|+|+|.|+..||..|++..    ..||+|
T Consensus         1 CpiC~~~~~---~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFK---DPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-S---SEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhC---CccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            899999996   45899999999999999999854    359987

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.56  E-value=2.2e-08  Score=67.56  Aligned_cols=44  Identities=30%  Similarity=0.841  Sum_probs=38.4

Q ss_pred             cccccccccccCCceEEccccceeccccchhhhccCCCcCcccc
Q 021640          184 HCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQ  227 (309)
Q Consensus       184 ~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~  227 (309)
                      .|.||++.|........++|+|+|+..||..+......||+||+
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            49999999965667889999999999999999866678999985

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

Probab=98.53  E-value=1.8e-08  Score=86.49  Aligned_cols=52  Identities=29%  Similarity=0.714  Sum_probs=42.7

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG  233 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~  233 (309)
                      +..-|+|||+.+... ..+-+.|||+||..||+.-|+....||+|++.|..+.
T Consensus       130 ~~~~CPiCl~~~sek-~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~  181 (187)
T KOG0320|consen  130 GTYKCPICLDSVSEK-VPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQ  181 (187)
T ss_pred             cccCCCceecchhhc-cccccccchhHHHHHHHHHHHhCCCCCCcccccchhh
Confidence            346799999998743 2244679999999999999999999999999876553

>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=98.53  E-value=3.2e-08  Score=65.36  Aligned_cols=39  Identities=38%  Similarity=1.086  Sum_probs=33.2

Q ss_pred             ccccccccccCCceEEccccceeccccchhhhc--cCCCcCcc
Q 021640          185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV--QHNSCPVC  225 (309)
Q Consensus       185 C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~--~~~sCP~C  225 (309)
                      |+||++.+...  +..++|+|.||..||..|++  ....||+|
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            89999988643  35899999999999999999  44569998

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 ....

>smart00504 Ubox Modified RING finger domain

Probab=98.53  E-value=3.4e-08  Score=71.16  Aligned_cols=48  Identities=25%  Similarity=0.501  Sum_probs=41.6

Q ss_pred             ccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCC
Q 021640          183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG  233 (309)
Q Consensus       183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~  233 (309)
                      ..|+||++.+..+   +.++|||+|+..||..|++.+.+||+|+..+..++
T Consensus         2 ~~Cpi~~~~~~~P---v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~   49 (63)
T smart00504        2 FLCPISLEVMKDP---VILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHED   49 (63)
T ss_pred             cCCcCCCCcCCCC---EECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhh
Confidence            4699999998754   77899999999999999999889999998885443

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

>PHA02926 zinc finger-like protein; Provisional

Probab=98.49  E-value=3.2e-08  Score=87.93  Aligned_cols=51  Identities=25%  Similarity=0.673  Sum_probs=38.1

Q ss_pred             cccccccccccccccCC------ceEEccccceeccccchhhhccC------CCcCccccccc
Q 021640          180 RSDSHCPVCQDKFELGS------EARQMPCNHIYHSDCIVPWLVQH------NSCPVCRQELP  230 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~------~~~~lpC~H~fh~~Ci~~Wl~~~------~sCP~CR~~l~  230 (309)
                      ..+.+|+||+|..-.+.      -....+|+|.||..||..|...+      .+||+||..+.
T Consensus       168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            34689999998863221      12344699999999999999753      35999998764

>smart00184 RING Ring finger

Probab=98.46  E-value=4.9e-08  Score=62.28  Aligned_cols=38  Identities=37%  Similarity=1.209  Sum_probs=32.8

Q ss_pred             ccccccccccCCceEEccccceeccccchhhhc-cCCCcCcc
Q 021640          185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV-QHNSCPVC  225 (309)
Q Consensus       185 C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~-~~~sCP~C  225 (309)
                      |+||++..   .....++|+|.||..||..|+. ....||+|
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            78999873   5678899999999999999998 55679987

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=98.43  E-value=7.8e-08  Score=93.37  Aligned_cols=51  Identities=31%  Similarity=0.702  Sum_probs=43.3

Q ss_pred             ccccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCC
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQ  232 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~  232 (309)
                      ++....|+||++.|...   +.++|+|.||..||..|+.....||+|+..+...
T Consensus        23 Le~~l~C~IC~d~~~~P---vitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~   73 (397)
T TIGR00599        23 LDTSLRCHICKDFFDVP---VLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES   73 (397)
T ss_pred             cccccCCCcCchhhhCc---cCCCCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence            45668999999999644   5789999999999999999888899999877543

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=98.39  E-value=9.3e-08  Score=71.48  Aligned_cols=51  Identities=33%  Similarity=0.770  Sum_probs=37.7

Q ss_pred             cccccccccc-----------ccCCceE--EccccceeccccchhhhccCCCcCcccccccCCC
Q 021640          183 SHCPVCQDKF-----------ELGSEAR--QMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG  233 (309)
Q Consensus       183 ~~C~IC~~~~-----------~~~~~~~--~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~  233 (309)
                      +.|+||...+           ..+++..  ---|.|.||..||..||..++.||++|+++...+
T Consensus        21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~~   84 (88)
T COG5194          21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLAD   84 (88)
T ss_pred             chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEec
Confidence            5677776655           2333322  2339999999999999999999999999875443

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

Probab=98.30  E-value=1.3e-07  Score=70.19  Aligned_cols=51  Identities=33%  Similarity=0.877  Sum_probs=36.9

Q ss_pred             cccccccccccccc--------CCc-eEEc-cccceeccccchhhhccCC---CcCcccccccC
Q 021640          181 SDSHCPVCQDKFEL--------GSE-ARQM-PCNHIYHSDCIVPWLVQHN---SCPVCRQELPL  231 (309)
Q Consensus       181 ~~~~C~IC~~~~~~--------~~~-~~~l-pC~H~fh~~Ci~~Wl~~~~---sCP~CR~~l~~  231 (309)
                      .+..|.||.-.|..        ++. ..++ -|.|.||..||.+||....   .||+||+++..
T Consensus        19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~   82 (84)
T KOG1493|consen   19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQF   82 (84)
T ss_pred             CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence            34589999988842        222 2222 2999999999999998543   59999998643

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

Probab=98.26  E-value=1.7e-07  Score=85.22  Aligned_cols=58  Identities=31%  Similarity=0.841  Sum_probs=46.4

Q ss_pred             ccccccccccccccCC-------ceEEccccceeccccchhhhc--cCCCcCcccccccCCCCCCCc
Q 021640          181 SDSHCPVCQDKFELGS-------EARQMPCNHIYHSDCIVPWLV--QHNSCPVCRQELPLQGSSSSR  238 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~-------~~~~lpC~H~fh~~Ci~~Wl~--~~~sCP~CR~~l~~~~~~~~~  238 (309)
                      ++..|+||-..+....       +.-+|.|+|+||..||.-|-.  ++++||.|++.+..+...++.
T Consensus       223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~rmfsnp  289 (328)
T KOG1734|consen  223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKRMFSNP  289 (328)
T ss_pred             CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhhhccCc
Confidence            4568999998875544       667899999999999999986  566899999988766554443

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

Probab=98.16  E-value=5.6e-07  Score=62.20  Aligned_cols=42  Identities=24%  Similarity=0.819  Sum_probs=33.8

Q ss_pred             cccccccccccCCceEEcccc-----ceeccccchhhhccC--CCcCccc
Q 021640          184 HCPVCQDKFELGSEARQMPCN-----HIYHSDCIVPWLVQH--NSCPVCR  226 (309)
Q Consensus       184 ~C~IC~~~~~~~~~~~~lpC~-----H~fh~~Ci~~Wl~~~--~sCP~CR  226 (309)
                      .|.||++ ...++....+||.     |.+|..||.+|+..+  .+||+|+
T Consensus         1 ~CrIC~~-~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHD-EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCC-CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4899998 4445567789985     899999999999654  4799995

Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class

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

Probab=98.10  E-value=7.7e-07  Score=80.94  Aligned_cols=50  Identities=24%  Similarity=0.736  Sum_probs=41.9

Q ss_pred             ccccccccccccccCCceEEccccceeccccchh-hhccCCC-cCcccccccCCC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVP-WLVQHNS-CPVCRQELPLQG  233 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~-Wl~~~~s-CP~CR~~l~~~~  233 (309)
                      .+..|.||++..   +....++|+|+||..||.. |-.++.- ||+||+.+..++
T Consensus       214 ~d~kC~lC~e~~---~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~  265 (271)
T COG5574         214 ADYKCFLCLEEP---EVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK  265 (271)
T ss_pred             cccceeeeeccc---CCcccccccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence            367899999876   4568999999999999999 8877776 999999876554

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

Probab=98.08  E-value=1e-06  Score=86.65  Aligned_cols=51  Identities=29%  Similarity=0.785  Sum_probs=40.8

Q ss_pred             cccccccccccccCCceEEccccceeccccchhhhccC-----CCcCcccccccCCCCC
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH-----NSCPVCRQELPLQGSS  235 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~-----~sCP~CR~~l~~~~~~  235 (309)
                      +..|+||++....   +..+.|||+||..||..++...     ..||+||..|..++..
T Consensus       186 ~~~CPICL~~~~~---p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~  241 (513)
T KOG2164|consen  186 DMQCPICLEPPSV---PVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLL  241 (513)
T ss_pred             CCcCCcccCCCCc---ccccccCceeeHHHHHHHHhhhcccCCccCCchhhhcccccee
Confidence            6789999987643   4677799999999999988754     4699999988765543

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

Probab=98.04  E-value=6.3e-07  Score=83.94  Aligned_cols=49  Identities=27%  Similarity=0.634  Sum_probs=43.1

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPL  231 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~  231 (309)
                      +....|.||.+.|..+   .++||+|.||.-||..+|..+..||.|+.++.+
T Consensus        21 D~lLRC~IC~eyf~ip---~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~E   69 (442)
T KOG0287|consen   21 DDLLRCGICFEYFNIP---MITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTE   69 (442)
T ss_pred             HHHHHHhHHHHHhcCc---eeccccchHHHHHHHHHhccCCCCCceecccch
Confidence            4457899999999765   789999999999999999999999999877643

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

Probab=98.01  E-value=1.7e-06  Score=58.11  Aligned_cols=34  Identities=26%  Similarity=0.877  Sum_probs=21.7

Q ss_pred             cccccccccc-CCceEEccccceeccccchhhhccC
Q 021640          185 CPVCQDKFEL-GSEARQMPCNHIYHSDCIVPWLVQH  219 (309)
Q Consensus       185 C~IC~~~~~~-~~~~~~lpC~H~fh~~Ci~~Wl~~~  219 (309)
                      |+||++ |.. ....+.|+|+|+|+.+||.+++...
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~   35 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKS   35 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcC
Confidence            899999 754 3346889999999999999999854

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

Probab=97.95  E-value=1.8e-06  Score=84.34  Aligned_cols=51  Identities=35%  Similarity=0.918  Sum_probs=39.8

Q ss_pred             ccccccccccccccCC--------------ceEEccccceeccccchhhhcc-CCCcCcccccccC
Q 021640          181 SDSHCPVCQDKFELGS--------------EARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQELPL  231 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~--------------~~~~lpC~H~fh~~Ci~~Wl~~-~~sCP~CR~~l~~  231 (309)
                      ....|+||+..+..-.              .-..+||.|+||..|+..|+.. +-.||+||..|++
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            3568999998863211              2345699999999999999994 4489999999874

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

Probab=97.89  E-value=4.4e-06  Score=62.47  Aligned_cols=49  Identities=27%  Similarity=0.494  Sum_probs=37.8

Q ss_pred             cccccccccccccCCceEEccccceeccccchhhhcc-CCCcCcccccccCCC
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQELPLQG  233 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~-~~sCP~CR~~l~~~~  233 (309)
                      ...|+|+.+.|..   .+.+||||.|...||..||.. +.+||+|+..+...+
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            4689999999964   488999999999999999998 788999998876543

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 ....

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

Probab=97.89  E-value=3.1e-06  Score=77.85  Aligned_cols=48  Identities=31%  Similarity=0.684  Sum_probs=41.8

Q ss_pred             ccccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccc
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL  229 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l  229 (309)
                      +...+.|-||.+.|..+   ..++|+|.||.-||...|..+.-||+||.+.
T Consensus        22 LDs~lrC~IC~~~i~ip---~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~   69 (391)
T COG5432          22 LDSMLRCRICDCRISIP---CETTCGHTFCSLCIRRHLGTQPFCPVCREDP   69 (391)
T ss_pred             chhHHHhhhhhheeecc---eecccccchhHHHHHHHhcCCCCCccccccH
Confidence            34557899999999765   7888999999999999999999999999643

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

Probab=97.88  E-value=3.3e-06  Score=62.75  Aligned_cols=50  Identities=20%  Similarity=0.594  Sum_probs=23.5

Q ss_pred             cccccccccccc-cCCc--eEEc--cccceeccccchhhhcc----C-------CCcCcccccccC
Q 021640          182 DSHCPVCQDKFE-LGSE--ARQM--PCNHIYHSDCIVPWLVQ----H-------NSCPVCRQELPL  231 (309)
Q Consensus       182 ~~~C~IC~~~~~-~~~~--~~~l--pC~H~fh~~Ci~~Wl~~----~-------~sCP~CR~~l~~  231 (309)
                      +..|.||+..+. .++.  ++.-  .|++.||..||..||..    +       ..||.|+++|..
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~   67 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW   67 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence            357999998865 3222  1221  38999999999999973    1       249999998753

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

Probab=97.84  E-value=2.4e-06  Score=88.73  Aligned_cols=51  Identities=25%  Similarity=0.950  Sum_probs=38.8

Q ss_pred             cccccccccccccccccCCceEEcc------ccceeccccchhhhccC--CCcCccccccc
Q 021640          178 HLRSDSHCPVCQDKFELGSEARQMP------CNHIYHSDCIVPWLVQH--NSCPVCRQELP  230 (309)
Q Consensus       178 ~~~~~~~C~IC~~~~~~~~~~~~lp------C~H~fh~~Ci~~Wl~~~--~sCP~CR~~l~  230 (309)
                      +..+-.+|+||...+..-+  +.||      |+|.||..||.+|++..  ++||+||.+++
T Consensus      1465 ~fsG~eECaICYsvL~~vd--r~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1465 KFSGHEECAICYSVLDMVD--RSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             hcCCcchhhHHHHHHHHHh--ccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            3456689999998764211  3333      99999999999999864  56999998775

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

Probab=97.77  E-value=5.5e-06  Score=65.05  Aligned_cols=51  Identities=31%  Similarity=0.725  Sum_probs=37.7

Q ss_pred             cccccccccccc------------cCCc--eEEccccceeccccchhhhccCCCcCcccccccCC
Q 021640          182 DSHCPVCQDKFE------------LGSE--ARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQ  232 (309)
Q Consensus       182 ~~~C~IC~~~~~------------~~~~--~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~  232 (309)
                      .+.|+||..-+.            ..++  +.---|.|.||..||..||+.++.||+|.++....
T Consensus        46 vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~~q  110 (114)
T KOG2930|consen   46 VDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWVFQ  110 (114)
T ss_pred             echhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcceeEe
Confidence            467888876541            1122  22233999999999999999999999998876543

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=97.76  E-value=1e-05  Score=75.91  Aligned_cols=53  Identities=25%  Similarity=0.488  Sum_probs=37.5

Q ss_pred             cccccccccccccCCce--EEccccceeccccchhhhc-cCCCcCcccccccCCCC
Q 021640          182 DSHCPVCQDKFELGSEA--RQMPCNHIYHSDCIVPWLV-QHNSCPVCRQELPLQGS  234 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~--~~lpC~H~fh~~Ci~~Wl~-~~~sCP~CR~~l~~~~~  234 (309)
                      +..|+||+.+--.....  ...+|+|.||..||...+. ....||+|+..+.....
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~f   58 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNF   58 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhc
Confidence            35799999863222222  2337999999999999554 44579999988765543

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).

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

Probab=97.75  E-value=1.1e-05  Score=58.37  Aligned_cols=55  Identities=27%  Similarity=0.540  Sum_probs=26.6

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCCCCCCc
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSSR  238 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~~~~~  238 (309)
                      +....|++|.+.+..  .+....|.|+|+..||..-+..  .||+|+.+...++...++
T Consensus         5 e~lLrCs~C~~~l~~--pv~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD~~~Nr   59 (65)
T PF14835_consen    5 EELLRCSICFDILKE--PVCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQDIQINR   59 (65)
T ss_dssp             HHTTS-SSS-S--SS---B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS----H
T ss_pred             HHhcCCcHHHHHhcC--CceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHHHHhhh
Confidence            445789999998863  3455669999999999886553  499999887766655443

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

Probab=97.74  E-value=9.8e-06  Score=78.57  Aligned_cols=48  Identities=33%  Similarity=0.895  Sum_probs=38.2

Q ss_pred             ccccccccccccccCC-ceEEccccceeccccchhhhccCCCcCccccccc
Q 021640          181 SDSHCPVCQDKFELGS-EARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~-~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      +..+|+||||.+.... .++...|.|.||..|+..|  ...+||+||....
T Consensus       174 ELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w--~~~scpvcR~~q~  222 (493)
T KOG0804|consen  174 ELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKW--WDSSCPVCRYCQS  222 (493)
T ss_pred             cCCCcchhHhhcCccccceeeeecccccchHHHhhc--ccCcChhhhhhcC
Confidence            4578999999986433 2355569999999999999  4568999998665

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

Probab=97.71  E-value=7.9e-06  Score=74.35  Aligned_cols=45  Identities=33%  Similarity=0.816  Sum_probs=39.1

Q ss_pred             ccccccccccccccccCCceEEccccceeccccchhhhccCCCcCccc
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCR  226 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR  226 (309)
                      +.+...|+||++.|...   +.++|+|.||..||..++.....||.||
T Consensus        10 ~~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~~~~~Cp~cr   54 (386)
T KOG2177|consen   10 LQEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWEGPLSCPVCR   54 (386)
T ss_pred             ccccccChhhHHHhhcC---ccccccchHhHHHHHHhcCCCcCCcccC
Confidence            34568999999999866   8999999999999999988445699999

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

Probab=97.57  E-value=1.8e-05  Score=73.27  Aligned_cols=54  Identities=26%  Similarity=0.728  Sum_probs=44.7

Q ss_pred             cccccccccccccCCceEEccccceeccccchhhhcc-----------------------CCCcCcccccccCCCCC
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ-----------------------HNSCPVCRQELPLQGSS  235 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~-----------------------~~sCP~CR~~l~~~~~~  235 (309)
                      ...|.|||.-|..++...+++|.|+||..|+..+|..                       ...|||||..|..+..+
T Consensus       115 ~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~~s  191 (368)
T KOG4445|consen  115 NGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEENS  191 (368)
T ss_pred             CCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccccc
Confidence            5689999999999988999999999999999888751                       12499999988655443

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

Probab=97.45  E-value=1.2e-05  Score=75.82  Aligned_cols=58  Identities=26%  Similarity=0.565  Sum_probs=43.4

Q ss_pred             eeeecccccccccccccccccccCCceEEccccceeccccchhhhcc-CCCcCcccccccC
Q 021640          172 VRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQELPL  231 (309)
Q Consensus       172 ~~~~~~~~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~-~~sCP~CR~~l~~  231 (309)
                      ..+.-..+..+..|+|||+.++..  ....-|.|.||.+||..-++. +++||.||+.+..
T Consensus        33 i~~~l~~~~~~v~c~icl~llk~t--mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S   91 (381)
T KOG0311|consen   33 IMVDLAMFDIQVICPICLSLLKKT--MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS   91 (381)
T ss_pred             heecHHHhhhhhccHHHHHHHHhh--cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence            344445566778999999988643  233339999999999888875 5679999987743

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

Probab=97.44  E-value=1.8e-05  Score=70.55  Aligned_cols=75  Identities=20%  Similarity=0.505  Sum_probs=56.4

Q ss_pred             cccccccccccccCCceEEccccceeccccchhhhcc--------CCCcCcccccccCCCCCCCcccCCCCCCCCCCCCC
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ--------HNSCPVCRQELPLQGSSSSRIHQSSSGQSRSTSFG  253 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~--------~~sCP~CR~~l~~~~~~~~~~~~~~~~~~~~~~~~  253 (309)
                      ...|..|...+..++. .+|.|.|+||++|+..|-..        ...||.|..+|.+.....+........+...++++
T Consensus        50 ~pNC~LC~t~La~gdt-~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~NlvsPva~aLre~L~qvNWa  128 (299)
T KOG3970|consen   50 NPNCRLCNTPLASGDT-TRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLVSPVAEALREQLKQVNWA  128 (299)
T ss_pred             CCCCceeCCccccCcc-eeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccccchhHHHHHHHHHhhhHH
Confidence            4579999999988864 45669999999999999863        34699999999888777666555555555555665


Q ss_pred             CCCC
Q 021640          254 SNGS  257 (309)
Q Consensus       254 ~~~~  257 (309)
                      .++-
T Consensus       129 RagL  132 (299)
T KOG3970|consen  129 RAGL  132 (299)
T ss_pred             hhcc
Confidence            5443

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

Probab=97.42  E-value=5e-05  Score=72.01  Aligned_cols=47  Identities=32%  Similarity=0.790  Sum_probs=39.6

Q ss_pred             ccccccccccccccCCceEEccccce-eccccchhhhccCCCcCccccccc
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHI-YHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~-fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      +..+|.||+.+-   ..+.+|||.|. .|..|-+.-.-+++.||+||+.+.
T Consensus       289 ~gkeCVIClse~---rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~  336 (349)
T KOG4265|consen  289 SGKECVICLSES---RDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIE  336 (349)
T ss_pred             CCCeeEEEecCC---cceEEecchhhehhHhHHHHHHHhhcCCCccccchH
Confidence            357899999775   46789999998 789998887667889999999874

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

Probab=97.38  E-value=2.5e-05  Score=80.02  Aligned_cols=49  Identities=24%  Similarity=0.591  Sum_probs=43.3

Q ss_pred             cccccccccccccCCceEEccccceeccccchhhhccCCCcCccccccc
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      ...|++|+..+..+......+|.|+||..||..|-+.-++||+||.++.
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~  171 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFG  171 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhh
Confidence            3579999999987776677789999999999999999999999998763

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

Probab=97.36  E-value=4.6e-05  Score=72.76  Aligned_cols=47  Identities=30%  Similarity=0.886  Sum_probs=35.4

Q ss_pred             ccccccccccccCCceEEcc-ccceeccccchhhhccC---CCcCcccccc
Q 021640          183 SHCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQH---NSCPVCRQEL  229 (309)
Q Consensus       183 ~~C~IC~~~~~~~~~~~~lp-C~H~fh~~Ci~~Wl~~~---~sCP~CR~~l  229 (309)
                      ..|.||.+-+-....+.-.. |||+||..|+..|+..-   ..||+|+-.+
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            47999966655544555444 99999999999999853   4699998333

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

Probab=97.28  E-value=9.1e-05  Score=68.76  Aligned_cols=48  Identities=21%  Similarity=0.460  Sum_probs=38.8

Q ss_pred             cccccccccccccCCceEEccccceeccccchhhhccCC-CcCcccccccCC
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN-SCPVCRQELPLQ  232 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~-sCP~CR~~l~~~  232 (309)
                      ..+|+||+....   ..+.|+|+|.||.-||+--..... +|++||.+++..
T Consensus         7 ~~eC~IC~nt~n---~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    7 KKECLICYNTGN---CPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDST   55 (324)
T ss_pred             CCcceeeeccCC---cCccccccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence            468999997754   458999999999999987666544 699999988654

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

Probab=97.16  E-value=0.00013  Score=69.88  Aligned_cols=49  Identities=31%  Similarity=0.733  Sum_probs=36.1

Q ss_pred             ccccccccccccccCC----ceEE-ccccceeccccchhhh--cc-----CCCcCcccccc
Q 021640          181 SDSHCPVCQDKFELGS----EARQ-MPCNHIYHSDCIVPWL--VQ-----HNSCPVCRQEL  229 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~----~~~~-lpC~H~fh~~Ci~~Wl--~~-----~~sCP~CR~~l  229 (309)
                      .+..|.||++......    .... .+|.|.||..||..|-  .+     ...||.||...
T Consensus       160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s  220 (344)
T KOG1039|consen  160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPS  220 (344)
T ss_pred             ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcc
Confidence            4578999999865332    0123 4499999999999998  34     46799999654

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

Probab=97.09  E-value=0.00022  Score=68.41  Aligned_cols=49  Identities=24%  Similarity=0.798  Sum_probs=39.8

Q ss_pred             ccccccccccccCCceEEccccceeccccchhhhcc--CCCcCcccccccCCCC
Q 021640          183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ--HNSCPVCRQELPLQGS  234 (309)
Q Consensus       183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~--~~sCP~CR~~l~~~~~  234 (309)
                      ..|.||-|.   ...+++-||+|..|..|+..|-..  .++||.||.+|.....
T Consensus       370 eLCKICaen---dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~  420 (563)
T KOG1785|consen  370 ELCKICAEN---DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEP  420 (563)
T ss_pred             HHHHHhhcc---CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEeccccc
Confidence            469999754   356888999999999999999853  5789999999865544

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

Probab=96.75  E-value=0.00088  Score=65.61  Aligned_cols=54  Identities=31%  Similarity=0.750  Sum_probs=44.2

Q ss_pred             ccccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCCC
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGS  234 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~  234 (309)
                      ++.+..|+||...+..+  +....|+|.||..||..|+..+..||.|+..+.....
T Consensus        18 ~~~~l~C~~C~~vl~~p--~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~   71 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDP--VQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEE   71 (391)
T ss_pred             CcccccCccccccccCC--CCCCCCCCcccccccchhhccCcCCcccccccchhhc
Confidence            56778999999988754  2225799999999999999999999999887754443

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

Probab=96.73  E-value=0.00068  Score=57.71  Aligned_cols=40  Identities=28%  Similarity=0.740  Sum_probs=32.2

Q ss_pred             Cceeeecccccc-cccccccccccccCCceEEccccceecc
Q 021640          170 PTVRITQRHLRS-DSHCPVCQDKFELGSEARQMPCNHIYHS  209 (309)
Q Consensus       170 p~~~~~~~~~~~-~~~C~IC~~~~~~~~~~~~lpC~H~fh~  209 (309)
                      |.+.+..+.+.. ..+|.||+|+++.++.+.+|||..+||+
T Consensus       164 PrlsYNdDVL~ddkGECvICLEdL~~GdtIARLPCLCIYHK  204 (205)
T KOG0801|consen  164 PRLSYNDDVLKDDKGECVICLEDLEAGDTIARLPCLCIYHK  204 (205)
T ss_pred             cccccccchhcccCCcEEEEhhhccCCCceeccceEEEeec
Confidence            444455554443 4689999999999999999999999997

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

Probab=96.68  E-value=0.00086  Score=47.75  Aligned_cols=41  Identities=24%  Similarity=0.763  Sum_probs=28.9

Q ss_pred             cccccccccccccCCceEEccccceeccccchhhhccC--CCcCc
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH--NSCPV  224 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~--~sCP~  224 (309)
                      ...|+|.+..|+  +.++...|+|+|-+..|..||.++  ..||+
T Consensus        11 ~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   11 SLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             -SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             ccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            478999999987  456777899999999999999543  35998

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

Probab=96.61  E-value=0.00074  Score=65.12  Aligned_cols=46  Identities=30%  Similarity=0.941  Sum_probs=35.7

Q ss_pred             cccccccccccccCC--ceEEccccceeccccchhhhccC--CCcCcccc
Q 021640          182 DSHCPVCQDKFELGS--EARQMPCNHIYHSDCIVPWLVQH--NSCPVCRQ  227 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~--~~~~lpC~H~fh~~Ci~~Wl~~~--~sCP~CR~  227 (309)
                      ..+|+||++.++..-  .+..+.|+|.|-.+||.+||.+.  ..||.|..
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~   53 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSG   53 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCC
Confidence            468999999986533  35566699999999999999632  24999963

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

Probab=96.58  E-value=0.00023  Score=49.73  Aligned_cols=46  Identities=22%  Similarity=0.642  Sum_probs=33.3

Q ss_pred             cccccccccccccCCceEEccccce-eccccchhhhc-cCCCcCccccccc
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHI-YHSDCIVPWLV-QHNSCPVCRQELP  230 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~-fh~~Ci~~Wl~-~~~sCP~CR~~l~  230 (309)
                      +++|.||+|--.   ..+...|+|. .|.+|-..-++ .+..||+||.++.
T Consensus         7 ~dECTICye~pv---dsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    7 SDECTICYEHPV---DSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             ccceeeeccCcc---hHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            378999987543   3355669997 67788655444 7889999998763

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

Probab=96.52  E-value=0.00078  Score=65.79  Aligned_cols=49  Identities=35%  Similarity=0.710  Sum_probs=41.6

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPL  231 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~  231 (309)
                      ..+..|.||+..+..   .+.+||+|.||..||..-+.....||.||..+..
T Consensus        82 ~sef~c~vc~~~l~~---pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   82 RSEFECCVCSRALYP---PVVTPCGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cchhhhhhhHhhcCC---CccccccccccHHHHHHHhccCCCCccccccccc
Confidence            567899999988854   4677999999999999977777789999998875

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

Probab=96.45  E-value=0.00083  Score=64.46  Aligned_cols=47  Identities=32%  Similarity=0.834  Sum_probs=39.1

Q ss_pred             cccccccccccccC-CceEEccccceeccccchhhhccCC--CcCccccc
Q 021640          182 DSHCPVCQDKFELG-SEARQMPCNHIYHSDCIVPWLVQHN--SCPVCRQE  228 (309)
Q Consensus       182 ~~~C~IC~~~~~~~-~~~~~lpC~H~fh~~Ci~~Wl~~~~--sCP~CR~~  228 (309)
                      +..|..|-+.+... +..-.|||.|+||..|+...|.++.  +||-||+-
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crkl  414 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKL  414 (518)
T ss_pred             hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHH
Confidence            57899999988543 4577899999999999999997654  69999953

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

Probab=96.35  E-value=0.0021  Score=43.87  Aligned_cols=40  Identities=25%  Similarity=0.792  Sum_probs=27.2

Q ss_pred             ccccccccccCCceEEcccc--c---eeccccchhhhcc--CCCcCcc
Q 021640          185 CPVCQDKFELGSEARQMPCN--H---IYHSDCIVPWLVQ--HNSCPVC  225 (309)
Q Consensus       185 C~IC~~~~~~~~~~~~lpC~--H---~fh~~Ci~~Wl~~--~~sCP~C  225 (309)
                      |-||++.-.... ....||.  -   ..|..||..|+..  ..+|++|
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            789998865543 5677853  3   8999999999984  4569987

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

Probab=96.12  E-value=0.0012  Score=58.08  Aligned_cols=44  Identities=23%  Similarity=0.570  Sum_probs=38.2

Q ss_pred             ccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccc
Q 021640          183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL  229 (309)
Q Consensus       183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l  229 (309)
                      -.|.||.++|+.+   +.+.|+|.||..|...-++....|-+|-+..
T Consensus       197 F~C~iCKkdy~sp---vvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t  240 (259)
T COG5152         197 FLCGICKKDYESP---VVTECGHSFCSLCAIRKYQKGDECGVCGKAT  240 (259)
T ss_pred             eeehhchhhccch---hhhhcchhHHHHHHHHHhccCCcceecchhh
Confidence            4799999999654   7788999999999999888889999997654

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

Probab=96.05  E-value=0.0011  Score=68.52  Aligned_cols=48  Identities=21%  Similarity=0.684  Sum_probs=38.1

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhc-cCCCcCcccccccC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV-QHNSCPVCRQELPL  231 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~-~~~sCP~CR~~l~~  231 (309)
                      +-..|++|-.-++   .++...|+|+||..||.+-+. ++..||.|-..+-.
T Consensus       642 ~~LkCs~Cn~R~K---d~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga  690 (698)
T KOG0978|consen  642 ELLKCSVCNTRWK---DAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA  690 (698)
T ss_pred             hceeCCCccCchh---hHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence            4578999996664   345666999999999999987 56679999887643

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

Probab=96.04  E-value=0.00089  Score=63.03  Aligned_cols=47  Identities=23%  Similarity=0.612  Sum_probs=38.5

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccc
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL  229 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l  229 (309)
                      ...+|.+|...|.+..  .+.-|-|.||+.||...|...++||+|...|
T Consensus        14 ~~itC~LC~GYliDAT--TI~eCLHTFCkSCivk~l~~~~~CP~C~i~i   60 (331)
T KOG2660|consen   14 PHITCRLCGGYLIDAT--TITECLHTFCKSCIVKYLEESKYCPTCDIVI   60 (331)
T ss_pred             cceehhhccceeecch--hHHHHHHHHHHHHHHHHHHHhccCCccceec
Confidence            4568999999886442  3334999999999999999999999997655

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

Probab=95.91  E-value=0.0026  Score=69.40  Aligned_cols=50  Identities=30%  Similarity=0.712  Sum_probs=39.7

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccC----------CCcCcccccc
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH----------NSCPVCRQEL  229 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~----------~sCP~CR~~l  229 (309)
                      +.++.|.||..+--....+++|-|+|+||..|...-|++.          .+||+|+.++
T Consensus      3484 D~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~I 3543 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKI 3543 (3738)
T ss_pred             ccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchh
Confidence            4578999999876555678899999999999997655532          3699998766

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

Probab=95.78  E-value=0.0057  Score=48.20  Aligned_cols=33  Identities=30%  Similarity=0.692  Sum_probs=28.1

Q ss_pred             cccccccccccccccCCceEEccccceeccccch
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIV  213 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~  213 (309)
                      ..+..|+||...+.. ......||+|+||..|+.
T Consensus        76 ~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   76 TESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence            345689999999876 578889999999999985

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=95.38  E-value=0.0037  Score=51.88  Aligned_cols=35  Identities=17%  Similarity=0.534  Sum_probs=29.9

Q ss_pred             cccccccccccccCCceEEcccc------ceeccccchhhh
Q 021640          182 DSHCPVCQDKFELGSEARQMPCN------HIYHSDCIVPWL  216 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~------H~fh~~Ci~~Wl  216 (309)
                      ..+|.||++.+...+.++.++|+      |.||.+|+.+|-
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            46899999999875578888886      999999999994

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

>PHA02862 5L protein; Provisional

Probab=95.27  E-value=0.0059  Score=51.19  Aligned_cols=45  Identities=20%  Similarity=0.675  Sum_probs=34.0

Q ss_pred             ccccccccccccCCceEEcccc-----ceeccccchhhhcc--CCCcCcccccccC
Q 021640          183 SHCPVCQDKFELGSEARQMPCN-----HIYHSDCIVPWLVQ--HNSCPVCRQELPL  231 (309)
Q Consensus       183 ~~C~IC~~~~~~~~~~~~lpC~-----H~fh~~Ci~~Wl~~--~~sCP~CR~~l~~  231 (309)
                      ..|-||+++-+.  .  .-||.     ...|.+|+..|+..  +.+|+.|+.+...
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            579999987432  2  46764     57999999999974  3469999987643

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

Probab=95.24  E-value=0.0072  Score=56.23  Aligned_cols=44  Identities=23%  Similarity=0.507  Sum_probs=38.6

Q ss_pred             ccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccc
Q 021640          183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL  229 (309)
Q Consensus       183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l  229 (309)
                      ..|-||...|..+   ++..|+|.||..|-..-++....|.+|-+..
T Consensus       242 f~c~icr~~f~~p---Vvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t  285 (313)
T KOG1813|consen  242 FKCFICRKYFYRP---VVTKCGHYFCEVCALKPYQKGEKCYVCSQQT  285 (313)
T ss_pred             ccccccccccccc---hhhcCCceeehhhhccccccCCcceeccccc
Confidence            3599999999755   7888999999999999888889999998765

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

Probab=95.17  E-value=0.012  Score=56.00  Aligned_cols=51  Identities=25%  Similarity=0.503  Sum_probs=42.6

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCCC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGS  234 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~  234 (309)
                      ++..|+||...   +-.++..||+|.=|..||.+-|...+.|=.|+..+.....
T Consensus       421 Ed~lCpICyA~---pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~~~l  471 (489)
T KOG4692|consen  421 EDNLCPICYAG---PINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVIDVIL  471 (489)
T ss_pred             ccccCcceecc---cchhhccCCCCchHHHHHHHHHhcCCeeeEecceeeehhc
Confidence            56789999744   3567889999999999999999999999999988764333

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

Probab=94.94  E-value=0.0051  Score=59.58  Aligned_cols=47  Identities=19%  Similarity=0.489  Sum_probs=38.0

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccC--------CCcCcccc
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH--------NSCPVCRQ  227 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~--------~sCP~CR~  227 (309)
                      ....|.||+++..-....+.|||+|+||+.|+..++..+        -.||-+..
T Consensus       183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             hcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            357899999997665889999999999999999998732        24877654

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=94.85  E-value=0.0099  Score=50.68  Aligned_cols=49  Identities=27%  Similarity=0.754  Sum_probs=35.7

Q ss_pred             cccccccccccccccCCceEEccccc-----eeccccchhhhccC--CCcCcccccccCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNH-----IYHSDCIVPWLVQH--NSCPVCRQELPLQ  232 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H-----~fh~~Ci~~Wl~~~--~sCP~CR~~l~~~  232 (309)
                      ..+..|-||.++-.  .  -..||..     ..|.+|+..|+..+  .+|++|+.+....
T Consensus         6 ~~~~~CRIC~~~~~--~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          6 LMDKCCWICKDEYD--V--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCCCeeEecCCCCC--C--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            34678999998743  1  2357543     67999999999854  4699999876443

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.62  E-value=0.029  Score=51.08  Aligned_cols=71  Identities=17%  Similarity=0.317  Sum_probs=53.5

Q ss_pred             hhhcCCceeeecccc----------cccccccccccccccCCceEEc-cccceeccccchhhhccCCCcCcccccccCCC
Q 021640          165 AIDAMPTVRITQRHL----------RSDSHCPVCQDKFELGSEARQM-PCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG  233 (309)
Q Consensus       165 ~i~~lp~~~~~~~~~----------~~~~~C~IC~~~~~~~~~~~~l-pC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~  233 (309)
                      .++.|-.++++....          .....|+||.+.+........| ||+|+|+.+|+.+.+.....||+|-.++...+
T Consensus       194 klkdL~~VkFT~l~s~~~et~l~a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrd  273 (303)
T KOG3039|consen  194 KLKDLFAVKFTPLNSEETETKLIAASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRD  273 (303)
T ss_pred             chhhcceeeeeecCCchhhhhhhhhccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccc
Confidence            455666666654332          1247899999999876655544 59999999999999999999999988887665


Q ss_pred             CC
Q 021640          234 SS  235 (309)
Q Consensus       234 ~~  235 (309)
                      ..
T Consensus       274 iI  275 (303)
T KOG3039|consen  274 II  275 (303)
T ss_pred             eE
Confidence            43

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

Probab=94.55  E-value=0.021  Score=52.65  Aligned_cols=48  Identities=31%  Similarity=0.687  Sum_probs=37.2

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhcc--CCCcCccccccc
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ--HNSCPVCRQELP  230 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~--~~sCP~CR~~l~  230 (309)
                      .+.+|++|.+.-..+  -...+|+|+||.-||..=+.-  ..+||.|-.++.
T Consensus       238 ~~~~C~~Cg~~PtiP--~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  238 SDTECPVCGEPPTIP--HVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             CCceeeccCCCCCCC--eeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            467999999775543  356669999999999886653  357999988775

>PF04641 Rtf2: Rtf2 RING-finger

Probab=94.48  E-value=0.059  Score=49.89  Aligned_cols=91  Identities=18%  Similarity=0.372  Sum_probs=59.5

Q ss_pred             chHHHHHHHHhcCCCCCCCcchhh---hhcCCceeeeccc------------ccccccccccccccccCCceEE-ccccc
Q 021640          142 GLEELFEQLSANGRRGPPPAARSA---IDAMPTVRITQRH------------LRSDSHCPVCQDKFELGSEARQ-MPCNH  205 (309)
Q Consensus       142 ~l~~l~~~l~~~~~~~~ppa~~~~---i~~lp~~~~~~~~------------~~~~~~C~IC~~~~~~~~~~~~-lpC~H  205 (309)
                      ..+.||+.|......+..+..-..   ++.|-.+.++...            ......|+|...+|......+. -||||
T Consensus        58 nKeaile~Ll~~~~~~~~~~~~~hI~~LKDl~~l~~~~n~~~~~~~~~~~~~~~~~~~CPvt~~~~~~~~~fv~l~~cG~  137 (260)
T PF04641_consen   58 NKEAILEFLLDKKKNKDLPKTFSHIKSLKDLVELKFTKNPSYKEEDKSSGDNSEGRFICPVTGKEFNGKHKFVYLRPCGC  137 (260)
T ss_pred             cHHHHHHHHHhcCcCCCCccccccccCccceeeEEeEecCccccccccccccCCceeECCCCCcccCCceeEEEEcCCCC
Confidence            568889998886543222332223   3444445555431            2345789999999955444444 47999


Q ss_pred             eeccccchhhhccCCCcCcccccccCCC
Q 021640          206 IYHSDCIVPWLVQHNSCPVCRQELPLQG  233 (309)
Q Consensus       206 ~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~  233 (309)
                      +|-..+|..- .....||+|-.++...+
T Consensus       138 V~s~~alke~-k~~~~Cp~c~~~f~~~D  164 (260)
T PF04641_consen  138 VFSEKALKEL-KKSKKCPVCGKPFTEED  164 (260)
T ss_pred             EeeHHHHHhh-cccccccccCCccccCC
Confidence            9999999886 23557999988776444

>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=94.36  E-value=0.01  Score=39.74  Aligned_cols=41  Identities=27%  Similarity=0.784  Sum_probs=23.8

Q ss_pred             ccccccccccCCceEEccccceeccccchhhhccCC--CcCcc
Q 021640          185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN--SCPVC  225 (309)
Q Consensus       185 C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~--sCP~C  225 (309)
                      |.+|.+....|.......|.-.+|..|+..+++...  .||.|
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            778888887664333334999999999999998665  69987

; PDB: 3NW0_A 2CT0_A.

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=94.34  E-value=0.034  Score=39.10  Aligned_cols=46  Identities=24%  Similarity=0.689  Sum_probs=33.9

Q ss_pred             ccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCC
Q 021640          183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG  233 (309)
Q Consensus       183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~  233 (309)
                      ..|..|...   +.+-.++||+|+.+..|..-+  +-+.||+|-+.+...+
T Consensus         8 ~~~~~~~~~---~~~~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~~~~   53 (55)
T PF14447_consen    8 QPCVFCGFV---GTKGTVLPCGHLICDNCFPGE--RYNGCPFCGTPFEFDD   53 (55)
T ss_pred             eeEEEcccc---ccccccccccceeeccccChh--hccCCCCCCCcccCCC
Confidence            456666643   345579999999999997654  6677999988876543

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

Probab=94.26  E-value=0.025  Score=54.10  Aligned_cols=43  Identities=35%  Similarity=0.756  Sum_probs=31.8

Q ss_pred             cccccccccccccCCceEEccccceeccccchhhhccCCCcCccccccc
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      .+.|.||+++..   ..+.+||||+-+  |..-- +...+||+||..+.
T Consensus       305 p~lcVVcl~e~~---~~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI~  347 (355)
T KOG1571|consen  305 PDLCVVCLDEPK---SAVFVPCGHVCC--CTLCS-KHLPQCPVCRQRIR  347 (355)
T ss_pred             CCceEEecCCcc---ceeeecCCcEEE--chHHH-hhCCCCchhHHHHH
Confidence            578999998875   478999999966  65442 22335999998763

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

Probab=94.19  E-value=0.029  Score=45.50  Aligned_cols=33  Identities=24%  Similarity=0.575  Sum_probs=29.0

Q ss_pred             CceecccCCCceeecCCCccCCCCCCCceEEec
Q 021640            6 NTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELD   38 (309)
Q Consensus         6 ~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~~   38 (309)
                      ...||..|+..+.....++.||.|+|..++-+.
T Consensus        69 ~~~~C~~C~~~~~~e~~~~~CP~C~s~~~~i~~  101 (115)
T COG0375          69 AECWCLDCGQEVELEELDYRCPKCGSINLRIIG  101 (115)
T ss_pred             cEEEeccCCCeecchhheeECCCCCCCceEEec
Confidence            568999999999888888889999999888764

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

Probab=94.02  E-value=0.016  Score=60.61  Aligned_cols=47  Identities=23%  Similarity=0.781  Sum_probs=35.1

Q ss_pred             ccccccccccccccCCceE-EccccceeccccchhhhccCC-------CcCcccc
Q 021640          181 SDSHCPVCQDKFELGSEAR-QMPCNHIYHSDCIVPWLVQHN-------SCPVCRQ  227 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~-~lpC~H~fh~~Ci~~Wl~~~~-------sCP~CR~  227 (309)
                      ...+|.||.+.+.....+- ...|.|+||..||..|.+...       .||.|..
T Consensus       190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs  244 (950)
T KOG1952|consen  190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS  244 (950)
T ss_pred             CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence            4578999999986544322 233999999999999997421       3999983

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

Probab=93.77  E-value=0.0033  Score=60.36  Aligned_cols=51  Identities=27%  Similarity=0.681  Sum_probs=43.6

Q ss_pred             cccccccccccccC-CceEEccccceeccccchhhhccCCCcCcccccccCC
Q 021640          182 DSHCPVCQDKFELG-SEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQ  232 (309)
Q Consensus       182 ~~~C~IC~~~~~~~-~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~  232 (309)
                      ...|+||.+.++.. +++..+-|+|.+|.+||.+||.....||.|+.+|+..
T Consensus       196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~  247 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPKN  247 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhhh
Confidence            45799999998755 5677888999999999999999988899999888543

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

Probab=93.74  E-value=0.032  Score=50.67  Aligned_cols=48  Identities=19%  Similarity=0.532  Sum_probs=35.3

Q ss_pred             cccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCCC
Q 021640          184 HCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGS  234 (309)
Q Consensus       184 ~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~  234 (309)
                      .|..|..--. ++...++.|.|+||..|...-.  ...||+|++.|.....
T Consensus         5 hCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~--~~~C~lCkk~ir~i~l   52 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLTACRHVFCEPCLKASS--PDVCPLCKKSIRIIQL   52 (233)
T ss_pred             EeccccccCC-CCceeeeechhhhhhhhcccCC--ccccccccceeeeeec
Confidence            5887775544 6778888999999999986532  2289999998754433

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

Probab=93.49  E-value=0.058  Score=51.01  Aligned_cols=46  Identities=24%  Similarity=0.481  Sum_probs=35.5

Q ss_pred             cccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccc
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL  229 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l  229 (309)
                      ...|+||+.....+.  +..--|-+||..||..++..++.|||=-.++
T Consensus       300 ~~~CpvClk~r~Npt--vl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~  345 (357)
T KOG0826|consen  300 REVCPVCLKKRQNPT--VLEVSGYVFCYPCIFSYVVNYGHCPVTGYPA  345 (357)
T ss_pred             cccChhHHhccCCCc--eEEecceEEeHHHHHHHHHhcCCCCccCCcc
Confidence            457999998876542  2333599999999999999999999865443

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

Probab=93.19  E-value=0.035  Score=38.04  Aligned_cols=44  Identities=25%  Similarity=0.702  Sum_probs=21.4

Q ss_pred             ccccccccccCCceEEcc--ccceeccccchhhhc-cCCCcCcccccc
Q 021640          185 CPVCQDKFELGSEARQMP--CNHIYHSDCIVPWLV-QHNSCPVCRQEL  229 (309)
Q Consensus       185 C~IC~~~~~~~~~~~~lp--C~H~fh~~Ci~~Wl~-~~~sCP~CR~~l  229 (309)
                      |++|.+++.. .....+|  |++.++..|...-++ ....||-||++.
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  889999999887775 467899999753

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

Probab=92.86  E-value=0.033  Score=51.87  Aligned_cols=42  Identities=29%  Similarity=0.720  Sum_probs=31.9

Q ss_pred             cccccccccccccCCceEEcccccee-ccccchhhhccCCCcCccccccc
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIY-HSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~f-h~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      ...|.||++.-   ...+.|+|||.. |..|-..    -+.||+||+.|.
T Consensus       300 ~~LC~ICmDaP---~DCvfLeCGHmVtCt~CGkr----m~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAP---RDCVFLECGHMVTCTKCGKR----MNECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCC---cceEEeecCcEEeehhhccc----cccCchHHHHHH
Confidence            56899998754   567899999974 5667544    237999998764

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

Probab=92.59  E-value=0.039  Score=51.37  Aligned_cols=45  Identities=29%  Similarity=0.821  Sum_probs=37.9

Q ss_pred             ccccccccccccCC-ceEEccccceeccccchhhhccCCCcCcccc
Q 021640          183 SHCPVCQDKFELGS-EARQMPCNHIYHSDCIVPWLVQHNSCPVCRQ  227 (309)
Q Consensus       183 ~~C~IC~~~~~~~~-~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~  227 (309)
                      ..|+||.+.+.... .+..++|+|.-|..|+......+.+||+|.+
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            34999998875544 5678899999999999998888889999988

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

Probab=92.27  E-value=0.046  Score=47.49  Aligned_cols=52  Identities=23%  Similarity=0.641  Sum_probs=36.5

Q ss_pred             cccccccccccccCC----ceEEccccceeccccchhhhcc----C-------CCcCcccccccCCC
Q 021640          182 DSHCPVCQDKFELGS----EARQMPCNHIYHSDCIVPWLVQ----H-------NSCPVCRQELPLQG  233 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~----~~~~lpC~H~fh~~Ci~~Wl~~----~-------~sCP~CR~~l~~~~  233 (309)
                      ...|.||+..--.|.    ..--..|+.-||.-|+..||+.    .       ..||.|..++..+.
T Consensus       165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKm  231 (234)
T KOG3268|consen  165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKM  231 (234)
T ss_pred             hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeec
Confidence            356999986543332    2234459999999999999973    1       24999998876553

>TIGR00100 hypA hydrogenase nickel insertion protein HypA

Probab=91.56  E-value=0.15  Score=41.46  Aligned_cols=32  Identities=22%  Similarity=0.282  Sum_probs=26.4

Q ss_pred             CceecccCCCceeecCCCccCCCCCCCceEEe
Q 021640            6 NTHWCYRCRRPVRLQGEDAVCLYCSGGFVQEL   37 (309)
Q Consensus         6 ~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~   37 (309)
                      ...||..|...+.+......||.|++..++=+
T Consensus        69 ~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~~i~  100 (115)
T TIGR00100        69 VECECEDCSEEVSPEIDLYRCPKCHGIMLQVR  100 (115)
T ss_pred             cEEEcccCCCEEecCCcCccCcCCcCCCcEEe
Confidence            57899999988887666788999999876655

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.

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

Probab=91.40  E-value=0.11  Score=48.72  Aligned_cols=47  Identities=23%  Similarity=0.691  Sum_probs=38.2

Q ss_pred             ccccccccccccCC---ceEEccccceeccccchhhhccCC-CcCcccccc
Q 021640          183 SHCPVCQDKFELGS---EARQMPCNHIYHSDCIVPWLVQHN-SCPVCRQEL  229 (309)
Q Consensus       183 ~~C~IC~~~~~~~~---~~~~lpC~H~fh~~Ci~~Wl~~~~-sCP~CR~~l  229 (309)
                      ..|-||-++|...+   ..+.|.|+|.|+..|+.+-+.... .||.||...
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            57999999997763   356777999999999988776543 599999885

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=91.07  E-value=0.17  Score=41.05  Aligned_cols=32  Identities=25%  Similarity=0.680  Sum_probs=25.3

Q ss_pred             CceecccCCCceeecCCC-ccCCCCCCCceEEe
Q 021640            6 NTHWCYRCRRPVRLQGED-AVCLYCSGGFVQEL   37 (309)
Q Consensus         6 ~~ywCh~C~r~v~~~~~~-~~CP~C~~gFvEE~   37 (309)
                      ..+||..|...+...... ..||.|++.-++=+
T Consensus        69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~  101 (114)
T PRK03681         69 AECWCETCQQYVTLLTQRVRRCPQCHGDMLRIV  101 (114)
T ss_pred             cEEEcccCCCeeecCCccCCcCcCcCCCCcEEc
Confidence            579999999888776544 67999998876554

>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=90.48  E-value=0.14  Score=41.37  Aligned_cols=32  Identities=19%  Similarity=0.332  Sum_probs=24.4

Q ss_pred             CceecccCCCceeecCCCccCCCCCCCceEEe
Q 021640            6 NTHWCYRCRRPVRLQGEDAVCLYCSGGFVQEL   37 (309)
Q Consensus         6 ~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~   37 (309)
                      ..+||..|.....+......||.|++..++=+
T Consensus        69 ~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~~i~  100 (113)
T PF01155_consen   69 ARARCRDCGHEFEPDEFDFSCPRCGSPDVEII  100 (113)
T ss_dssp             -EEEETTTS-EEECHHCCHH-SSSSSS-EEEE
T ss_pred             CcEECCCCCCEEecCCCCCCCcCCcCCCcEEc
Confidence            57899999999998877789999999977554

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.

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

Probab=90.33  E-value=0.1  Score=54.83  Aligned_cols=43  Identities=33%  Similarity=0.828  Sum_probs=33.5

Q ss_pred             cccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccc
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL  229 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l  229 (309)
                      ...|..|--.+..+  .+..-|+|.||.+|+.   .....||-|+.++
T Consensus       840 ~skCs~C~~~LdlP--~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  840 VSKCSACEGTLDLP--FVHFLCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeeecccCCccccc--eeeeecccHHHHHhhc---cCcccCCccchhh
Confidence            35799998877654  5666799999999998   3455799998744

>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional

Probab=90.30  E-value=0.23  Score=40.23  Aligned_cols=32  Identities=28%  Similarity=0.734  Sum_probs=25.6

Q ss_pred             CceecccCCCceeecCCCccCCCCCCCceEEe
Q 021640            6 NTHWCYRCRRPVRLQGEDAVCLYCSGGFVQEL   37 (309)
Q Consensus         6 ~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~   37 (309)
                      ..+||..|..........+.||.|++.-++=+
T Consensus        69 ~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~~i~  100 (113)
T PRK12380         69 AQAWCWDCSQVVEIHQHDAQCPHCHGERLRVD  100 (113)
T ss_pred             cEEEcccCCCEEecCCcCccCcCCCCCCcEEc
Confidence            57899999988877666677999998766544

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=90.20  E-value=0.16  Score=35.73  Aligned_cols=33  Identities=39%  Similarity=0.887  Sum_probs=28.1

Q ss_pred             cccccccccccccCCceEEcc-ccceeccccchh
Q 021640          182 DSHCPVCQDKFELGSEARQMP-CNHIYHSDCIVP  214 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lp-C~H~fh~~Ci~~  214 (309)
                      ...|.+|-+.|+.++.+++-| |+-.||.+|...
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            457999999998888888888 999999999543

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

Probab=90.13  E-value=0.12  Score=49.29  Aligned_cols=47  Identities=28%  Similarity=0.739  Sum_probs=36.9

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhh--hccCCCcCcccccc
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPW--LVQHNSCPVCRQEL  229 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~W--l~~~~sCP~CR~~l  229 (309)
                      +++..|-||-+..   ..+.++||+|..|.-|-...  |-..+.||+||.+.
T Consensus        59 Een~~C~ICA~~~---TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~  107 (493)
T COG5236          59 EENMNCQICAGST---TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET  107 (493)
T ss_pred             cccceeEEecCCc---eEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence            4567899999876   35689999999999997543  33577899999865

>PHA03096 p28-like protein; Provisional

Probab=90.09  E-value=0.076  Score=49.87  Aligned_cols=36  Identities=17%  Similarity=0.469  Sum_probs=27.5

Q ss_pred             ccccccccccccCC----ceEEcc-ccceeccccchhhhcc
Q 021640          183 SHCPVCQDKFELGS----EARQMP-CNHIYHSDCIVPWLVQ  218 (309)
Q Consensus       183 ~~C~IC~~~~~~~~----~~~~lp-C~H~fh~~Ci~~Wl~~  218 (309)
                      ..|.||++......    .-..|+ |.|.||..||..|...
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~  219 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTE  219 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHh
Confidence            68999999865321    223455 9999999999999864

>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=90.02  E-value=0.099  Score=35.61  Aligned_cols=44  Identities=25%  Similarity=0.687  Sum_probs=25.4

Q ss_pred             cccccccccccCCceEEccc-cceeccccchhhhccCCCcCcccccccCC
Q 021640          184 HCPVCQDKFELGSEARQMPC-NHIYHSDCIVPWLVQHNSCPVCRQELPLQ  232 (309)
Q Consensus       184 ~C~IC~~~~~~~~~~~~lpC-~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~  232 (309)
                      .|.-|+-..  .   ....| .|+.+..|+...|.+...||+|.++||.+
T Consensus         4 nCKsCWf~~--k---~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen    4 NCKSCWFAN--K---GLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK   48 (50)
T ss_dssp             ---SS-S----S---SEEE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred             cChhhhhcC--C---CeeeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence            466666332  1   24447 59999999999999999999999999864

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.

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

Probab=89.53  E-value=0.38  Score=46.55  Aligned_cols=29  Identities=24%  Similarity=0.923  Sum_probs=22.2

Q ss_pred             ccceeccccchhhhcc-------------CCCcCcccccccC
Q 021640          203 CNHIYHSDCIVPWLVQ-------------HNSCPVCRQELPL  231 (309)
Q Consensus       203 C~H~fh~~Ci~~Wl~~-------------~~sCP~CR~~l~~  231 (309)
                      |.-..|.+|+-+|+..             +-.||+||+.+..
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi  352 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI  352 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence            5677888999999863             2359999998754

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

>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional

Probab=89.31  E-value=0.28  Score=40.00  Aligned_cols=32  Identities=22%  Similarity=0.312  Sum_probs=24.7

Q ss_pred             CceecccCCCceeecCCC-ccCCCCCCCceEEe
Q 021640            6 NTHWCYRCRRPVRLQGED-AVCLYCSGGFVQEL   37 (309)
Q Consensus         6 ~~ywCh~C~r~v~~~~~~-~~CP~C~~gFvEE~   37 (309)
                      ..+||..|...+...... ..||.|++..++=+
T Consensus        70 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~  102 (117)
T PRK00564         70 VELECKDCSHVFKPNALDYGVCEKCHSKNVIIT  102 (117)
T ss_pred             CEEEhhhCCCccccCCccCCcCcCCCCCceEEe
Confidence            578999999887765433 45999999877654

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

Probab=89.12  E-value=0.41  Score=32.20  Aligned_cols=32  Identities=28%  Similarity=0.533  Sum_probs=26.2

Q ss_pred             CceecccCCCceeecC--CCccCCCCCCCceEEe
Q 021640            6 NTHWCYRCRRPVRLQG--EDAVCLYCSGGFVQEL   37 (309)
Q Consensus         6 ~~ywCh~C~r~v~~~~--~~~~CP~C~~gFvEE~   37 (309)
                      ..|-|-.|...+....  ..+.||+|++-++...
T Consensus         2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~   35 (46)
T PRK00398          2 AEYKCARCGREVELDEYGTGVRCPYCGYRILFKE   35 (46)
T ss_pred             CEEECCCCCCEEEECCCCCceECCCCCCeEEEcc
Confidence            4688999999998766  3689999999888544

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

Probab=89.07  E-value=0.15  Score=48.01  Aligned_cols=43  Identities=23%  Similarity=0.724  Sum_probs=29.6

Q ss_pred             ccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccc
Q 021640          183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL  229 (309)
Q Consensus       183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l  229 (309)
                      -.|--|-..+.  -.-+.+||+|+||.+|-..  ...+.||.|-..|
T Consensus        91 HfCd~Cd~PI~--IYGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen   91 HFCDRCDFPIA--IYGRMIPCKHVFCLECARS--DSDKICPLCDDRV  133 (389)
T ss_pred             EeecccCCcce--eeecccccchhhhhhhhhc--CccccCcCcccHH
Confidence            35666754433  3457889999999999643  3456899996443

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

Probab=88.97  E-value=0.2  Score=47.45  Aligned_cols=42  Identities=31%  Similarity=0.706  Sum_probs=33.4

Q ss_pred             cccccccccccccCCceEEccc--cceeccccchhhhccCCCcCccccccc
Q 021640          182 DSHCPVCQDKFELGSEARQMPC--NHIYHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC--~H~fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      -.+|+||.+.+..+    .+.|  ||+.|..|-.   +..+.||.||.++.
T Consensus        48 lleCPvC~~~l~~P----i~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   48 LLDCPVCFNPLSPP----IFQCDNGHLACSSCRT---KVSNKCPTCRLPIG   91 (299)
T ss_pred             hccCchhhccCccc----ceecCCCcEehhhhhh---hhcccCCccccccc
Confidence            46899999998765    5667  6999999865   35678999998875

>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=88.84  E-value=0.25  Score=29.46  Aligned_cols=23  Identities=26%  Similarity=0.545  Sum_probs=18.9

Q ss_pred             cccCCCceeecCCCccCCCCCCCce
Q 021640           10 CYRCRRPVRLQGEDAVCLYCSGGFV   34 (309)
Q Consensus        10 Ch~C~r~v~~~~~~~~CP~C~~gFv   34 (309)
                      |-.|...|..  ...+||+|+..|.
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            7789998844  5789999999885

Several members are annotated as putative helicases.

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

Probab=88.72  E-value=0.24  Score=28.93  Aligned_cols=21  Identities=29%  Similarity=0.732  Sum_probs=17.3

Q ss_pred             cccCCCceeecC--CCccCCCCC
Q 021640           10 CYRCRRPVRLQG--EDAVCLYCS   30 (309)
Q Consensus        10 Ch~C~r~v~~~~--~~~~CP~C~   30 (309)
                      |..|++.|....  -.+.||.|+
T Consensus         1 C~sC~~~i~~r~~~v~f~CPnCG   23 (24)
T PF07754_consen    1 CTSCGRPIAPREQAVPFPCPNCG   23 (24)
T ss_pred             CccCCCcccCcccCceEeCCCCC
Confidence            788999997765  457999997

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

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=87.88  E-value=0.4  Score=40.03  Aligned_cols=32  Identities=16%  Similarity=0.244  Sum_probs=24.3

Q ss_pred             CceecccCCCceeec---------------------CCCccCCCCCCCceEEe
Q 021640            6 NTHWCYRCRRPVRLQ---------------------GEDAVCLYCSGGFVQEL   37 (309)
Q Consensus         6 ~~ywCh~C~r~v~~~---------------------~~~~~CP~C~~gFvEE~   37 (309)
                      ..|||..|.......                     ...+.||.|++.-++=+
T Consensus        69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~  121 (135)
T PRK03824         69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIV  121 (135)
T ss_pred             eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEe
Confidence            679999999887765                     23467999998766544

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

Probab=87.60  E-value=0.11  Score=54.33  Aligned_cols=51  Identities=25%  Similarity=0.544  Sum_probs=41.1

Q ss_pred             ccccccccccccCCceEEccccceeccccchhhhccCC--CcCcccccccCCCCCCC
Q 021640          183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN--SCPVCRQELPLQGSSSS  237 (309)
Q Consensus       183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~--sCP~CR~~l~~~~~~~~  237 (309)
                      ..|.||++    .+.+...+|+|.||..|+..-+....  .||+||..+..+.....
T Consensus       455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~s~  507 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLLSA  507 (674)
T ss_pred             cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHhhc
Confidence            68999998    36778889999999999988887543  49999988866665543

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

Probab=86.59  E-value=0.26  Score=46.17  Aligned_cols=42  Identities=29%  Similarity=0.774  Sum_probs=32.8

Q ss_pred             ccccccccccccCCceEEcc-ccceeccccchhhhc-cCCCcCcccc
Q 021640          183 SHCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLV-QHNSCPVCRQ  227 (309)
Q Consensus       183 ~~C~IC~~~~~~~~~~~~lp-C~H~fh~~Ci~~Wl~-~~~sCP~CR~  227 (309)
                      +.|+.|...+...   .+++ |+|.||..||..-|. ....||.|..
T Consensus       275 LkCplc~~Llrnp---~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRNP---MKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhCc---ccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            6799998877543   4455 899999999987665 4567999954

>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=86.23  E-value=0.42  Score=40.89  Aligned_cols=33  Identities=27%  Similarity=0.674  Sum_probs=22.1

Q ss_pred             cccccccccccccCCceEEcccc-------------ceeccccchhhhc
Q 021640          182 DSHCPVCQDKFELGSEARQMPCN-------------HIYHSDCIVPWLV  217 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~-------------H~fh~~Ci~~Wl~  217 (309)
                      +..|+||+|--   ..+++|-|.             -.-|..||+++-+
T Consensus         2 d~~CpICme~P---HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    2 DVTCPICMEHP---HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CccCceeccCC---CceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence            46899999653   556666653             2347789887654

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.

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

Probab=86.04  E-value=0.36  Score=49.38  Aligned_cols=51  Identities=27%  Similarity=0.746  Sum_probs=41.7

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCCCCCCc
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSSR  238 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~~~~~  238 (309)
                      ....|.||+++.    ..+..+|.   |..|+.+|+..+.+||+|++.+..++.....
T Consensus       478 ~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~~~~~  528 (543)
T KOG0802|consen  478 PNDVCAICYQEM----SARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDDFLSKN  528 (543)
T ss_pred             ccCcchHHHHHH----Hhcccccc---chhHHHhhhhhccccCCCchhhhcccccCcc
Confidence            457899999987    44677788   9999999999999999999988766655443

>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional

Probab=85.54  E-value=0.52  Score=38.80  Aligned_cols=31  Identities=16%  Similarity=0.257  Sum_probs=22.8

Q ss_pred             CceecccCCCceeecCC-------CccCCCCCCCceEEe
Q 021640            6 NTHWCYRCRRPVRLQGE-------DAVCLYCSGGFVQEL   37 (309)
Q Consensus         6 ~~ywCh~C~r~v~~~~~-------~~~CP~C~~gFvEE~   37 (309)
                      ..+|| .|.....+...       ...||.|++.-++=+
T Consensus        69 ~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~  106 (124)
T PRK00762         69 VEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHIL  106 (124)
T ss_pred             eeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEe
Confidence            57899 99988665421       256999998877655

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

Probab=85.16  E-value=0.31  Score=51.19  Aligned_cols=52  Identities=19%  Similarity=0.648  Sum_probs=38.4

Q ss_pred             cccccccccccccCCceEEcccc-----ceeccccchhhhccCC--CcCcccccccCCCC
Q 021640          182 DSHCPVCQDKFELGSEARQMPCN-----HIYHSDCIVPWLVQHN--SCPVCRQELPLQGS  234 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~-----H~fh~~Ci~~Wl~~~~--sCP~CR~~l~~~~~  234 (309)
                      +..|.||..+-.. +....-||+     .+.|.+|+.+|+.-+.  .|-+|+.++.-++-
T Consensus        12 ~~~CRICr~e~~~-d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~I   70 (1175)
T COG5183          12 KRSCRICRTEDIR-DDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDI   70 (1175)
T ss_pred             chhceeecCCCCC-CCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeee
Confidence            4689999987433 445556776     4689999999998554  49999988755443

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=85.12  E-value=0.58  Score=40.95  Aligned_cols=32  Identities=13%  Similarity=0.274  Sum_probs=25.6

Q ss_pred             CCceecccCCCceeecC---CCccCCCCCCCceEE
Q 021640            5 RNTHWCYRCRRPVRLQG---EDAVCLYCSGGFVQE   36 (309)
Q Consensus         5 ~~~ywCh~C~r~v~~~~---~~~~CP~C~~gFvEE   36 (309)
                      ...|.|-.|...+...-   .++.||.|++-++|.
T Consensus       115 ~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~~  149 (178)
T PRK06266        115 NMFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEEY  149 (178)
T ss_pred             CCEEECCCCCcEEeHHHHhhcCCcCCCCCCCCeec
Confidence            37899999998886542   579999999987763

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

Probab=84.98  E-value=0.26  Score=52.20  Aligned_cols=38  Identities=24%  Similarity=0.680  Sum_probs=30.1

Q ss_pred             cccccccccccccccccCCceEEccccceeccccchhhh
Q 021640          178 HLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWL  216 (309)
Q Consensus       178 ~~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl  216 (309)
                      .++..+.|.+|...+.. ..-.+.||+|.||++||.+-.
T Consensus       813 v~ep~d~C~~C~~~ll~-~pF~vf~CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  813 VLEPQDSCDHCGRPLLI-KPFYVFPCGHCFHRDCLIRHV  850 (911)
T ss_pred             EecCccchHHhcchhhc-CcceeeeccchHHHHHHHHHH
Confidence            34567899999988754 366788899999999997654

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

Probab=84.61  E-value=0.45  Score=46.20  Aligned_cols=49  Identities=20%  Similarity=0.430  Sum_probs=40.5

Q ss_pred             ccccccccccccccccCCceEEccccceeccccchhhhccCC---CcCcccc
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN---SCPVCRQ  227 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~---sCP~CR~  227 (309)
                      ..+.-.|+|=.+.-.....+..|.|||+..++-|.+..+.+.   .||+|=.
T Consensus       331 fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~  382 (394)
T KOG2817|consen  331 FHSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPV  382 (394)
T ss_pred             ccceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence            345678999998888878899999999999999999776554   4999943

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

Probab=84.57  E-value=0.32  Score=50.71  Aligned_cols=40  Identities=28%  Similarity=0.785  Sum_probs=30.1

Q ss_pred             cccccccccccCCceEEccccceeccccchhhhccCCCcCc
Q 021640          184 HCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPV  224 (309)
Q Consensus       184 ~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~  224 (309)
                      .|+||--.+ .+.......|+|+-|.+|...|++....||.
T Consensus      1030 ~C~~C~l~V-~gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1030 QCAICHLAV-RGSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             eeeeEeeEe-eccchhhccccccccHHHHHHHHhcCCcCCC
Confidence            455554332 3445566779999999999999999999985

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=84.14  E-value=0.58  Score=26.98  Aligned_cols=23  Identities=17%  Similarity=0.621  Sum_probs=18.2

Q ss_pred             ecccCCCceeecCCCccCCCCCCCc
Q 021640            9 WCYRCRRPVRLQGEDAVCLYCSGGF   33 (309)
Q Consensus         9 wCh~C~r~v~~~~~~~~CP~C~~gF   33 (309)
                      ||.+|-.+|..  ...+||.|+..|
T Consensus         1 ~Cp~CG~~~~~--~~~fC~~CG~~l   23 (23)
T PF13240_consen    1 YCPNCGAEIED--DAKFCPNCGTPL   23 (23)
T ss_pred             CCcccCCCCCC--cCcchhhhCCcC
Confidence            68999999853  577899998653

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

Probab=83.96  E-value=0.72  Score=41.39  Aligned_cols=39  Identities=26%  Similarity=0.737  Sum_probs=27.9

Q ss_pred             cccccccccccCCceEEccccce-eccccchhhhccCCCcCcccccc
Q 021640          184 HCPVCQDKFELGSEARQMPCNHI-YHSDCIVPWLVQHNSCPVCRQEL  229 (309)
Q Consensus       184 ~C~IC~~~~~~~~~~~~lpC~H~-fh~~Ci~~Wl~~~~sCP~CR~~l  229 (309)
                      .|-+|.+.   ...|..+||.|+ +|..|=..    -..||+|+...
T Consensus       160 ~Cr~C~~~---~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~  199 (207)
T KOG1100|consen  160 SCRKCGER---EATVLLLPCRHLCLCGICDES----LRICPICRSPK  199 (207)
T ss_pred             cceecCcC---CceEEeecccceEeccccccc----CccCCCCcChh
Confidence            38888644   456899999987 66778543    34599998644

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

Probab=83.75  E-value=0.36  Score=53.15  Aligned_cols=44  Identities=25%  Similarity=0.637  Sum_probs=37.0

Q ss_pred             cccccccccccccCCceEEccccceeccccchhhhccCCCcCcccc
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQ  227 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~  227 (309)
                      -..|.||++.+...  ..+.-|+|.++..|+..|+..+..||+|+.
T Consensus      1153 ~~~c~ic~dil~~~--~~I~~cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1153 HFVCEICLDILRNQ--GGIAGCGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred             ccchHHHHHHHHhc--CCeeeechhHhhhHHHHHHHHhccCcchhh
Confidence            35899999998632  245559999999999999999999999973

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=83.14  E-value=0.7  Score=39.62  Aligned_cols=32  Identities=13%  Similarity=0.170  Sum_probs=24.6

Q ss_pred             CCceecccCCCceeecC---CCccCCCCCCCceEEe
Q 021640            5 RNTHWCYRCRRPVRLQG---EDAVCLYCSGGFVQEL   37 (309)
Q Consensus         5 ~~~ywCh~C~r~v~~~~---~~~~CP~C~~gFvEE~   37 (309)
                      ...|.|-.|...+...-   .+++||.|++-+ +++
T Consensus       107 ~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L-~~~  141 (158)
T TIGR00373       107 NMFFICPNMCVRFTFNEAMELNFTCPRCGAML-DYL  141 (158)
T ss_pred             CCeEECCCCCcEeeHHHHHHcCCcCCCCCCEe-eec
Confidence            47899999998876532   579999999874 444

This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.

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

Probab=82.64  E-value=0.74  Score=31.70  Aligned_cols=33  Identities=27%  Similarity=0.530  Sum_probs=25.7

Q ss_pred             CCceecccCCCceeecC--CCccCCCCCCCceEEe
Q 021640            5 RNTHWCYRCRRPVRLQG--EDAVCLYCSGGFVQEL   37 (309)
Q Consensus         5 ~~~ywCh~C~r~v~~~~--~~~~CP~C~~gFvEE~   37 (309)
                      +..|-|-.|.+.|....  .++.||+|++-.+-..
T Consensus         4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~K~   38 (49)
T COG1996           4 MMEYKCARCGREVELDQETRGIRCPYCGSRILVKE   38 (49)
T ss_pred             eEEEEhhhcCCeeehhhccCceeCCCCCcEEEEec
Confidence            46799999999997432  6789999998765443

>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=81.72  E-value=1.6  Score=27.25  Aligned_cols=27  Identities=22%  Similarity=0.482  Sum_probs=20.6

Q ss_pred             eecccCCCceeecC-CCccCCCCCCCce
Q 021640            8 HWCYRCRRPVRLQG-EDAVCLYCSGGFV   34 (309)
Q Consensus         8 ywCh~C~r~v~~~~-~~~~CP~C~~gFv   34 (309)
                      |-|-.|...|.+.. +.+.||+|+.-.+
T Consensus         1 Y~C~~Cg~~~~~~~~~~irC~~CG~RIl   28 (32)
T PF03604_consen    1 YICGECGAEVELKPGDPIRCPECGHRIL   28 (32)
T ss_dssp             EBESSSSSSE-BSTSSTSSBSSSS-SEE
T ss_pred             CCCCcCCCeeEcCCCCcEECCcCCCeEE
Confidence            67999999999876 5578999998654

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 ....

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=81.69  E-value=1.3  Score=29.74  Aligned_cols=31  Identities=16%  Similarity=0.351  Sum_probs=25.9

Q ss_pred             ceecccCCCceeecC-CCccCCCCCCCceEEe
Q 021640            7 THWCYRCRRPVRLQG-EDAVCLYCSGGFVQEL   37 (309)
Q Consensus         7 ~ywCh~C~r~v~~~~-~~~~CP~C~~gFvEE~   37 (309)
                      .|-|-.|..++.+.. ..+.||+|++-.+--.
T Consensus         2 ~Y~C~~Cg~~~~~~~~~~irC~~CG~rIlyK~   33 (44)
T smart00659        2 IYICGECGRENEIKSKDVVRCRECGYRILYKK   33 (44)
T ss_pred             EEECCCCCCEeecCCCCceECCCCCceEEEEe
Confidence            488999999999875 5689999999877554

present in RNA polymerase I, II and III

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

Probab=81.46  E-value=0.5  Score=44.20  Aligned_cols=51  Identities=20%  Similarity=0.569  Sum_probs=37.1

Q ss_pred             cccccccccccccCCc-eEEcccc-----ceeccccchhhhcc--CCCcCcccccccCC
Q 021640          182 DSHCPVCQDKFELGSE-ARQMPCN-----HIYHSDCIVPWLVQ--HNSCPVCRQELPLQ  232 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~-~~~lpC~-----H~fh~~Ci~~Wl~~--~~sCP~CR~~l~~~  232 (309)
                      ...|-||.++...... ....||.     +..|..|+..|+..  ...|.+|.......
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~  136 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV  136 (323)
T ss_pred             CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence            4689999987643221 4677764     67899999999984  45699998765443

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

Probab=80.94  E-value=0.84  Score=32.91  Aligned_cols=27  Identities=22%  Similarity=0.626  Sum_probs=20.3

Q ss_pred             ecccCCCceeecCCCccCCCCCCC-ceEEe
Q 021640            9 WCYRCRRPVRLQGEDAVCLYCSGG-FVQEL   37 (309)
Q Consensus         9 wCh~C~r~v~~~~~~~~CP~C~~g-FvEE~   37 (309)
                      =|+.|.+-+..  +.-+||.|++. |.||-
T Consensus         6 AC~~Ck~l~~~--d~e~CP~Cgs~~~te~W   33 (64)
T COG2093           6 ACKNCKRLTPE--DTEICPVCGSTDLTEEW   33 (64)
T ss_pred             HHhhccccCCC--CCccCCCCCCcccchhh
Confidence            38999876632  34589999998 87775

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	309
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		1e-15
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		5e-12
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		2e-07
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		7e-06
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		2e-05
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		7e-04

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

Iteration: 1
 Score = 80.1 bits (196), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 31/55 (56%), Positives = 41/55 (74%)
Query: 175 TQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL 229
           T+ H+ S   CPVC++ + LG   RQ+PCNH++H  CIVPWL QH+SCPVCR+ L
Sbjct: 8   TEEHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSL 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 = 68.2 bits (165), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 159 PPAARSAIDAMPTVRITQRH--LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWL 216
           PPA++ +IDA+P + +T+ H  +  +  CP+C  ++  G  A ++PC+H +H  C+  WL
Sbjct: 15  PPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWL 74
Query: 217 VQHNSCPVCRQELP 230
            +  +CPVCR   P
Sbjct: 75  QKSGTCPVCRCMFP 88

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 16/45 (35%), Positives = 28/45 (62%)
Query: 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL 229
           C +C    E G + R++PC H++H  C+  WL+ +  CP+CR ++
Sbjct: 17  CTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDI 61

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 169 MPTVRIT-QRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQ 227
           +P+ R     H    + C VC   FE     R +PCNH +H+ C+  WL  + +CP+CR 
Sbjct: 9   LPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRA 68
Query: 228 E 228
           +
Sbjct: 69  D 69

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/43 (46%), Positives = 29/43 (67%), Gaps = 1/43 (2%)
Query: 185 CPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQHNSCPVCR 226
           C VC  + E G EAR +P C H +H++C+  WL  H++CP+CR
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVC 225
           C VC + F+   E    PC H +H  C++ WL     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	309
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	3e-42
2ect_A	78	Ring finger protein 126; metal binding protein, st	5e-31
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	9e-26
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	2e-24
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	7e-24
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	6e-20
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	3e-17
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	1e-16
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	7e-16
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	6e-15
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	9e-14
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	4e-13
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	2e-12
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	3e-10
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	3e-10
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	3e-10
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	9e-10
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	2e-09
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	3e-09
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	4e-09
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	5e-09
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	4e-08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	6e-08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-06
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	6e-08
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	3e-07
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	1e-06
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	1e-06
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	1e-06
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	3e-06
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	3e-06
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	4e-06
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	4e-06
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	6e-06
1z6u_A	150	NP95-like ring finger protein isoform B; structura	8e-06
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	9e-06
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	1e-05
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	1e-05
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	2e-05
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	2e-05
3nw0_A	238	Non-structural maintenance of chromosomes element	2e-05
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	4e-05
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	6e-05
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	1e-04
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	2e-04
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	3e-04
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	4e-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 =  139 bits (353), Expect = 3e-42
 Identities = 27/90 (30%), Positives = 46/90 (51%), Gaps = 4/90 (4%)

Query: 143 LEELFEQLSANGRRGPPPAARSAIDAMPTVRITQRHLRSDS--HCPVCQDKFELGSEARQ 200
           +         +     PPA++ +IDA+P + +T+ H        CP+C  ++  G  A +
Sbjct: 1   MGHHHHH--HSHMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATE 58

Query: 201 MPCNHIYHSDCIVPWLVQHNSCPVCRQELP 230
           +PC+H +H  C+  WL +  +CPVCR   P
Sbjct: 59  LPCHHYFHKPCVSIWLQKSGTCPVCRCMFP 88

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

 Score =  110 bits (277), Expect = 5e-31
 Identities = 33/71 (46%), Positives = 48/71 (67%)

Query: 175 TQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGS 234
           T+ H+ S   CPVC++ + LG   RQ+PCNH++H  CIVPWL QH+SCPVCR+ L  Q +
Sbjct: 8   TEEHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNT 67

Query: 235 SSSRIHQSSSG 245
           +++    +  G
Sbjct: 68  ATNPPGLTGVG 78

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

 Score = 96.6 bits (241), Expect = 9e-26
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 161 AARSAIDAMPTVRIT-QRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH 219
            +  +   +P+ R     H    + C VC   FE     R +PCNH +H+ C+  WL  +
Sbjct: 1   GSSGSSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKAN 60

Query: 220 NSCPVCRQEL 229
            +CP+CR + 
Sbjct: 61  RTCPICRADS 70

>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 = 93.2 bits (232), Expect = 2e-24
 Identities = 19/57 (33%), Positives = 33/57 (57%)

Query: 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSS 237
           ++  C +C    E G + R++PC H++H  C+  WL+ +  CP+CR ++  Q  S S
Sbjct: 13  TEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQLPSES 69

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

 Score = 91.8 bits (228), Expect = 7e-24
 Identities = 20/71 (28%), Positives = 28/71 (39%), Gaps = 4/71 (5%)

Query: 175 TQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGS 234
             + L     C VC + F+   E    PC H +H  C++ WL     CP+C   +     
Sbjct: 8   KVKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQ 67

Query: 235 SSSRIHQSSSG 245
            S      SSG
Sbjct: 68  LSG----PSSG 74

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

 Score = 80.9 bits (200), Expect = 6e-20
 Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 4/63 (6%)

Query: 175 TQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGS 234
             + L  +  C +C D          +PC H +   CI  W  +H +CP+CR ++     
Sbjct: 8   RVKQLTDEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANE 63

Query: 235 SSS 237
           SS 
Sbjct: 64  SSG 66

>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 = 73.1 bits (180), Expect = 3e-17
 Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 1/47 (2%)

Query: 181 SDSHCPVCQDKFELGSE-ARQMPCNHIYHSDCIVPWLVQHNSCPVCR 226
             S CP+C +        A  +PC H+ H  C    L +   CP+C 
Sbjct: 4   GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCS 50

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

 Score = 71.8 bits (177), Expect = 1e-16
 Identities = 20/48 (41%), Positives = 31/48 (64%), Gaps = 1/48 (2%)

Query: 185 CPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQHNSCPVCRQELPL 231
           C VC  + E G EAR +P C H +H++C+  WL  H++CP+CR  + +
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV 55

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

 Score = 70.1 bits (172), Expect = 7e-16
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 2/49 (4%)

Query: 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL 229
               CP+C +     + +  +PC H +   CI  W+ Q+ +CP+C+  +
Sbjct: 4   VAERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPV 50

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

 Score = 68.0 bits (166), Expect = 6e-15
 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 182 DSHCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQHNSCPVCRQELPLQ 232
              C  CQ + +          CNH +H+ C+  W+ Q+N CP+C+Q+  +Q
Sbjct: 26  MDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQ 77

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

 Score = 64.2 bits (156), Expect = 9e-14
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 4/49 (8%)

Query: 185 CPVCQDKFE----LGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL 229
           CP+C D +      G       C H++ S C+   L   N+CP CR+++
Sbjct: 18  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66

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

 Score = 62.5 bits (152), Expect = 4e-13
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 4/49 (8%)

Query: 185 CPVCQDKFELGSEARQM----PCNHIYHSDCIVPWLVQHNSCPVCRQEL 229
           CP+C D +    +  ++     C H++ S C+   L   N+CP CR+++
Sbjct: 6   CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54

>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 = 61.0 bits (148), Expect = 2e-12
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 4/49 (8%)

Query: 185 CPVCQDKFELGSEARQM----PCNHIYHSDCIVPWLVQHNSCPVCRQEL 229
           CP+C D +    +  ++     C H++ S C+   L   N+CP CR+++
Sbjct: 13  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61

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

 Score = 54.8 bits (132), Expect = 3e-10
 Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 3/52 (5%)

Query: 179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP 230
             +   C +C            +PC H++   C+         C +CRQE+P
Sbjct: 12  SLTVPECAICLQTCV---HPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIP 60

>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 = 55.7 bits (134), Expect = 3e-10
 Identities = 23/85 (27%), Positives = 34/85 (40%), Gaps = 5/85 (5%)

Query: 179 LRSDSHCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLV-QHNSCPVCRQELPLQGSSS 236
           +     C +C +K     +AR  P C+ +    CI  WL  Q   CP CR  L L+   +
Sbjct: 19  IAEVFRCFICMEKLR---DARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVN 75

Query: 237 SRIHQSSSGQSRSTSFGSNGSGREN 261
            R  +  + Q  +    S     EN
Sbjct: 76  CRWAEEVTQQLDTLQLCSLTKHEEN 100

>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 = 3e-10
 Identities = 18/65 (27%), Positives = 24/65 (36%), Gaps = 8/65 (12%)

Query: 177 RHLRSDSHCPVCQDKFELGSEARQM-PCNHIYHSDCIVPWLVQHNSCPVCRQEL----PL 231
             L     C +C+       +A  +  C H +   CIV      N CP C   +    PL
Sbjct: 10  SELTPYILCSICKGYL---IDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPL 66

Query: 232 QGSSS 236
            G SS
Sbjct: 67  SGPSS 71

>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 = 54.4 bits (131), Expect = 9e-10
 Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 2/59 (3%)

Query: 171 TVRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL 229
           T RI    L     C +C   F        + C H +   CIV +L     CP+C  ++
Sbjct: 4   TTRIKITELNPHLMCVLCGGYFI--DATTIIECLHSFCKTCIVRYLETSKYCPICDVQV 60

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

 Score = 53.2 bits (128), Expect = 2e-09
 Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 4/61 (6%)

Query: 170 PTVRITQRHLRSDSHCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQHNSCPVCRQE 228
           P      + +     C +C + F     A  +P C+H Y S CI  +L     CP C   
Sbjct: 10  PPGLAVMKTIDDLLRCGICFEYFN---IAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVT 66

Query: 229 L 229
           +
Sbjct: 67  V 67

>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 = 52.9 bits (126), Expect = 3e-09
 Identities = 14/50 (28%), Positives = 17/50 (34%), Gaps = 1/50 (2%)

Query: 184 HCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQHNSCPVCRQELPLQ 232
            C   Q              CNH +H  CI  WL     CP+  +E   Q
Sbjct: 53  ECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQ 102

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

 Score = 53.9 bits (129), Expect = 4e-09
 Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 3/52 (5%)

Query: 179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP 230
           L ++  C +C + F    EA  + C H + S CI  W+ +   CP+CR+++ 
Sbjct: 61  LENELQCIICSEYF---IEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIK 109

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

 Score = 51.4 bits (123), Expect = 5e-09
 Identities = 9/44 (20%), Positives = 15/44 (34%), Gaps = 3/44 (6%)

Query: 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQE 228
           C +C+  F+         C H +   C +        C +C Q 
Sbjct: 18  CFICRQAFQ---NPVVTKCRHYFCESCALEHFRATPRCYICDQP 58

>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 = 50.2 bits (119), Expect = 4e-08
 Identities = 14/50 (28%), Positives = 17/50 (34%), Gaps = 1/50 (2%)

Query: 184 HCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQHNSCPVCRQELPLQ 232
            C   Q              CNH +H  CI  WL     CP+  +E   Q
Sbjct: 64  ECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQ 113

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

 Score = 49.8 bits (118), Expect = 6e-08
 Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 4/50 (8%)

Query: 185 CPVCQDKFELGSEARQ----MPCNHIYHSDCIVPWLVQHNSCPVCRQELP 230
           CP+C D +    +  +      C H++ S C+   L   N+CP CR+++ 
Sbjct: 10  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN 59

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

 Score = 45.5 bits (107), Expect = 2e-06
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 4/49 (8%)

Query: 185 CPVCQDKF----ELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL 229
           CP+C D +    + G       C H++ S C+   L   N+CP CR+++
Sbjct: 75  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 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 = 52.5 bits (125), Expect = 6e-08
 Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 4/51 (7%)

Query: 180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV-QHNSCPVCRQEL 229
            +   C +C +      + +  PC H+  + C+  W   +   CP CR E+
Sbjct: 330 STFQLCKICAEND---KDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEI 377

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

 Score = 45.9 bits (109), Expect = 3e-07
 Identities = 9/46 (19%), Positives = 16/46 (34%), Gaps = 4/46 (8%)

Query: 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN-SCPVCRQEL 229
           C  C          +Q  C H +   C+   L   +  C  C++ +
Sbjct: 18  CEKCHLVLC---SPKQTECGHRFCESCMAALLSSSSPKCTACQESI 60

>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 = 44.5 bits (105), Expect = 1e-06
 Identities = 10/48 (20%), Positives = 14/48 (29%), Gaps = 4/48 (8%)

Query: 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNS--CPVCRQELP 230
           C +C      G       C    H  C+  +   +    CP C    P
Sbjct: 18  CNICHSLLIQGQSCET--CGIRMHLPCVAKYFQSNAEPRCPHCNDYWP 63

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

 Score = 46.1 bits (109), Expect = 1e-06
 Identities = 17/88 (19%), Positives = 29/88 (32%), Gaps = 12/88 (13%)

Query: 144 EELFEQLSANGRRGPPPAARSAIDAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMPC 203
            +L+ ++ A+ +  P              ++    +     C  CQ+            C
Sbjct: 22  AKLWNEVLASLKDRPASG--------SPFQLFLSKVEETFQCICCQELVF---RPITTVC 70

Query: 204 NHIYHSDCIVPWL-VQHNSCPVCRQELP 230
            H    DC+      Q  SCP CR +L 
Sbjct: 71  QHNVCKDCLDRSFRAQVFSCPACRYDLG 98

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

 Score = 43.9 bits (104), Expect = 1e-06
 Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 6/47 (12%)

Query: 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPL 231
           C  CQ + +     + +PC H   S C+    +Q   CP+C+   PL
Sbjct: 9   CQQCQAEAK---CPKLLPCLHTLCSGCLEASGMQ---CPICQAPWPL 49

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

 Score = 44.5 bits (105), Expect = 3e-06
 Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 4/61 (6%)

Query: 179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN-SCPVCRQELPLQGSSSS 237
             S+  C +C +      E   +PCNH     C    + + +  CP CR+ +       +
Sbjct: 12  SLSECQCGICMEILV---EPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSSWTRYHT 68

Query: 238 R 238
           R
Sbjct: 69  R 69

>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 = 44.4 bits (104), Expect = 3e-06
 Identities = 16/93 (17%), Positives = 27/93 (29%), Gaps = 24/93 (25%)

Query: 154 GRRGPPPAARSAIDAMPTVRITQRHLRSDSHCPVCQDKFELGSEA--------------- 198
           G  G        I         +  +  +  C +C +K  + S                 
Sbjct: 1   GSSGSSGEPEQVIR----KYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVG 56

Query: 199 RQMPCNHIYHSDCIVPWLVQHN-----SCPVCR 226
           R   C+H +H  C++      N      CP C+
Sbjct: 57  RLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCK 89

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

 Score = 44.4 bits (105), Expect = 4e-06
 Identities = 15/56 (26%), Positives = 20/56 (35%), Gaps = 4/56 (7%)

Query: 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNS-CPVCRQELPLQGSSSSRI 239
           CP+C        EA Q PC H +   CI+  +      CPV  + L          
Sbjct: 21  CPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNF 73

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

 Score = 43.2 bits (102), Expect = 4e-06
 Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 6/60 (10%)

Query: 175 TQRHLRSDSHCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQHN--SCPVCRQELPL 231
               +  +  C +C+D      +A  +P C + Y  +CI   L++ +  +CP C Q    
Sbjct: 8   EDDPIPDELLCLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS 64

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

 Score = 42.8 bits (100), Expect = 6e-06
 Identities = 12/53 (22%), Positives = 17/53 (32%), Gaps = 2/53 (3%)

Query: 180 RSDSHCPVCQDKFEL-GSEARQMPCNHIYHSDCIVPWLVQHN-SCPVCRQELP 230
                CP+C +  E+         C +     C        N  CP CR+  P
Sbjct: 9   EDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYP 61

>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 = 44.2 bits (104), Expect = 8e-06
 Identities = 15/55 (27%), Positives = 20/55 (36%), Gaps = 4/55 (7%)

Query: 177 RHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWL-VQHNSCPVCRQELP 230
           + L     C  CQ+      +     C H    DC+      Q  SCP CR +L 
Sbjct: 73  KKLEQSFMCVCCQELV---YQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLG 124

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

 Score = 45.6 bits (107), Expect = 9e-06
 Identities = 13/64 (20%), Positives = 20/64 (31%), Gaps = 16/64 (25%)

Query: 182 DSHCPVCQDKFELGSEARQM-----PCNHIYHSDCIVPWL-----------VQHNSCPVC 225
           +  C +C      G E   +      C    H+ C+  W            V    CP C
Sbjct: 308 ELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFC 367

Query: 226 RQEL 229
           + +L
Sbjct: 368 KAKL 371

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

 Score = 44.3 bits (104), Expect = 1e-05
 Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 4/54 (7%)

Query: 178 HLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNS-CPVCRQELP 230
            L S   CP+C        EA Q PC H +   CI+  +      CPV  + L 
Sbjct: 14  PLESKYECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILL 64

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

 Score = 42.1 bits (99), Expect = 1e-05
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 6/56 (10%)

Query: 179 LRSDSHCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQHN--SCPVCRQELPL 231
           +  +  C +C+D      +A  +P C + Y  +CI   L++ +  +CP C Q    
Sbjct: 10  IPDELLCLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS 62

>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 = 42.2 bits (99), Expect = 2e-05
 Identities = 16/67 (23%), Positives = 23/67 (34%), Gaps = 6/67 (8%)

Query: 167 DAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQHNSCPVC 225
            A    R     L     C  C +      E   +  C HI+ S+C+   +     CPVC
Sbjct: 7   GAWAHSRAALDRLEKLLRCSRCTNIL---REPVCLGGCEHIFCSNCVSDCI--GTGCPVC 61

Query: 226 RQELPLQ 232
                +Q
Sbjct: 62  YTPAWIQ 68

>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 = 42.2 bits (99), Expect = 2e-05
 Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 4/53 (7%)

Query: 178 HLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNS-CPVCRQEL 229
           H      C +C+       +  +  C H++   CI+  L    S CP CR   
Sbjct: 19  HFVKSISCQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPC 68

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

 Score = 44.0 bits (103), Expect = 2e-05
 Identities = 12/70 (17%), Positives = 22/70 (31%), Gaps = 6/70 (8%)

Query: 163 RSAIDAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNS- 221
           R+ ++      I + +  +   C +C      G       C    H  C+  +   +   
Sbjct: 163 RAILEMEQY--IRETYPDAVKICNICHSLLIQGQSCET--CGIRMHLPCVAKYFQSNAEP 218

Query: 222 -CPVCRQELP 230
            CP C    P
Sbjct: 219 RCPHCNDYWP 228

>3htk_C E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae} Length = 267

 Score = 43.4 bits (101), Expect = 4e-05
 Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 6/52 (11%)

Query: 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNS--CPV--CRQELPLQ 232
           CP+    +E  +      CNH++  D I  +L  + +  CP   C Q + ++
Sbjct: 184 CPITCKPYE--APLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMR 233

>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 = 41.3 bits (96), Expect = 6e-05
 Identities = 13/53 (24%), Positives = 17/53 (32%), Gaps = 4/53 (7%)

Query: 179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNS-CPVCRQELP 230
           L +   C  C++         Q  C H Y S C+   L      C  C  E  
Sbjct: 28  LEAKYLCSACRNVLR---RPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGI 77

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

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 6/55 (10%)

Query: 179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN---SCPVCRQELP 230
           ++    CP+C +      E     C+HI+   C++  L Q      CP+C+ ++ 
Sbjct: 18  MQKILECPICLELI---KEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDIT 69

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

 Score = 40.7 bits (95), Expect = 2e-04
 Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 5/69 (7%)

Query: 163 RSAIDAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQHN- 220
           + AI     + ++ R L S+  CP+C D  +          C H + +DCI+  L   N 
Sbjct: 35  QEAITDGLEIVVSPRSLHSELMCPICLDMLK---NTMTTKECLHRFCADCIITALRSGNK 91

Query: 221 SCPVCRQEL 229
            CP CR++L
Sbjct: 92  ECPTCRKKL 100

>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 = 37.6 bits (87), Expect = 3e-04
 Identities = 13/51 (25%), Positives = 18/51 (35%), Gaps = 3/51 (5%)

Query: 182 DSHCPVCQDKFELGSEARQM--PCNHIYHSDCIVPWLVQH-NSCPVCRQEL 229
           D  CP C+         + M   C H     C+    V+   +CP C   L
Sbjct: 3   DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 53

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

 Score = 37.8 bits (88), Expect = 4e-04
 Identities = 11/53 (20%), Positives = 18/53 (33%), Gaps = 4/53 (7%)

Query: 185 CPVCQDKFELGSEARQM-PCNHIYHSDCIVPWLVQHN---SCPVCRQELPLQG 233
           CP+C + F       ++  C H     C+   L        CP C +   +  
Sbjct: 18  CPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITS 70

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	309
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.67
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.61
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.52
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	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
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.36
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.35
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.35
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.33
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.31
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.31
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.27
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.27
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.25
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.25
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.25
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.24
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.23
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.2
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.19
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.16
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.14
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.13
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.12
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.1
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.1
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.09
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.08
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.07
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.07
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.06
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.05
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.02
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.02
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.0
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	98.98
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	98.98
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	98.98
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	98.97
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	98.97
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.95
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.93
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.92
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	98.92
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.89
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	98.87
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.83
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.82
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.82
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.82
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	98.8
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.79
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.79
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.75
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.73
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.65
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.53
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.53
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.5
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.5
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.42
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.41
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.36
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.35
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.35
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.26
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.23
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.18
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.16
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	97.8
3nw0_A	238	Non-structural maintenance of chromosomes element	97.73
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	95.61
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	93.04
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	92.1
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	91.98
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	90.23
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	89.98
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	89.57
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	89.22
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	88.17
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	88.03
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	87.92
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	87.38
3a43_A	139	HYPD, hydrogenase nickel incorporation protein HYP	86.74
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	86.3
4ayb_P	48	DNA-directed RNA polymerase; transferase, multi-su	86.21
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	86.19
1we9_A	64	PHD finger family protein; structural genomics, PH	85.65
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	85.16
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	85.03
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	84.28
2yt5_A	66	Metal-response element-binding transcription facto	83.95
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	83.95

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

Probab=99.67  E-value=3.2e-17  Score=126.67  Aligned_cols=77  Identities=35%  Similarity=0.906  Sum_probs=67.9

Q ss_pred             CCCCCCcchhhhhcCCceeeeccc--ccccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccC
Q 021640          155 RRGPPPAARSAIDAMPTVRITQRH--LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPL  231 (309)
Q Consensus       155 ~~~~ppa~~~~i~~lp~~~~~~~~--~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~  231 (309)
                      .....+++++.|++||.+.+....  ...+..|+||++.|..++.++.|+|+|.||..||..||+.+.+||+||+.+..
T Consensus        11 ~~~~~~~s~~~i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           11 MVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFPP   89 (91)
T ss_dssp             SSCCCCCCHHHHHTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTCBCTTTCCBSSC
T ss_pred             CcCCCCCCHHHHHhCCCeeecccccccCCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCCcCcCcCccCCC
Confidence            446778999999999999887654  34567899999999988889999999999999999999999999999998864

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

Probab=99.61  E-value=2e-16  Score=117.51  Aligned_cols=71  Identities=28%  Similarity=0.717  Sum_probs=61.3

Q ss_pred             chhhhhcCCceeeeccc-ccccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCC
Q 021640          162 ARSAIDAMPTVRITQRH-LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQ  232 (309)
Q Consensus       162 ~~~~i~~lp~~~~~~~~-~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~  232 (309)
                      +...|+.||.+++.... ..+...|+||++.|..++.++.|+|+|+||..||.+||+.+.+||+||+.+...
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            45678889998887654 345678999999999988899999999999999999999999999999988653

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

Probab=99.52  E-value=1.3e-14  Score=108.25  Aligned_cols=58  Identities=52%  Similarity=1.225  Sum_probs=51.1

Q ss_pred             ccccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCCCCC
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSS  236 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~~~  236 (309)
                      ......|+||++.|..+..++.|+|+|.||..||..|++.+.+||+||+.+.......
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   69 (78)
T 2ect_A           12 VGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTAT   69 (78)
T ss_dssp             SSSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCCCSCSCC
T ss_pred             CCCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccCCcccCC
Confidence            3456799999999998888899999999999999999999999999999987665543

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

Probab=99.49  E-value=1e-14  Score=101.45  Aligned_cols=51  Identities=39%  Similarity=0.974  Sum_probs=46.7

Q ss_pred             cccccccccccccccCCceEEcc-ccceeccccchhhhccCCCcCccccccc
Q 021640          180 RSDSHCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lp-C~H~fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      +++..|+||++.|..++.+..++ |+|.||..||.+|++.+.+||+||+.+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            45678999999999888889998 9999999999999999999999999875

>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=1.3e-14  Score=105.66  Aligned_cols=55  Identities=31%  Similarity=0.954  Sum_probs=49.0

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGS  234 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~  234 (309)
                      .....|+||++.|..++.++.++|+|.||..||..|+..+.+||+||..|.....
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   66 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQLP   66 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCSCCC
T ss_pred             CCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccCcCC
Confidence            4467899999999888889999999999999999999999999999999876543

>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=105.38  Aligned_cols=54  Identities=28%  Similarity=0.776  Sum_probs=48.5

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG  233 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~  233 (309)
                      .....|+||++.|..+..++.|+|+|.||..||..|++.+.+||+||+.+....
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLA   66 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCSBCTTTCCBCSSCC
T ss_pred             CCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCCcCCCcCccccccc
Confidence            456789999999998888899999999999999999999999999999886543

>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=99.36  E-value=2.7e-13  Score=107.72  Aligned_cols=50  Identities=26%  Similarity=0.614  Sum_probs=43.1

Q ss_pred             ccccccccccccccCC---------------ceEEccccceeccccchhhhccCCCcCccccccc
Q 021640          181 SDSHCPVCQDKFELGS---------------EARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~---------------~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      .+..|+||++.|...-               .++.++|+|.||..||.+||..+.+||+||+++.
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            4578999999987541               3677899999999999999999999999999864

>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=99.35  E-value=2.9e-13  Score=93.88  Aligned_cols=50  Identities=28%  Similarity=0.736  Sum_probs=43.5

Q ss_pred             ccccccccccccccC-CceEEccccceeccccchhhhccCCCcCccccccc
Q 021640          181 SDSHCPVCQDKFELG-SEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~-~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      ....|+||++.|..+ +.++.++|+|.||..||.+|++.+.+||+||+.+.
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            356899999998653 35788999999999999999999999999999874

>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=99.35  E-value=4e-13  Score=107.23  Aligned_cols=52  Identities=23%  Similarity=0.621  Sum_probs=42.6

Q ss_pred             ccccccccccccccCC---------------ceEEccccceeccccchhhh-----ccCCCcCcccccccCC
Q 021640          181 SDSHCPVCQDKFELGS---------------EARQMPCNHIYHSDCIVPWL-----VQHNSCPVCRQELPLQ  232 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~---------------~~~~lpC~H~fh~~Ci~~Wl-----~~~~sCP~CR~~l~~~  232 (309)
                      .+..|+||++.|..+.               .++.++|+|+||..||..||     ..+.+||+||..+...
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            3468999999996543               34578999999999999999     4567899999988654

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

Probab=99.33  E-value=2.1e-13  Score=102.89  Aligned_cols=50  Identities=28%  Similarity=0.734  Sum_probs=41.1

Q ss_pred             cccccccccccc-----------cCCceEEcc-ccceeccccchhhhccCCCcCcccccccC
Q 021640          182 DSHCPVCQDKFE-----------LGSEARQMP-CNHIYHSDCIVPWLVQHNSCPVCRQELPL  231 (309)
Q Consensus       182 ~~~C~IC~~~~~-----------~~~~~~~lp-C~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~  231 (309)
                      +..|+||++.|.           .++.++.++ |+|.||..||.+||+.+++||+||+.+..
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            456888887774           345566666 99999999999999999999999998754

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

Probab=99.31  E-value=4.5e-13  Score=97.70  Aligned_cols=54  Identities=26%  Similarity=0.672  Sum_probs=46.3

Q ss_pred             cccccccccccccccC----CceEEccccceeccccchhhhccCCCcCcccccccCCC
Q 021640          180 RSDSHCPVCQDKFELG----SEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG  233 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~----~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~  233 (309)
                      .++..|+||++.|...    ..++.++|+|.||..||.+|++.+.+||+||+.+...+
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   65 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR   65 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCCCS
T ss_pred             CCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccChhh
Confidence            3567899999998653    45688999999999999999999999999999987544

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

Probab=99.31  E-value=3.8e-13  Score=97.36  Aligned_cols=52  Identities=27%  Similarity=0.694  Sum_probs=44.8

Q ss_pred             cccccccccccccccC----CceEEccccceeccccchhhhccCCCcCcccccccC
Q 021640          180 RSDSHCPVCQDKFELG----SEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPL  231 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~----~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~  231 (309)
                      .....|+||++.|...    ..++.++|+|.||..||..|+..+.+||+||+.|..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            4567899999999753    345889999999999999999999999999998753

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

Probab=99.27  E-value=1.2e-12  Score=95.43  Aligned_cols=51  Identities=27%  Similarity=0.755  Sum_probs=44.6

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGS  234 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~  234 (309)
                      .....|+||++.+..    +.++|+|.||..||..|+..+.+||+||+.+.....
T Consensus        13 ~~~~~C~IC~~~~~~----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   63 (70)
T 2ecn_A           13 TDEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANE   63 (70)
T ss_dssp             CCCCCCSSSCCSCCS----EEETTTEEECHHHHHHSSCCCSSCHHHHHCTTCCCC
T ss_pred             CCCCCCeeCCcCccC----cccCCCCcccHHHHHHHHHCcCcCCCcCCcccCCCc
Confidence            456789999999864    789999999999999999999999999999875543

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

Probab=99.27  E-value=8.3e-13  Score=94.10  Aligned_cols=52  Identities=27%  Similarity=0.677  Sum_probs=44.7

Q ss_pred             cccccccccccccC----CceEEccccceeccccchhhhccCCCcCcccccccCCC
Q 021640          182 DSHCPVCQDKFELG----SEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG  233 (309)
Q Consensus       182 ~~~C~IC~~~~~~~----~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~  233 (309)
                      ...|+||++.+...    ..+..++|+|.||..||..|++.+.+||+||+.+...+
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   58 (64)
T 2xeu_A            3 MVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR   58 (64)
T ss_dssp             CCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTTTC
T ss_pred             CCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCccc
Confidence            46899999998753    45578899999999999999999999999999886543

>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=99.25  E-value=4.8e-13  Score=107.98  Aligned_cols=51  Identities=25%  Similarity=0.616  Sum_probs=1.0

Q ss_pred             ccccccccccccccC-------------C--ceEEccccceeccccchhhhccCCCcCcccccccC
Q 021640          181 SDSHCPVCQDKFELG-------------S--EARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPL  231 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~-------------~--~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~  231 (309)
                      .++.|+||++.|...             +  .+..++|+|.||..||.+||..+.+||+||+++..
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~~  112 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEF  112 (117)
T ss_dssp             CC----------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeeee
Confidence            357899999999652             1  23346899999999999999999999999998643

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

Probab=99.25  E-value=2.9e-12  Score=96.64  Aligned_cols=53  Identities=25%  Similarity=0.696  Sum_probs=44.6

Q ss_pred             ccccccccccccccCCceEEcccc-----ceeccccchhhhccCC--CcCcccccccCCCC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCN-----HIYHSDCIVPWLVQHN--SCPVCRQELPLQGS  234 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~-----H~fh~~Ci~~Wl~~~~--sCP~CR~~l~~~~~  234 (309)
                      ++..|.||+++|..++.+ ++||.     |.||..||.+||..++  +||+||+.+..+..
T Consensus        14 ~~~~C~IC~~~~~~~~~l-~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~~   73 (80)
T 2d8s_A           14 SQDICRICHCEGDDESPL-ITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMETK   73 (80)
T ss_dssp             TSCCCSSSCCCCCSSSCE-ECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCCC
T ss_pred             CCCCCeEcCccccCCCee-EeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCcc
Confidence            457899999999876655 69996     9999999999998764  89999999876554

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

Probab=99.25  E-value=2.6e-12  Score=92.94  Aligned_cols=49  Identities=27%  Similarity=0.777  Sum_probs=43.0

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPL  231 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~  231 (309)
                      .+..|+||++.+..  .++.++|+|.||..||..|++.+.+||+||+.+..
T Consensus         4 ~~~~C~IC~~~~~~--~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCeeCCccccC--CcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            45689999999863  46889999999999999999999999999998853

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

Probab=99.24  E-value=2.7e-12  Score=94.27  Aligned_cols=55  Identities=22%  Similarity=0.463  Sum_probs=45.0

Q ss_pred             ccccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCCCC
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSS  235 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~~  235 (309)
                      ++....|+||++.|..  .+..++|+|.||..||..|+..+.+||+||+.+...+..
T Consensus        12 ~~~~~~C~IC~~~~~~--p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   66 (72)
T 2djb_A           12 LTPYILCSICKGYLID--ATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPL   66 (72)
T ss_dssp             CCGGGSCTTTSSCCSS--CEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSCSC
T ss_pred             cCCCCCCCCCChHHHC--cCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCccccc
Confidence            3456789999999864  233349999999999999999989999999998765543

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

Probab=99.23  E-value=3e-12  Score=93.77  Aligned_cols=50  Identities=24%  Similarity=0.612  Sum_probs=43.2

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQ  232 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~  232 (309)
                      .....|+||++.+..   .+.++|+|.||..||..|+..+.+||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   62 (71)
T 2d8t_A           13 LTVPECAICLQTCVH---PVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPED   62 (71)
T ss_dssp             SSCCBCSSSSSBCSS---EEEETTTEEEEHHHHHHCTTCSSBCSSSCCBCCHH
T ss_pred             CCCCCCccCCcccCC---CEEccCCCHHHHHHHHHHHHCCCcCcCcCchhCHh
Confidence            345789999999853   47889999999999999999999999999988643

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

Probab=99.20  E-value=5.1e-12  Score=95.76  Aligned_cols=55  Identities=24%  Similarity=0.616  Sum_probs=46.3

Q ss_pred             cccccccccccccccccCCc-eEEccccceeccccchhhhccC---CCcCcccccccCC
Q 021640          178 HLRSDSHCPVCQDKFELGSE-ARQMPCNHIYHSDCIVPWLVQH---NSCPVCRQELPLQ  232 (309)
Q Consensus       178 ~~~~~~~C~IC~~~~~~~~~-~~~lpC~H~fh~~Ci~~Wl~~~---~sCP~CR~~l~~~  232 (309)
                      .+.+...|+||++.|...+. .+.++|+|.||..||..|+..+   ..||+||+.+...
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           11 ALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             CCCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             hccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            34566789999999976543 7889999999999999999876   6899999987654

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

Probab=99.19  E-value=1e-11  Score=91.80  Aligned_cols=53  Identities=26%  Similarity=0.657  Sum_probs=43.3

Q ss_pred             ccccccccccccccccCCceEEcc-ccceeccccchhhhccC--CCcCcccccccCCCC
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQH--NSCPVCRQELPLQGS  234 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lp-C~H~fh~~Ci~~Wl~~~--~sCP~CR~~l~~~~~  234 (309)
                      +.....|+||++.|..   .+.++ |+|.||..||..|+..+  .+||+||+.+...+.
T Consensus        12 ~~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~~   67 (74)
T 2yur_A           12 IPDELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA   67 (74)
T ss_dssp             SCGGGSCSSSCCCCTT---CEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTTT
T ss_pred             CCCCCCCcCCChHHhC---CeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCccc
Confidence            3456789999999964   47799 99999999999999865  689999997654433

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

Probab=99.16  E-value=1.3e-11  Score=90.39  Aligned_cols=52  Identities=23%  Similarity=0.645  Sum_probs=43.0

Q ss_pred             ccccccccccccccccCCceEEccccceeccccchhhhc---cCCCcCcccccccCCC
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV---QHNSCPVCRQELPLQG  233 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~---~~~sCP~CR~~l~~~~  233 (309)
                      +.....|+||++.|.   ..+.++|+|.||..||..|++   ....||+||+.+..++
T Consensus        17 ~~~~~~C~IC~~~~~---~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           17 LQEEVICPICLDILQ---KPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCCCBCTTTCSBCS---SEEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             CccCCEeccCCcccC---CeEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            345678999999986   457789999999999999997   3557999999886543

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

Probab=99.14  E-value=8.3e-12  Score=103.25  Aligned_cols=50  Identities=30%  Similarity=0.853  Sum_probs=43.3

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQ  232 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~  232 (309)
                      +.+..|+||++.|.   .++.+||+|.||..||..|+..+.+||+||+.+...
T Consensus        51 ~~~~~C~iC~~~~~---~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           51 ENELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             HHHSBCTTTCSBCS---SEEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             cccCCCcccCcccC---CceECCCCCCccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            34568999999985   357899999999999999999999999999988543

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

Probab=99.13  E-value=1.1e-11  Score=89.28  Aligned_cols=50  Identities=18%  Similarity=0.523  Sum_probs=41.9

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhc-cCCCcCcccccccCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV-QHNSCPVCRQELPLQ  232 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~-~~~sCP~CR~~l~~~  232 (309)
                      .+...|+||++.+..+   +.++|+|.||..||..|+. ....||+||+.+..+
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCSP---KQTECGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             CCCEECTTTCCEESSC---CCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             CcCCCCCCCChHhcCe---eECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            4567899999998644   4589999999999999995 556899999988654

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

Probab=99.12  E-value=1.6e-11  Score=92.05  Aligned_cols=48  Identities=19%  Similarity=0.518  Sum_probs=42.3

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccCCCcCccccccc
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      .....|+||++.|..   .+.++|+|.||..||..|+....+||+||+.+.
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQN---PVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCCS---EEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhcC---eeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            345789999999854   467999999999999999999899999999885

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

Probab=99.10  E-value=1.6e-11  Score=91.22  Aligned_cols=51  Identities=24%  Similarity=0.628  Sum_probs=43.0

Q ss_pred             ccccccccccccccccCCceEEccccceeccccchhhhcc-------CCCcCcccccccCC
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ-------HNSCPVCRQELPLQ  232 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~-------~~sCP~CR~~l~~~  232 (309)
                      +.+...|+||++.|...   +.++|+|.||..||..|+..       ...||+||..+...
T Consensus         9 ~~~~~~C~IC~~~~~~p---~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~   66 (79)
T 2egp_A            9 VQEEVTCPICLELLTEP---LSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFE   66 (79)
T ss_dssp             CCCCCEETTTTEECSSC---CCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSS
T ss_pred             cccCCCCcCCCcccCCe---eECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHh
Confidence            34568899999998643   56899999999999999987       56799999988654

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

Probab=99.10  E-value=2.7e-11  Score=90.01  Aligned_cols=51  Identities=20%  Similarity=0.455  Sum_probs=43.5

Q ss_pred             ccccccccccccccccCCceEEccccceeccccchhhhcc-CCCcCcccccccCC
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQELPLQ  232 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~-~~sCP~CR~~l~~~  232 (309)
                      +.+...|+||++.|..   .+.++|+|.||..||..|+.. +.+||+||..+...
T Consensus         5 ~~~~~~C~IC~~~~~~---Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~   56 (78)
T 1t1h_A            5 FPEYFRCPISLELMKD---PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             CSSSSSCTTTSCCCSS---EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             CcccCCCCCccccccC---CEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChh
Confidence            3456789999999864   477899999999999999987 77899999988654

>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=99.09  E-value=5.9e-12  Score=98.56  Aligned_cols=52  Identities=31%  Similarity=0.713  Sum_probs=43.9

Q ss_pred             ccccccccccccccccCCceEE-ccccceeccccchhhhccC-CCcCcccccccCCC
Q 021640          179 LRSDSHCPVCQDKFELGSEARQ-MPCNHIYHSDCIVPWLVQH-NSCPVCRQELPLQG  233 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~-lpC~H~fh~~Ci~~Wl~~~-~sCP~CR~~l~~~~  233 (309)
                      +.+...|+||++.|..   .+. ++|+|.||..||..|+... .+||+||..+....
T Consensus        19 l~~~~~C~IC~~~~~~---p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (100)
T 3lrq_A           19 IAEVFRCFICMEKLRD---ARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRE   72 (100)
T ss_dssp             HHHHTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCccCCccccC---ccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHHH
Confidence            4556789999999963   456 9999999999999999987 68999999986543

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

Probab=99.08  E-value=3.7e-11  Score=89.13  Aligned_cols=53  Identities=19%  Similarity=0.504  Sum_probs=43.7

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccC--CCcCcccccccCCCCC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH--NSCPVCRQELPLQGSS  235 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~--~sCP~CR~~l~~~~~~  235 (309)
                      ....|+||++.+..+.  +...|+|.||..||.+||+.+  .+||+||.++..+...
T Consensus        14 ~i~~C~IC~~~i~~g~--~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~~~   68 (74)
T 2ct0_A           14 AVKICNICHSLLIQGQ--SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIPK   68 (74)
T ss_dssp             SSCBCSSSCCBCSSSE--ECSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCCCC
T ss_pred             CCCcCcchhhHcccCC--ccCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCCCC
Confidence            4578999999998653  333799999999999999987  7899999998755544

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

Probab=99.07  E-value=5.5e-11  Score=89.12  Aligned_cols=53  Identities=23%  Similarity=0.670  Sum_probs=44.0

Q ss_pred             ccccccccccccccccCCceEEccccceeccccchhhhcc------CCCcCcccccccCCCC
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ------HNSCPVCRQELPLQGS  234 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~------~~sCP~CR~~l~~~~~  234 (309)
                      +.+...|+||++.|..   .+.++|+|.||..||..|+..      ...||+||..+...+.
T Consensus        16 ~~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~   74 (85)
T 2ecv_A           16 VKEEVTCPICLELLTQ---PLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENI   74 (85)
T ss_dssp             CCCCCCCTTTCSCCSS---CBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSSC
T ss_pred             ccCCCCCCCCCcccCC---ceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHhc
Confidence            3456789999999864   367899999999999999987      6789999998875443

>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=3.4e-11  Score=95.25  Aligned_cols=56  Identities=23%  Similarity=0.552  Sum_probs=45.4

Q ss_pred             ecccccccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCC
Q 021640          175 TQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQ  232 (309)
Q Consensus       175 ~~~~~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~  232 (309)
                      ..+.+.....|+||++.|..  .+..++|+|.||..||..|+..+.+||+||..+...
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~--p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A            8 KITELNPHLMCVLCGGYFID--ATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             EHHHHGGGTBCTTTSSBCSS--EEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             chhccCCcCCCccCChHHhC--cCEeCCCCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            33445667899999999863  333349999999999999999999999999988653

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

Probab=99.06  E-value=3.9e-11  Score=89.94  Aligned_cols=52  Identities=27%  Similarity=0.729  Sum_probs=43.7

Q ss_pred             ccccccccccccccccCCceEEccccceeccccchhhhcc------CCCcCcccccccCCC
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ------HNSCPVCRQELPLQG  233 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~------~~sCP~CR~~l~~~~  233 (309)
                      +.....|+||++.|..+   +.++|+|.||..||..|+..      ...||+||..+..+.
T Consensus        16 ~~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~   73 (85)
T 2ecw_A           16 IKEEVTCPICLELLKEP---VSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGN   73 (85)
T ss_dssp             CCTTTSCTTTCSCCSSC---EECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTC
T ss_pred             CccCCCCcCCChhhCcc---eeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHh
Confidence            34567899999998643   67899999999999999987      668999999887543

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

Probab=99.05  E-value=4.2e-11  Score=97.03  Aligned_cols=54  Identities=26%  Similarity=0.661  Sum_probs=46.2

Q ss_pred             ccccccccccccccC----CceEEccccceeccccchhhhccCCCcCcccccccCCCC
Q 021640          181 SDSHCPVCQDKFELG----SEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGS  234 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~----~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~  234 (309)
                      +...|+||++.|..+    ..++.++|+|.||..||..||+.+.+||+||+.+.....
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l   63 (133)
T 4ap4_A            6 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   63 (133)
T ss_dssp             CSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCE
T ss_pred             CCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCccccc
Confidence            457899999999753    455889999999999999999999999999998865543

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

Probab=99.02  E-value=7.7e-11  Score=83.97  Aligned_cols=44  Identities=27%  Similarity=0.715  Sum_probs=37.3

Q ss_pred             ccccccccccccccccCCceEEccccceeccccchhhhc---cCCCcCcc
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV---QHNSCPVC  225 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~---~~~sCP~C  225 (309)
                      +.+...|+||++.|..   .+.++|+|.||..||..|++   ....||+|
T Consensus        17 ~~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           17 LQEEVICPICLDILQK---PVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCBCTTTCSBCSS---CEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             CccCCCCCcCCchhCC---eEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            3556789999999864   47789999999999999998   45579998

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

Probab=99.02  E-value=3.8e-11  Score=93.44  Aligned_cols=49  Identities=29%  Similarity=0.642  Sum_probs=42.1

Q ss_pred             cccccccccccccccCCceEEc-cccceeccccchhhhccCCCcCcccccccC
Q 021640          180 RSDSHCPVCQDKFELGSEARQM-PCNHIYHSDCIVPWLVQHNSCPVCRQELPL  231 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~l-pC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~  231 (309)
                      .+...|+||++.|..   .+.+ +|+|.||..||..|+..+.+||+||..+..
T Consensus        20 ~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           20 DDLLRCGICFEYFNI---AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             HHHTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCCCCcccCChhhCC---cCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            345789999999864   3555 899999999999999999999999998864

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

Probab=99.00  E-value=3.3e-11  Score=101.26  Aligned_cols=51  Identities=27%  Similarity=0.544  Sum_probs=43.4

Q ss_pred             ccccccccccccccccCCceEEccccceeccccchhhhccCC-CcCcccccccCC
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN-SCPVCRQELPLQ  232 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~-sCP~CR~~l~~~  232 (309)
                      +.....|+||++.|..   .+.++|+|.||..||..|+.... +||+||..+...
T Consensus        75 l~~~~~C~IC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           75 LEQSFMCVCCQELVYQ---PVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHHHTBCTTTSSBCSS---EEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CccCCEeecCChhhcC---CEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            3456789999999864   46799999999999999998765 799999998765

>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=6.7e-11  Score=100.49  Aligned_cols=52  Identities=33%  Similarity=0.756  Sum_probs=42.5

Q ss_pred             cccccccccccccccccCCceEEccccceeccccchhhhcc-CCCcCcccccccC
Q 021640          178 HLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQELPL  231 (309)
Q Consensus       178 ~~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~-~~sCP~CR~~l~~  231 (309)
                      .+.....|+||++.|..  .+..++|+|.||..||..|+.. +..||+||..+..
T Consensus        50 ~~~~~~~C~IC~~~~~~--p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           50 SLHSELMCPICLDMLKN--TMTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             CCHHHHBCTTTSSBCSS--EEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             hCCCCCCCcccChHhhC--cCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            34456799999999874  3444599999999999999997 6789999998853

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

Probab=98.98  E-value=1.3e-10  Score=88.96  Aligned_cols=49  Identities=29%  Similarity=0.718  Sum_probs=41.4

Q ss_pred             ccccccccccccccccCCceEEcc-ccceeccccchhhhccC--CCcCccccccc
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQH--NSCPVCRQELP  230 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lp-C~H~fh~~Ci~~Wl~~~--~sCP~CR~~l~  230 (309)
                      +.....|+||++.|..   .+.++ |+|.||..||..|+...  ..||+||..+.
T Consensus        10 ~~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           10 IPDELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CCTTTEETTTTEECSS---CEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CCcCCCCCCCChhhcC---ceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            4566899999999964   47889 99999999999999754  58999999873

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

Probab=98.98  E-value=1e-10  Score=81.59  Aligned_cols=44  Identities=30%  Similarity=0.825  Sum_probs=36.6

Q ss_pred             ccccccccccccccccCCceEEccccceeccccchhhh---ccCCCcCcc
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWL---VQHNSCPVC  225 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl---~~~~sCP~C  225 (309)
                      +.....|+||++.+..+   +.++|+|.||..||..|+   ....+||+|
T Consensus        12 ~~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           12 LQVEASCSVCLEYLKEP---VIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             SCCCCBCSSSCCBCSSC---CCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cccCCCCccCCcccCcc---EeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            34567899999999654   668999999999999995   456789998

>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=98.97  E-value=1.2e-10  Score=94.37  Aligned_cols=49  Identities=27%  Similarity=0.527  Sum_probs=42.0

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccCC-CcCcccccccC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN-SCPVCRQELPL  231 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~-sCP~CR~~l~~  231 (309)
                      .....|+||++.|.   ..+.++|+|.||..||..|+..+. +||+||..+..
T Consensus        50 ~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           50 EETFQCICCQELVF---RPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHHTBCTTTSSBCS---SEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             ccCCCCCcCChHHc---CcEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            45678999999996   447789999999999999998554 89999999865

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

Probab=98.97  E-value=1.7e-10  Score=82.79  Aligned_cols=52  Identities=27%  Similarity=0.579  Sum_probs=41.1

Q ss_pred             ccccccccc-ccccCCc-eEEccccceeccccchhhhcc-CCCcCcccccccCCC
Q 021640          182 DSHCPVCQD-KFELGSE-ARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQELPLQG  233 (309)
Q Consensus       182 ~~~C~IC~~-~~~~~~~-~~~lpC~H~fh~~Ci~~Wl~~-~~sCP~CR~~l~~~~  233 (309)
                      +..|+||++ .|..+.. ++.++|+|.||..||..|+.. ...||+||+.+...+
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   57 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSN   57 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCC
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCcccccc
Confidence            467999999 7765533 256899999999999999765 457999999886543

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

Probab=98.95  E-value=1.3e-10  Score=94.06  Aligned_cols=52  Identities=27%  Similarity=0.705  Sum_probs=44.5

Q ss_pred             ccccccccccccccC----CceEEccccceeccccchhhhccCCCcCcccccccCC
Q 021640          181 SDSHCPVCQDKFELG----SEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQ  232 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~----~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~  232 (309)
                      ....|+||++.|...    ..++.++|+|.||..||.+||+.+++||+||..+..+
T Consensus        71 ~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  126 (133)
T 4ap4_A           71 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK  126 (133)
T ss_dssp             SSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChh
Confidence            457899999998652    3457889999999999999999999999999988654

>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=4.2e-10  Score=78.65  Aligned_cols=47  Identities=28%  Similarity=0.654  Sum_probs=39.5

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG  233 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~  233 (309)
                      +...|+||++.|...   +.|+|+|.||..||..|   ...||+||+.+..+.
T Consensus         5 ~~~~C~IC~~~~~~p---~~l~CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T 1bor_A            5 QFLRCQQCQAEAKCP---KLLPCLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CCSSCSSSCSSCBCC---SCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             cCCCceEeCCccCCe---EEcCCCCcccHHHHccC---CCCCCcCCcEeecCC
Confidence            457899999999754   78999999999999885   568999999886544

>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=98.92  E-value=1.7e-10  Score=92.07  Aligned_cols=49  Identities=24%  Similarity=0.657  Sum_probs=41.7

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhcc-CCCcCcccccccC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQELPL  231 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~-~~sCP~CR~~l~~  231 (309)
                      .++..|+||++.|..   .+.++|+|.||..||..|+.. ..+||+||..+..
T Consensus        13 ~~~~~C~iC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           13 LSECQCGICMEILVE---PVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHHBCTTTCSBCSS---CEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCCccCCcccCc---eeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            345789999999864   478899999999999999986 5689999998753

>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=98.92  E-value=1.8e-10  Score=91.17  Aligned_cols=50  Identities=24%  Similarity=0.713  Sum_probs=41.8

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccCC---CcCcccccccCCC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN---SCPVCRQELPLQG  233 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~---sCP~CR~~l~~~~  233 (309)
                      ....|+||++.|..+   +.++|+|.||..||..|+..+.   +||+||..+....
T Consensus        20 ~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   72 (112)
T 1jm7_A           20 KILECPICLELIKEP---VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS   72 (112)
T ss_dssp             HHTSCSSSCCCCSSC---CBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTT
T ss_pred             CCCCCcccChhhcCe---EECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhh
Confidence            456899999998643   5689999999999999998654   7999999887543

>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=98.89  E-value=2.2e-10  Score=95.23  Aligned_cols=52  Identities=25%  Similarity=0.519  Sum_probs=43.6

Q ss_pred             cccccccccccccccccCCceEEccccceeccccchhhhccCC-CcCcccccccCC
Q 021640          178 HLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN-SCPVCRQELPLQ  232 (309)
Q Consensus       178 ~~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~-sCP~CR~~l~~~  232 (309)
                      .+++...|+||++.|..+   +.++|+|.||..||..|+.... +||+||.++..+
T Consensus        27 ~l~~~~~C~IC~~~~~~p---v~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   79 (141)
T 3knv_A           27 KLEAKYLCSACRNVLRRP---FQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYE   79 (141)
T ss_dssp             GCCGGGBCTTTCSBCSSE---EECTTSCEEEHHHHHHHGGGSCEECHHHHHTTCCC
T ss_pred             cCCcCcCCCCCChhhcCc---EECCCCCccCHHHHHHHHhcCCCCCCCCCCccccc
Confidence            445678999999998644   6789999999999999998665 899999987543

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

Probab=98.87  E-value=3.7e-10  Score=90.77  Aligned_cols=51  Identities=31%  Similarity=0.637  Sum_probs=43.2

Q ss_pred             ccccccccccccccccCCceEEccccceeccccchhhhccCC-CcCcccccccCC
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN-SCPVCRQELPLQ  232 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~-sCP~CR~~l~~~  232 (309)
                      +.+...|+||++.+..   .+.++|+|.||..||..|+.... +||+||..+...
T Consensus        15 ~~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           15 LESKYECPICLMALRE---AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             CCGGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCcCChhhcC---eEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            4556799999999864   47789999999999999998765 899999988653

>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=98.83  E-value=1e-09  Score=87.98  Aligned_cols=49  Identities=24%  Similarity=0.594  Sum_probs=41.0

Q ss_pred             cccccccccccccccCCceEEc-cccceeccccchhhhccCCCcCcccccccCCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQM-PCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG  233 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~l-pC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~  233 (309)
                      .....|+||++.|..   .+.+ +|+|.||..||..|+.  ..||+||..+....
T Consensus        20 ~~~~~C~IC~~~~~~---pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~   69 (117)
T 1jm7_B           20 EKLLRCSRCTNILRE---PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQD   69 (117)
T ss_dssp             HHTTSCSSSCSCCSS---CBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSS
T ss_pred             hhCCCCCCCChHhhC---ccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCcccc
Confidence            356789999999964   3666 9999999999999998  78999999885443

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

Probab=98.82  E-value=3.9e-10  Score=107.95  Aligned_cols=48  Identities=25%  Similarity=0.770  Sum_probs=41.7

Q ss_pred             cccccccccccccCCceEEccccceeccccchhhhc-cCCCcCcccccccCC
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV-QHNSCPVCRQELPLQ  232 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~-~~~sCP~CR~~l~~~  232 (309)
                      ...|+||++.+.   .++.+||+|.||..||..|+. .+.+||+||..+...
T Consensus       332 ~~~C~ICle~~~---~pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          332 FQLCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             SSBCTTTSSSBC---CEEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCCccCcCCC---CeEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            368999999884   468899999999999999998 678999999988643

>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=98.82  E-value=1.1e-09  Score=85.85  Aligned_cols=51  Identities=18%  Similarity=0.227  Sum_probs=44.4

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG  233 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~  233 (309)
                      .....|+||++.|..   .+.++|||.|+..||..||..+.+||+|+..+....
T Consensus        27 p~~~~CpI~~~~m~d---PV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~   77 (100)
T 2kre_A           27 PDEFRDPLMDTLMTD---PVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTESM   77 (100)
T ss_dssp             STTTBCTTTCSBCSS---EEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCTTS
T ss_pred             cHhhCCcCccCcccC---CeECCCCCEEchHHHHHHHHcCCCCCCCCCCCChhh
Confidence            346789999999964   478899999999999999998889999999887544

>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=98.82  E-value=4.3e-10  Score=89.89  Aligned_cols=51  Identities=22%  Similarity=0.521  Sum_probs=42.9

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhcc-CCCcCcccccccCCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQELPLQG  233 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~-~~sCP~CR~~l~~~~  233 (309)
                      .+...|+||++.|..   .+.++|+|.||..||..|+.. ..+||+||..+...+
T Consensus        21 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (116)
T 1rmd_A           21 VKSISCQICEHILAD---PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (116)
T ss_dssp             HHHTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             cCCCCCCCCCcHhcC---cEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhh
Confidence            346789999999853   467899999999999999987 678999999886543

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

Probab=98.80  E-value=2.9e-09  Score=79.64  Aligned_cols=55  Identities=22%  Similarity=0.558  Sum_probs=42.1

Q ss_pred             ccccccccccccccccCCceEEcc--ccceeccccchhhhcc-CCCcCcccccccCCCC
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMP--CNHIYHSDCIVPWLVQ-HNSCPVCRQELPLQGS  234 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lp--C~H~fh~~Ci~~Wl~~-~~sCP~CR~~l~~~~~  234 (309)
                      ++++..|+||++.+...+ ++.+|  |||.||..||..++.. ...||+||+.+.....
T Consensus         8 ~~~~~~CpICle~~~~~d-~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~   65 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEIDD-INFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPA   65 (78)
T ss_dssp             CCCCCBCTTTCCBCCTTT-TTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSS
T ss_pred             cccCCcCCccCccCcccc-ccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCch
Confidence            356678999999886532 33444  9999999999998753 5679999998875544

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

Probab=98.79  E-value=1.1e-09  Score=83.10  Aligned_cols=50  Identities=16%  Similarity=0.236  Sum_probs=43.7

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQ  232 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~  232 (309)
                      .....|+||++.|..   .+.++|||.|+..||..|+..+.+||+|+..+...
T Consensus        12 p~~~~CpI~~~~m~d---PV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~   61 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTD---PVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTES   61 (85)
T ss_dssp             CTTTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             chheECcccCchhcC---CeECCCCCEECHHHHHHHHhcCCCCCCCcCCCChH
Confidence            356789999999964   48899999999999999999888999999988654

>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=98.79  E-value=2.1e-09  Score=83.96  Aligned_cols=52  Identities=13%  Similarity=0.152  Sum_probs=44.9

Q ss_pred             cccccccccccccccCCceEEcccc-ceeccccchhhhccCCCcCcccccccCCCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCN-HIYHSDCIVPWLVQHNSCPVCRQELPLQGS  234 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~-H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~  234 (309)
                      .....|+||++.|..   .+.++|+ |.|+..||..||..+.+||+||..+.....
T Consensus        20 p~~~~CpI~~~~m~d---PV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~L   72 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQI   72 (98)
T ss_dssp             CTTTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTS
T ss_pred             cHhcCCcCccccccC---CeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCChhhc
Confidence            346789999999964   4789999 999999999999988899999999876543

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=98.75  E-value=8.8e-10  Score=81.42  Aligned_cols=44  Identities=23%  Similarity=0.691  Sum_probs=37.9

Q ss_pred             cccccccccccccccCCceEEccccce-eccccchhhhccCCCcCccccccc
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHI-YHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~-fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      ++...|+||++.+.   .++.+||+|. ||..|+..|    ..||+||+.+.
T Consensus        22 ~~~~~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~   66 (74)
T 4ic3_A           22 QEEKLCKICMDRNI---AIVFVPCGHLVTCKQCAEAV----DKCPMCYTVIT   66 (74)
T ss_dssp             HHHTBCTTTSSSBC---CEEEETTCCBCCCHHHHTTC----SBCTTTCCBCS
T ss_pred             ccCCCCCCCCCCCC---CEEEcCCCChhHHHHhhhcC----ccCCCcCcCcc
Confidence            34578999999874   4678899999 999999999    78999999875

>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=98.73  E-value=3.1e-09  Score=76.35  Aligned_cols=47  Identities=23%  Similarity=0.509  Sum_probs=39.3

Q ss_pred             ccccccccccccccCCceEEc--cccce-eccccchhhhccCCCcCccccccc
Q 021640          181 SDSHCPVCQDKFELGSEARQM--PCNHI-YHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~l--pC~H~-fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      ++..|.||++.+..   +..+  ||+|. |+..|+..|++.+..||+||+.+.
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            45689999988643   3444  99999 899999999998889999999874

>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=98.65  E-value=7.7e-09  Score=74.00  Aligned_cols=47  Identities=19%  Similarity=0.475  Sum_probs=38.9

Q ss_pred             ccccccccccccccCCceEEc--cccce-eccccchhhhccCCCcCccccccc
Q 021640          181 SDSHCPVCQDKFELGSEARQM--PCNHI-YHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~l--pC~H~-fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      ....|.||++.+..   ...+  ||+|. |+..|+..|.+.+..||+||+.+.
T Consensus         6 ~~~~C~IC~~~~~~---~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            6 LLKPCSLCEKRPRD---GNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GGSBCTTTSSSBSC---EEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             cCCCCcccCCcCCC---eEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            35689999987642   3444  99998 999999999988889999999874

>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=98.53  E-value=1.5e-08  Score=86.09  Aligned_cols=51  Identities=29%  Similarity=0.624  Sum_probs=42.9

Q ss_pred             ccccccccccccccccCCceEEccccceeccccchhhhccCC-CcCcccccccCC
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN-SCPVCRQELPLQ  232 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~-sCP~CR~~l~~~  232 (309)
                      +.+...|+||++.|..+   +.++|+|.||..||..|+.... +||+||..+...
T Consensus        15 ~~~~~~C~IC~~~~~~p---v~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           15 LESKYECPICLMALREA---VQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             CCGGGBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCChhhcCc---EECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            45678999999998643   6789999999999999998654 899999988653

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

Probab=98.53  E-value=1.5e-08  Score=95.05  Aligned_cols=52  Identities=23%  Similarity=0.599  Sum_probs=39.8

Q ss_pred             cccccccccccccccCCce-----EEccccceeccccchhhhccC-----------CCcCcccccccC
Q 021640          180 RSDSHCPVCQDKFELGSEA-----RQMPCNHIYHSDCIVPWLVQH-----------NSCPVCRQELPL  231 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~-----~~lpC~H~fh~~Ci~~Wl~~~-----------~sCP~CR~~l~~  231 (309)
                      +...+|+||++.+..+..+     ....|+|.||..||.+||+..           .+||+||++|..
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~  373 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLST  373 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCc
Confidence            3467899999998762222     124699999999999999752           469999998753

>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=98.50  E-value=1.4e-08  Score=78.44  Aligned_cols=49  Identities=24%  Similarity=0.609  Sum_probs=39.9

Q ss_pred             cccccccccccccccCCceEEcc-ccceeccccchhhhccC------CCcCc--cccc-ccC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQH------NSCPV--CRQE-LPL  231 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lp-C~H~fh~~Ci~~Wl~~~------~sCP~--CR~~-l~~  231 (309)
                      .....|+||++.|..   .+.++ |+|.|+..||..||..+      .+||+  |++. +..
T Consensus         5 ~~~~~CPI~~~~~~d---PV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~   63 (94)
T 2yu4_A            5 SSGFTCPITKEEMKK---PVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRK   63 (94)
T ss_dssp             SSCCBCTTTCSBCSS---EEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCG
T ss_pred             CcEeECcCcCchhcC---CEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCH
Confidence            345789999999964   47786 99999999999999864      48999  9866 543

>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=98.50  E-value=3e-08  Score=89.87  Aligned_cols=49  Identities=16%  Similarity=0.116  Sum_probs=41.4

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccC-CCcCcccccccCC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH-NSCPVCRQELPLQ  232 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~-~sCP~CR~~l~~~  232 (309)
                      ....|+||++.|..   .+.++|||.||..||..|+..+ .+||+||..+...
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            45789999999964   4789999999999999999864 4599999988543

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.42  E-value=3e-08  Score=73.18  Aligned_cols=44  Identities=23%  Similarity=0.699  Sum_probs=36.1

Q ss_pred             ccccccccccccccCCceEEccccce-eccccchhhhccCCCcCcccccccC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHI-YHSDCIVPWLVQHNSCPVCRQELPL  231 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~-fh~~Ci~~Wl~~~~sCP~CR~~l~~  231 (309)
                      +...|+||++.+.   .++.+||+|. ||..|+..    ...||+||..+..
T Consensus        24 ~~~~C~IC~~~~~---~~~~~pCgH~~~C~~C~~~----~~~CP~Cr~~i~~   68 (75)
T 2ecg_A           24 EEKLCKICMDRNI---AIVFVPCGHLVTCKQCAEA----VDKCPMCYTVITF   68 (75)
T ss_dssp             HHHSCSSSCSSCC---CBCCSSSCCCCBCHHHHHH----CSBCTTTCCBCCC
T ss_pred             CCCCCCcCCCCCC---CEEEecCCCHHHHHHHhhC----CCCCccCCceecC
Confidence            3467999999874   4578999999 99999964    3689999998854

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=98.41  E-value=5.2e-08  Score=69.15  Aligned_cols=48  Identities=25%  Similarity=0.696  Sum_probs=37.3

Q ss_pred             ccccccccccccccCCceEEcccc--c---eeccccchhhhcc--CCCcCcccccccC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCN--H---IYHSDCIVPWLVQ--HNSCPVCRQELPL  231 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~--H---~fh~~Ci~~Wl~~--~~sCP~CR~~l~~  231 (309)
                      +...|.||+++.  ++. ..+||.  +   .||..||.+|+..  +.+||+|+..+..
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            457899999874  233 368954  4   9999999999974  5689999988753

>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=98.36  E-value=5.8e-08  Score=72.61  Aligned_cols=44  Identities=30%  Similarity=0.658  Sum_probs=37.0

Q ss_pred             ccccccccccccccCCceEEccccce-eccccchhhhccCCCcCcccccccC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHI-YHSDCIVPWLVQHNSCPVCRQELPL  231 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~-fh~~Ci~~Wl~~~~sCP~CR~~l~~  231 (309)
                      ....|.||++.+.   .++.+||+|. |+..|+..|.    .||+||..+..
T Consensus        17 ~~~~C~IC~~~~~---~~v~~pCgH~~~C~~C~~~~~----~CP~Cr~~i~~   61 (79)
T 2yho_A           17 EAMLCMVCCEEEI---NSTFCPCGHTVCCESCAAQLQ----SCPVCRSRVEH   61 (79)
T ss_dssp             HHTBCTTTSSSBC---CEEEETTCBCCBCHHHHTTCS----BCTTTCCBCCE
T ss_pred             CCCEeEEeCcccC---cEEEECCCCHHHHHHHHHhcC----cCCCCCchhhC
Confidence            4568999998764   5688999999 9999999873    89999998754

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.35  E-value=1.8e-07  Score=67.88  Aligned_cols=45  Identities=29%  Similarity=0.682  Sum_probs=37.1

Q ss_pred             ccccccccccccccCCceEEccccce-eccccchhhhccCCCcCcccccccCC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHI-YHSDCIVPWLVQHNSCPVCRQELPLQ  232 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~-fh~~Ci~~Wl~~~~sCP~CR~~l~~~  232 (309)
                      ....|.||++.+.   .++.+||+|. |+..|+..    ...||+||..+...
T Consensus        14 ~~~~C~IC~~~~~---~~v~~pCgH~~~C~~C~~~----~~~CP~CR~~i~~~   59 (68)
T 2ea5_A           14 NSKDCVVCQNGTV---NWVLLPCRHTCLCDGCVKY----FQQCPMCRQFVQES   59 (68)
T ss_dssp             CSSCCSSSSSSCC---CCEETTTTBCCSCTTHHHH----CSSCTTTCCCCCCE
T ss_pred             CCCCCCCcCcCCC---CEEEECCCChhhhHHHHhc----CCCCCCCCcchhce
Confidence            4578999998763   5689999999 99999974    46899999988543

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

Probab=98.35  E-value=8.9e-08  Score=82.55  Aligned_cols=50  Identities=16%  Similarity=0.094  Sum_probs=42.2

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccC-CCcCcccccccCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH-NSCPVCRQELPLQ  232 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~-~sCP~CR~~l~~~  232 (309)
                      .....|+||++.|..   ++.++|||.|+..||..|+..+ .+||+|+..+...
T Consensus       104 p~~f~CPI~~elm~D---PV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~  154 (179)
T 2f42_A          104 PDYLCGKISFELMRE---PCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQD  154 (179)
T ss_dssp             CGGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             cHhhcccCccccCCC---CeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChh
Confidence            356789999999964   4788999999999999999864 4799999988654

>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=98.26  E-value=1.8e-07  Score=71.78  Aligned_cols=48  Identities=21%  Similarity=0.602  Sum_probs=38.4

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhcc--------CCCcCc--cccc
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ--------HNSCPV--CRQE  228 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~--------~~sCP~--CR~~  228 (309)
                      +..+|+||++++.....+..++|+|.||.+||..++..        ...||.  |+..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            34689999999876644445579999999999999873        136999  9987

>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=98.23  E-value=4.1e-07  Score=86.11  Aligned_cols=44  Identities=30%  Similarity=0.785  Sum_probs=38.1

Q ss_pred             cccccccccccccccCCceEEccccce-eccccchhhhccCCCcCccccccc
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHI-YHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~-fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      +++..|+||++.+.   .++.+||+|. ||..|+..|    ..||+||..+.
T Consensus       293 ~~~~~C~IC~~~~~---~~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~  337 (345)
T 3t6p_A          293 QEERTCKVCMDKEV---SVVFIPCGHLVVCQECAPSL----RKCPICRGIIK  337 (345)
T ss_dssp             HTTCBCTTTSSSBC---CEEEETTCCEEECTTTGGGC----SBCTTTCCBCC
T ss_pred             cCCCCCCccCCcCC---ceEEcCCCChhHhHHHHhcC----CcCCCCCCCcc
Confidence            45678999999885   4688899999 999999998    67999999875

>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=98.18  E-value=2e-07  Score=66.27  Aligned_cols=49  Identities=8%  Similarity=0.186  Sum_probs=42.2

Q ss_pred             ccccccccccccCCceEEc-cccceeccccchhhhccCCCcCcccccccCCCC
Q 021640          183 SHCPVCQDKFELGSEARQM-PCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGS  234 (309)
Q Consensus       183 ~~C~IC~~~~~~~~~~~~l-pC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~  234 (309)
                      ..|+||++.+.++   +.+ +|||+|...||.+||+.+.+||+++..|..++.
T Consensus         4 ~~CpIs~~~m~dP---V~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~L   53 (61)
T 2bay_A            4 MLCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEI   53 (61)
T ss_dssp             CCCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGC
T ss_pred             EEecCCCCCCCCC---EEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhhc
Confidence            5799999999743   666 899999999999999988899999998876554

>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=98.16  E-value=4.1e-07  Score=82.46  Aligned_cols=52  Identities=25%  Similarity=0.617  Sum_probs=41.9

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccC--CCcCc--ccccccCCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH--NSCPV--CRQELPLQG  233 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~--~sCP~--CR~~l~~~~  233 (309)
                      .....|+||++.|..  .|+.+.|||.|+..||..|+..+  .+||+  |++.+...+
T Consensus       179 ~~el~CPIcl~~f~D--PVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~d  234 (267)
T 3htk_C          179 KIELTCPITCKPYEA--PLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRD  234 (267)
T ss_dssp             BCCSBCTTTSSBCSS--EEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGG
T ss_pred             ceeeECcCccCcccC--CeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhh
Confidence            456789999999964  35556899999999999999864  36999  999875443

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

Probab=97.80  E-value=5.3e-06  Score=64.19  Aligned_cols=45  Identities=24%  Similarity=0.665  Sum_probs=37.2

Q ss_pred             cccccccccccCCceEEccccceeccccchhhhc-cCCCcCccccccc
Q 021640          184 HCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV-QHNSCPVCRQELP  230 (309)
Q Consensus       184 ~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~-~~~sCP~CR~~l~  230 (309)
                      .|.+|--.+.  ...+.+||+|+||.+|+..|.+ ..++||.|+..+.
T Consensus         3 fC~~C~~Pi~--iygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~   48 (101)
T 3vk6_A            3 FCDKCGLPIK--VYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQ   48 (101)
T ss_dssp             BCTTTCSBCS--EEEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCS
T ss_pred             ecCccCCCeE--EEeeeccccccHHHHHHHHHHhccCCCCcCcCCeee
Confidence            5888876665  4678999999999999999985 4678999998773

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

Probab=97.73  E-value=8.9e-06  Score=73.09  Aligned_cols=53  Identities=19%  Similarity=0.492  Sum_probs=42.6

Q ss_pred             cccccccccccccCCceEEccccceeccccchhhhccCC--CcCcccccccCCCCCC
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN--SCPVCRQELPLQGSSS  236 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~--sCP~CR~~l~~~~~~~  236 (309)
                      ...|.||.+.+..+  .+.-.|+|.||..|+..|++.+.  .||.|+..++......
T Consensus       180 i~~C~iC~~iv~~g--~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~~~~~  234 (238)
T 3nw0_A          180 VKICNICHSLLIQG--QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIPKV  234 (238)
T ss_dssp             CCBCTTTCSBCSSC--EECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSCCCCC
T ss_pred             CCcCcchhhHHhCC--cccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCC
Confidence            56899999998765  23334999999999999998654  7999999988775543

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=93.04  E-value=0.06  Score=38.34  Aligned_cols=45  Identities=24%  Similarity=0.555  Sum_probs=32.3

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccCC----CcCccccc
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN----SCPVCRQE  228 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~----sCP~CR~~  228 (309)
                      ....|.||.+.   ++-+.--.|...||..|+.+.|....    .||.|+..
T Consensus        11 ~~~~C~vC~~~---~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~   59 (66)
T 2lri_C           11 PGARCGVCGDG---TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGD   59 (66)
T ss_dssp             TTCCCTTTSCC---TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTC
T ss_pred             CCCCcCCCCCC---CeEEECCCCCCceecccCCCccCcCCCCCEECccccCC
Confidence            34679999753   33333334999999999999987543    49999754

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=92.10  E-value=0.052  Score=41.28  Aligned_cols=35  Identities=14%  Similarity=0.415  Sum_probs=26.2

Q ss_pred             cccccccccccccCCceEEccccceeccccchh-hh
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVP-WL  216 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~-Wl  216 (309)
                      +..|.||.+.+.......-+.|+|.|+..|+.. |.
T Consensus         3 e~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~~h~   38 (101)
T 2jun_A            3 KVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKATHP   38 (101)
T ss_dssp             CCBCTTCCSSSCCBCCEEETTTTEEECHHHHHHHSC
T ss_pred             CCCCcCCCCCCCCCceEECCcCChHHhHHHCHHHhc
Confidence            468999998754333333489999999999998 54

>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}

Probab=91.98  E-value=0.1  Score=41.30  Aligned_cols=33  Identities=21%  Similarity=0.285  Sum_probs=27.7

Q ss_pred             CceecccCCCceeecCCCc-cCCCCCCCceEEec
Q 021640            6 NTHWCYRCRRPVRLQGEDA-VCLYCSGGFVQELD   38 (309)
Q Consensus         6 ~~ywCh~C~r~v~~~~~~~-~CP~C~~gFvEE~~   38 (309)
                      ..|||..|...+....... .||.|++..++-+.
T Consensus        72 ~~~~C~~CG~~~e~~~~~~~~CP~Cgs~~~~i~~  105 (119)
T 2kdx_A           72 VELECKDCSHVFKPNALDYGVCEKCHSKNVIITQ  105 (119)
T ss_dssp             CEEECSSSSCEECSCCSTTCCCSSSSSCCCEEEE
T ss_pred             ceEEcCCCCCEEeCCCCCCCcCccccCCCcEEec
Confidence            5799999999998766667 99999999877553

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=90.23  E-value=0.14  Score=35.03  Aligned_cols=45  Identities=31%  Similarity=0.752  Sum_probs=31.0

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccCC----CcCcccc
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN----SCPVCRQ  227 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~----sCP~CR~  227 (309)
                      ..+..|.||.+.   ++-+.--.|...||..|+.+-|....    .||.|..
T Consensus         7 ~~~~~C~vC~~~---g~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            7 GHEDFCSVCRKS---GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SSCCSCSSSCCS---SCCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCccCCCC---CeEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            346789999864   33333334899999999998665432    3888854

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=89.98  E-value=0.37  Score=36.22  Aligned_cols=46  Identities=33%  Similarity=0.660  Sum_probs=32.5

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccCC----CcCccccc
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN----SCPVCRQE  228 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~----sCP~CR~~  228 (309)
                      ..+..|.||.+.   ++-+..-.|.-.||..|+.+=|....    .||.|+..
T Consensus        23 ~n~~~C~vC~~~---g~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~   72 (88)
T 1fp0_A           23 DSATICRVCQKP---GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   72 (88)
T ss_dssp             SSSSCCSSSCSS---SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCC
T ss_pred             CCCCcCcCcCCC---CCEEECCCCCCceecccCCCCCCCCcCCCcCCccccCC
Confidence            456789999854   33333334889999999988776432    49999764

>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=89.57  E-value=0.26  Score=34.29  Aligned_cols=46  Identities=30%  Similarity=0.591  Sum_probs=31.5

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccCC----CcCcccccc
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN----SCPVCRQEL  229 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~----sCP~CR~~l  229 (309)
                      .+..|.||.+.   ++-+.--.|...||..|+.+-|....    .||.|+...
T Consensus         8 ~~~~C~vC~~~---g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            8 HMEFCRVCKDG---GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SCSSCTTTCCC---SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCcCCCCCCC---CCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            45789999852   33233334889999999997665432    499997643

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=89.22  E-value=0.19  Score=34.99  Aligned_cols=46  Identities=33%  Similarity=0.678  Sum_probs=31.5

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccCC----CcCccccc
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN----SCPVCRQE  228 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~----sCP~CR~~  228 (309)
                      ..+..|.||.+.   ++-+.--.|...||..|+.+-|....    .||.|++.
T Consensus         9 ~~~~~C~vC~~~---g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A            9 DHQDYCEVCQQG---GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             CCCSSCTTTSCC---SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCCccCCCC---CcEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            346789999863   33223334889999999998665322    49999764

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=88.17  E-value=0.39  Score=33.87  Aligned_cols=45  Identities=29%  Similarity=0.657  Sum_probs=31.4

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccCC----CcCccccc
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN----SCPVCRQE  228 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~----sCP~CR~~  228 (309)
                      .+..|.||.+.   ++-+..-.|...||..|+.+-|....    .||.|...
T Consensus         7 ~~~~C~vC~~~---g~ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~   55 (66)
T 1xwh_A            7 NEDECAVCRDG---GELICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQA   55 (66)
T ss_dssp             CCCSBSSSSCC---SSCEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHT
T ss_pred             CCCCCccCCCC---CCEEEcCCCChhhcccccCCCcCcCCCCCeECccccCc
Confidence            46789999853   33333334899999999997665432    49999753

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=88.03  E-value=0.13  Score=35.52  Aligned_cols=47  Identities=30%  Similarity=0.743  Sum_probs=32.7

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccCC----CcCccccccc
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN----SCPVCRQELP  230 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~----sCP~CR~~l~  230 (309)
                      .+..|.||...   ++-+.--.|...||..|+.+-|....    .||.|.....
T Consensus         4 ~~~~C~vC~~~---g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~   54 (60)
T 2puy_A            4 HEDFCSVCRKS---GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQML   54 (60)
T ss_dssp             CCSSCTTTCCC---SSCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHHH
T ss_pred             CCCCCcCCCCC---CcEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccChhh
Confidence            45789999863   33333334899999999997665432    4999976543

>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=87.92  E-value=0.18  Score=37.54  Aligned_cols=32  Identities=25%  Similarity=0.768  Sum_probs=23.6

Q ss_pred             cccccccccccccccCCceEEcc---ccceeccccchhh
Q 021640          180 RSDSHCPVCQDKFELGSEARQMP---CNHIYHSDCIVPW  215 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lp---C~H~fh~~Ci~~W  215 (309)
                      ..+..|.||.. |...   .++|   |+-+||..|+.+-
T Consensus        13 ~~D~~C~VC~~-~t~~---~l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           13 VNDEMCDVCEV-WTAE---SLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTTCC-CCSS---CCSSCSSSSSCCCHHHHHHH
T ss_pred             CCCcccCcccc-cccc---ceeccccccccccHhhcccc
Confidence            45789999963 3333   3455   8999999999885

>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=87.38  E-value=0.32  Score=41.15  Aligned_cols=46  Identities=30%  Similarity=0.694  Sum_probs=32.3

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccCC----CcCcccccc
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN----SCPVCRQEL  229 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~----sCP~CR~~l  229 (309)
                      .+..|.||.+.   ++-+..-.|...||..|+.+-|....    .||.|+..-
T Consensus         3 ~~~~C~~C~~~---g~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A            3 NEDWCAVCQNG---GELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             SCSSCTTTCCC---SSCEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCccccCCCC---CeeeecCCCCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            45679999843   33233333899999999998876432    499998643

>3a43_A HYPD, hydrogenase nickel incorporation protein HYPA; [NIFE] hydrogenase maturation, zinc-finger, nickel binding, metal-binding; HET: FME; 2.30A {Pyrococcus kodakaraensis} PDB: 3a44_A*

Probab=86.74  E-value=0.33  Score=39.53  Aligned_cols=32  Identities=16%  Similarity=0.342  Sum_probs=25.8

Q ss_pred             CceecccCCCceeecC-----------C----------CccCCCCCCCceEEe
Q 021640            6 NTHWCYRCRRPVRLQG-----------E----------DAVCLYCSGGFVQEL   37 (309)
Q Consensus         6 ~~ywCh~C~r~v~~~~-----------~----------~~~CP~C~~gFvEE~   37 (309)
                      ..+||..|...+....           .          ...||.|++.-++-+
T Consensus        69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~h~~p~~~~~~~~CP~Cgs~~~~i~  121 (139)
T 3a43_A           69 AVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFEVV  121 (139)
T ss_dssp             CEEEETTTCCEEEGGGCTTCCSCCCGGGCCCCGGGCGGGCSCSSSSCCCEEEE
T ss_pred             CcEECCCCCCEEecccccccccccccccccccccccccCCcCccccCCccEEe
Confidence            5799999999987654           3          578999999987744

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=86.30  E-value=0.32  Score=32.31  Aligned_cols=44  Identities=32%  Similarity=0.639  Sum_probs=28.7

Q ss_pred             cccccccccccCCceEEccccceeccccchhhhccCC----CcCcccc
Q 021640          184 HCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN----SCPVCRQ  227 (309)
Q Consensus       184 ~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~----sCP~CR~  227 (309)
                      .|.||...-..++-+.--.|...||..|+.+=|....    .||.|+.
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            5889986532222233334899999999987555322    4999964

>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=86.21  E-value=0.34  Score=31.97  Aligned_cols=32  Identities=16%  Similarity=0.399  Sum_probs=24.2

Q ss_pred             CceecccCCCceeecC----CCccCCCCCCCceEEe
Q 021640            6 NTHWCYRCRRPVRLQG----EDAVCLYCSGGFVQEL   37 (309)
Q Consensus         6 ~~ywCh~C~r~v~~~~----~~~~CP~C~~gFvEE~   37 (309)
                      +.|-|-.|-+++....    .++.||+|+=-.|..+
T Consensus         2 ~iY~C~rCg~~fs~~el~~lP~IrCpyCGyrii~Kv   37 (48)
T 4ayb_P            2 AVYRCGKCWKTFTDEQLKVLPGVRCPYCGYKIIFMV   37 (48)
T ss_dssp             ---CCCCTTTTCCCCCSCCCSSSCCTTTCCSCEECC
T ss_pred             cEEEeeccCCCccHHHHhhCCCcccCccCcEEEEEe
Confidence            4689999999997653    7889999998877665

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=86.19  E-value=0.38  Score=34.61  Aligned_cols=49  Identities=24%  Similarity=0.499  Sum_probs=33.1

Q ss_pred             ccccccccccccccCCceEE-ccccceeccccchhhhcc----CCCcCccccccc
Q 021640          181 SDSHCPVCQDKFELGSEARQ-MPCNHIYHSDCIVPWLVQ----HNSCPVCRQELP  230 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~-lpC~H~fh~~Ci~~Wl~~----~~sCP~CR~~l~  230 (309)
                      +...|.||..... ++..+. =.|.--||..|+..-+..    .-.||.|+..+.
T Consensus        17 ~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~   70 (75)
T 2k16_A           17 QIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIK   70 (75)
T ss_dssp             EEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHC
T ss_pred             CCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchh
Confidence            4567999987643 322222 238999999999776543    235999987664

>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=85.65  E-value=0.46  Score=33.06  Aligned_cols=48  Identities=19%  Similarity=0.512  Sum_probs=32.5

Q ss_pred             cccccccccccccccCCc-eEEccccceeccccchhhhc-----cCCCcCcccc
Q 021640          180 RSDSHCPVCQDKFELGSE-ARQMPCNHIYHSDCIVPWLV-----QHNSCPVCRQ  227 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~-~~~lpC~H~fh~~Ci~~Wl~-----~~~sCP~CR~  227 (309)
                      ++...|+||...+..+.. +..-.|..-||..|+.--..     ..-.||.|+.
T Consensus         4 ~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~   57 (64)
T 1we9_A            4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcC
Confidence            345689999988753332 33334899999999865432     2346999975

>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=85.16  E-value=0.33  Score=36.69  Aligned_cols=49  Identities=27%  Similarity=0.431  Sum_probs=32.4

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccCC----CcCcccccc
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN----SCPVCRQEL  229 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~----sCP~CR~~l  229 (309)
                      +...|.||...-....-+..=-|...||..|+.+=|....    .||.|+...
T Consensus        15 ~~~~C~vC~~~~~~~~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~~~   67 (92)
T 2e6r_A           15 DSYICQVCSRGDEDDKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILAE   67 (92)
T ss_dssp             CCCCCSSSCCSGGGGGCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHHHH
T ss_pred             CCCCCccCCCcCCCCCEEEcCCCCchhccccCCCCcccCCCCCcCCccCcCcc
Confidence            4568999987533222222333899999999987665432    499997643

>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=85.03  E-value=0.61  Score=36.11  Aligned_cols=47  Identities=26%  Similarity=0.552  Sum_probs=30.8

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccC----CCcCccc
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH----NSCPVCR  226 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~----~sCP~CR  226 (309)
                      ..+..|.||.+.-+..+-+.--.|...||..||...+...    -.||.|+
T Consensus         5 ~~~~~C~~C~~~g~~~~ll~C~~C~~~~H~~Cl~~~~~~~~~~~W~C~~C~   55 (111)
T 2ysm_A            5 SSGANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPECK   55 (111)
T ss_dssp             CCCSCBTTTCCCCCTTTSEECSSSCCEECTTTTTCCCCTTTSTTCCCTTTC
T ss_pred             CCCCCCcCCCCCCCCcCCeECCCCCCCcChHHhCCccccccccCccCCcCC
Confidence            3567899998653222224444599999999999887531    1366654

>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2

Probab=84.28  E-value=0.63  Score=34.77  Aligned_cols=51  Identities=24%  Similarity=0.587  Sum_probs=33.5

Q ss_pred             cccccccccccccc-CCceEEc-cccceeccccchhhhcc--------CCCcCcccccccC
Q 021640          181 SDSHCPVCQDKFEL-GSEARQM-PCNHIYHSDCIVPWLVQ--------HNSCPVCRQELPL  231 (309)
Q Consensus       181 ~~~~C~IC~~~~~~-~~~~~~l-pC~H~fh~~Ci~~Wl~~--------~~sCP~CR~~l~~  231 (309)
                      .+..|.||...-.. ...+..- -|...||..|+.+-|..        .=.|+.|+.....
T Consensus        15 ~~~~C~vC~~~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~~~~~p~g~W~C~~C~~~~~~   75 (88)
T 1wev_A           15 MGLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMKR   75 (88)
T ss_dssp             HCCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHCC
T ss_pred             CCCcCCCCCCCCCCCCCceEECCCCCCeEcCccCCCcccccccCCCCCCeeCccccchhhh
Confidence            35689999875322 1222222 38999999999987752        1249999876543

>2yt5_A Metal-response element-binding transcription factor 2; zinc-regulated factor 1, ZIRF1, metal-response element DNA-binding protein M96; NMR {Mus musculus}

Probab=83.95  E-value=0.46  Score=33.21  Aligned_cols=50  Identities=22%  Similarity=0.468  Sum_probs=32.8

Q ss_pred             ccccccccccccccc--CCceEEccccceeccccchhhhcc-------CCCcCcccccc
Q 021640          180 RSDSHCPVCQDKFEL--GSEARQMPCNHIYHSDCIVPWLVQ-------HNSCPVCRQEL  229 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~--~~~~~~lpC~H~fh~~Ci~~Wl~~-------~~sCP~CR~~l  229 (309)
                      .++..|.||......  +.-+.--.|...||..|+.+-|..       .=.|+.|....
T Consensus         4 ~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~   62 (66)
T 2yt5_A            4 GSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFAT   62 (66)
T ss_dssp             CCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTT
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCcc
Confidence            345789999976432  222222338999999999986642       12499997644

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=83.95  E-value=0.44  Score=41.18  Aligned_cols=46  Identities=30%  Similarity=0.686  Sum_probs=31.4

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccCC----CcCcccccc
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN----SCPVCRQEL  229 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~----sCP~CR~~l  229 (309)
                      .+..|.||...   ++-+..=.|...||..|+.+.|....    .||.|+..-
T Consensus         6 ~~~~C~~C~~~---g~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A            6 NEDWCAVCQNG---GDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             SCSSBTTTCCC---EEEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCCCCCCCC---CceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            45789999743   22112222889999999998876432    499998643

---

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	309
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	6e-18
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	8e-15
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	4e-13
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	9e-13
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	1e-11
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	3e-11
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	2e-09
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	1e-08
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	1e-07
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	1e-07
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	2e-07
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	1e-06
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	2e-05
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	3e-04

>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 = 74.1 bits (182), Expect = 6e-18
 Identities = 20/51 (39%), Positives = 31/51 (60%), Gaps = 1/51 (1%)

Query: 182 DSHCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQHNSCPVCRQELPL 231
              C VC  + E G EAR +P C H +H++C+  WL  H++CP+CR  + +
Sbjct: 5   GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV 55

>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 = 65.7 bits (160), Expect = 8e-15
 Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 2/46 (4%)

Query: 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP 230
           CP+C +     + +  +PC H +   CI  W+ Q+ +CP+C+  + 
Sbjct: 8   CPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE 51

>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 = 62.1 bits (150), Expect = 4e-13
 Identities = 15/67 (22%), Positives = 22/67 (32%), Gaps = 15/67 (22%)

Query: 181 SDSHCPVCQDKFELGSEARQ---------------MPCNHIYHSDCIVPWLVQHNSCPVC 225
              +C +C++         Q                 CNH +H  CI  WL     CP+ 
Sbjct: 20  VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLD 79

Query: 226 RQELPLQ 232
            +E   Q
Sbjct: 80  NREWEFQ 86

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.8 bits (147), Expect = 9e-13
 Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 4/50 (8%)

Query: 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWL-VQHNSCPVCRQEL 229
           +   C +C +  +   + +  PC H+  + C+  W   +   CP CR E+
Sbjct: 22  TFQLCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEI 68

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.8 bits (137), Expect = 1e-11
 Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 6/48 (12%)

Query: 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQ 232
           C  CQ + +     + +PC H   S C+         CP+C+   PL 
Sbjct: 9   CQQCQAEAK---CPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLG 50

>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 = 55.9 bits (134), Expect = 3e-11
 Identities = 12/51 (23%), Positives = 16/51 (31%), Gaps = 3/51 (5%)

Query: 182 DSHCPVCQDKFELGSEARQM--PCNHIYHSDCIVPWL-VQHNSCPVCRQEL 229
           D  CP C+         + M   C H     C+         +CP C   L
Sbjct: 3   DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 53

>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 = 52.0 bits (124), Expect = 2e-09
 Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 6/62 (9%)

Query: 172 VRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN---SCPVCRQE 228
           V+     ++    CP+C +  +   E     C+HI+   C++  L Q      CP+C+ +
Sbjct: 11  VQNVINAMQKILECPICLELIK---EPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKND 67

Query: 229 LP 230
           + 
Sbjct: 68  IT 69

>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 = 48.2 bits (114), Expect = 1e-08
 Identities = 12/48 (25%), Positives = 17/48 (35%), Gaps = 2/48 (4%)

Query: 185 CPVCQDKFELG-SEARQMPCNHIYHSDCIVPWLVQHN-SCPVCRQELP 230
           CP+C +  E+         C +     C        N  CP CR+  P
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYP 50

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.4 bits (110), Expect = 1e-07
 Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 17/68 (25%)

Query: 176 QRHLRSDSH-------------CPVCQDKFELGSEARQMPCNHIYHSDCIVPWL-VQHNS 221
           + HL +                C +C+       +  +  C H++   CI+  L V  + 
Sbjct: 4   KIHLSTKLLAVDFPAHFVKSISCQICEHILA---DPVETSCKHLFCRICILRCLKVMGSY 60

Query: 222 CPVCRQEL 229
           CP CR   
Sbjct: 61  CPSCRYPC 68

>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 = 46.7 bits (110), Expect = 1e-07
 Identities = 15/65 (23%), Positives = 21/65 (32%), Gaps = 4/65 (6%)

Query: 168 AMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQ 227
           A    R     L     C  C +            C HI+ S+C+   +     CPVC  
Sbjct: 8   AWAHSRAALDRLEKLLRCSRCTNILR--EPVCLGGCEHIFCSNCVSDCI--GTGCPVCYT 63

Query: 228 ELPLQ 232
              +Q
Sbjct: 64  PAWIQ 68

>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 = 45.2 bits (106), Expect = 2e-07
 Identities = 8/53 (15%), Positives = 17/53 (32%), Gaps = 4/53 (7%)

Query: 184 HCPVCQDKFELGSEARQMP--CNHIYHSDCIVPWL--VQHNSCPVCRQELPLQ 232
            C +C ++                  H  C+  WL   ++ +C +C      +
Sbjct: 8   VCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNTR 60

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 42.8 bits (100), Expect = 1e-06
 Identities = 4/48 (8%), Positives = 14/48 (29%), Gaps = 2/48 (4%)

Query: 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQ 232
           C +                  I+    +  ++    + P+  + L ++
Sbjct: 3   CAISGKVPR--RPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE 48

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.8 bits (94), Expect = 2e-05
 Identities = 10/69 (14%), Positives = 21/69 (30%), Gaps = 5/69 (7%)

Query: 163 RSAIDAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV----- 217
           + A +    + + +  + S                 R   C+H +H  C++         
Sbjct: 21  KVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKD 80

Query: 218 QHNSCPVCR 226
               CP C+
Sbjct: 81  GSLQCPSCK 89

>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 = 37.4 bits (86), Expect = 3e-04
 Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 10/62 (16%)

Query: 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN--------SCP--VCRQELP 230
             S C +C  ++ +        C  I+ + C+  ++            SCP   C ++  
Sbjct: 4   GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGH 63

Query: 231 LQ 232
           LQ
Sbjct: 64  LQ 65

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	309
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.62
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.41
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.34
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.32
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.31
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.24
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.22
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.12
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.1
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.04
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.03
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.98
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.87
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	98.82
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.77
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.53
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.23
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	92.7
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	92.28
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	89.54
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	88.11
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	87.21
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	81.31

>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=99.62  E-value=8.9e-17  Score=111.29  Aligned_cols=51  Identities=39%  Similarity=0.974  Sum_probs=46.6

Q ss_pred             cccccccccccccccCCceEEcc-ccceeccccchhhhccCCCcCccccccc
Q 021640          180 RSDSHCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lp-C~H~fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      +++.+|+||+++|..++.++.++ |+|.||..||.+||+.+++||+||+.|.
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            45678999999999999998886 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=99.41  E-value=4.1e-14  Score=101.77  Aligned_cols=47  Identities=28%  Similarity=0.859  Sum_probs=42.1

Q ss_pred             cccccccccccccCCceEEccccceeccccchhhhccCCCcCccccccc
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP  230 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~  230 (309)
                      .+.|+||++.|.  +.++.++|+|.||..||..||+.+.+||+||+++.
T Consensus         5 ~d~C~IC~~~~~--~~~~~~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~   51 (68)
T d1chca_           5 AERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCSSCCSCCC--SCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCccCCcCcc--CCcEEeCCCCcCcHHHHHHHHHhCCcCCCCCcchH
Confidence            467999999986  35678999999999999999999999999999874

>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=99.34  E-value=4.6e-13  Score=105.41  Aligned_cols=54  Identities=20%  Similarity=0.596  Sum_probs=42.2

Q ss_pred             ccccccccccccccC---------------CceEEccccceeccccchhhhccC-----CCcCcccccccCCCC
Q 021640          181 SDSHCPVCQDKFELG---------------SEARQMPCNHIYHSDCIVPWLVQH-----NSCPVCRQELPLQGS  234 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~---------------~~~~~lpC~H~fh~~Ci~~Wl~~~-----~sCP~CR~~l~~~~~  234 (309)
                      .+..|+||++.|...               ..+.+++|+|+||..||..||+..     .+||+||..+..+..
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~~~   97 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTG   97 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSS
T ss_pred             ccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccCcC
Confidence            356799999998532               245678899999999999999753     379999988755543

>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=99.32  E-value=1.9e-13  Score=103.04  Aligned_cols=51  Identities=25%  Similarity=0.615  Sum_probs=42.6

Q ss_pred             ccccccccccccccCC---------------ceEEccccceeccccchhhhccCCCcCcccccccC
Q 021640          181 SDSHCPVCQDKFELGS---------------EARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPL  231 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~---------------~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~  231 (309)
                      .++.|+||++.+....               .+..++|+|+||..||.+||+.+++||+||+++..
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   85 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEF   85 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCCE
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCCcCCCCCCcccc
Confidence            3467999998875422               36778899999999999999999999999998753

>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=99.31  E-value=1.2e-13  Score=94.10  Aligned_cols=48  Identities=23%  Similarity=0.545  Sum_probs=40.5

Q ss_pred             cccccccccccCCc-eEEccccceeccccchhhhccC-CCcCcccccccC
Q 021640          184 HCPVCQDKFELGSE-ARQMPCNHIYHSDCIVPWLVQH-NSCPVCRQELPL  231 (309)
Q Consensus       184 ~C~IC~~~~~~~~~-~~~lpC~H~fh~~Ci~~Wl~~~-~sCP~CR~~l~~  231 (309)
                      +|+||+++|..++. ++.++|+|.||..||.+|++.+ .+||+||+++..
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            69999999976654 4556899999999999999865 469999998864

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=1.2e-12  Score=93.10  Aligned_cols=51  Identities=24%  Similarity=0.526  Sum_probs=40.5

Q ss_pred             cccccccccccccCC--ceEEccccceeccccchhhhcc-CCCcCcccccccCC
Q 021640          182 DSHCPVCQDKFELGS--EARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQELPLQ  232 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~--~~~~lpC~H~fh~~Ci~~Wl~~-~~sCP~CR~~l~~~  232 (309)
                      +..|+||++.+..+.  .+..++|+|.||..||..|+.. +.+||+||+.|...
T Consensus         3 d~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~   56 (65)
T d1g25a_           3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCcccc
Confidence            468999999864432  3466789999999999999965 55799999988543

>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=99.22  E-value=1.7e-12  Score=95.89  Aligned_cols=48  Identities=25%  Similarity=0.785  Sum_probs=41.1

Q ss_pred             ccccccccccccCCceEEccccceeccccchhhhcc-CCCcCcccccccCCC
Q 021640          183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQELPLQG  233 (309)
Q Consensus       183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~-~~sCP~CR~~l~~~~  233 (309)
                      ..|+||++.+.   .++.++|+|.||..||..||.. +++||+||+.|....
T Consensus        24 ~~C~IC~~~~~---~~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~   72 (79)
T d1fbva4          24 QLCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE   72 (79)
T ss_dssp             TBCTTTSSSBC---CEECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCC
T ss_pred             CCCccCCCcCC---CeEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCc
Confidence            46999999874   5688999999999999999974 578999999986544

>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=99.12  E-value=1.1e-11  Score=85.44  Aligned_cols=46  Identities=28%  Similarity=0.681  Sum_probs=38.8

Q ss_pred             cccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCC
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG  233 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~  233 (309)
                      ...|+||++.|..   .+.+||+|.||..||..|   +.+||+||+.+....
T Consensus         6 ~l~C~IC~~~~~~---p~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T d1bora_           6 FLRCQQCQAEAKC---PKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CSSCSSSCSSCBC---CSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             CCCCcccCcccCC---CEEecCCCHHhHHHHHcC---CCcCcCCCCcccCCC
Confidence            3689999999964   478999999999999887   567999999986543

>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=99.10  E-value=5.3e-12  Score=87.06  Aligned_cols=48  Identities=8%  Similarity=0.212  Sum_probs=40.9

Q ss_pred             cccccccccccCCceEEc-cccceeccccchhhhccCCCcCcccccccCCCC
Q 021640          184 HCPVCQDKFELGSEARQM-PCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGS  234 (309)
Q Consensus       184 ~C~IC~~~~~~~~~~~~l-pC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~  234 (309)
                      .|+||++.|+.   .+.+ .|||+||.+||.+||+.+.+||+||+.+..++.
T Consensus         2 ~C~Ic~~~~~~---Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dL   50 (56)
T d2baya1           2 LCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEI   50 (56)
T ss_dssp             CCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGC
T ss_pred             CCccCCchHHh---cCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhc
Confidence            69999999863   3555 599999999999999999999999998876543

>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=99.04  E-value=1.6e-11  Score=94.77  Aligned_cols=51  Identities=24%  Similarity=0.722  Sum_probs=41.8

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccCC---CcCcccccccCCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN---SCPVCRQELPLQG  233 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~---sCP~CR~~l~~~~  233 (309)
                      +....|+||++.|..   ++.++|+|.||..||..|+....   .||+||..+...+
T Consensus        19 ~~~l~CpIC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   72 (103)
T d1jm7a_          19 QKILECPICLELIKE---PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS   72 (103)
T ss_dssp             HHHTSCSSSCCCCSS---CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTT
T ss_pred             ccCcCCCccCchhCC---eEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhh
Confidence            345689999999964   46789999999999999997653   6999999886544

>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=99.03  E-value=1.7e-11  Score=91.79  Aligned_cols=50  Identities=22%  Similarity=0.589  Sum_probs=41.5

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhcc-CCCcCcccccccCCC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQELPLQG  233 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~-~~sCP~CR~~l~~~~  233 (309)
                      ....|+||++.|.   .++.++|+|.||..||..|++. +.+||+||..+...+
T Consensus        22 ~~l~C~IC~~~~~---~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~   72 (86)
T d1rmda2          22 KSISCQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (86)
T ss_dssp             HHTBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             cCcCCccCCcchh---cceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChhh
Confidence            4578999999985   4578999999999999999974 457999999875443

>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=98.98  E-value=7.1e-11  Score=90.08  Aligned_cols=50  Identities=24%  Similarity=0.515  Sum_probs=40.0

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCCC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGS  234 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~  234 (309)
                      ....|+||++.|..+  +...+|+|.||..||..|+.  +.||+||..+...+.
T Consensus        21 ~~l~C~IC~~~~~~p--v~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~l   70 (97)
T d1jm7b_          21 KLLRCSRCTNILREP--VCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDL   70 (97)
T ss_dssp             HTTSCSSSCSCCSSC--BCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSC
T ss_pred             hcCCCccCCchhhcC--ceeCCCCCchhHHHHHHHHh--ccccccCCcCchhhC
Confidence            456899999999643  44458999999999999985  469999988765443

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=98.87  E-value=2.1e-10  Score=79.83  Aligned_cols=49  Identities=18%  Similarity=0.492  Sum_probs=37.6

Q ss_pred             cccccccccccccccCCceEEcc-----ccceeccccchhhhc--cCCCcCcccccccC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMP-----CNHIYHSDCIVPWLV--QHNSCPVCRQELPL  231 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lp-----C~H~fh~~Ci~~Wl~--~~~sCP~CR~~l~~  231 (309)
                      ++...|.||++++...   ...|     |+|.||..||..|+.  .+.+||+||+++..
T Consensus         4 ed~~~C~IC~~~~~~~---~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           4 EDVPVCWICNEELGNE---RFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEECSCC---CCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCCccCCccCCCc---eeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            3457899999987643   2333     469999999999996  34589999998753

>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=98.82  E-value=6e-10  Score=81.85  Aligned_cols=50  Identities=16%  Similarity=0.112  Sum_probs=41.9

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhcc-CCCcCcccccccCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQELPLQ  232 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~-~~sCP~CR~~l~~~  232 (309)
                      -+...|+||++.|..   .+.++|||.|+..||..||.. +.+||+||..+...
T Consensus         5 P~~l~CpIc~~l~~d---Pv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~   55 (80)
T d2c2la2           5 PDYLCGKISFELMRE---PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQE   55 (80)
T ss_dssp             CSTTBCTTTCSBCSS---EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGG
T ss_pred             CccccCcCcCchhhh---hcccCCcCeecHHHHHHHHhcCCccCCCcccccccc
Confidence            356789999999964   368999999999999999975 45799999987544

>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=98.77  E-value=1.1e-09  Score=79.96  Aligned_cols=51  Identities=20%  Similarity=0.436  Sum_probs=42.8

Q ss_pred             cccccccccccccccCCceEEccccceeccccchhhhccC-CCcCcccccccCCC
Q 021640          180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH-NSCPVCRQELPLQG  233 (309)
Q Consensus       180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~-~sCP~CR~~l~~~~  233 (309)
                      .++..|+||++.|..   .+.++|+|.|+..||..|++.+ ..||+|+..+...+
T Consensus         6 P~~l~CpIc~~~m~d---PV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~   57 (78)
T d1t1ha_           6 PEYFRCPISLELMKD---PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAG   57 (78)
T ss_dssp             SSSSSCTTTSCCCSS---EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCC
T ss_pred             CccCCCcCcCchhhC---ceEccCCCcchHHHHHHHHHHCCCCCCcccccCCccc
Confidence            356789999999964   4688999999999999999865 56999999886544

>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=98.53  E-value=1.5e-08  Score=77.25  Aligned_cols=52  Identities=13%  Similarity=0.165  Sum_probs=43.7

Q ss_pred             ccccccccccccccCCceEEcccc-ceeccccchhhhccCCCcCcccccccCCCCC
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCN-HIYHSDCIVPWLVQHNSCPVCRQELPLQGSS  235 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~-H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~~  235 (309)
                      .+..|+||++.|..   +++++|+ |.|+..||..||..+.+||+|+..|..+...
T Consensus        21 ~~f~CPI~~~lm~d---PV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L~   73 (98)
T d1wgma_          21 DEFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIR   73 (98)
T ss_dssp             TTTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSE
T ss_pred             HHhCCcCchhHHHH---HHhcccccchhhHHHHHHHHHhcCCcccccccccchhhc
Confidence            35799999999964   4788866 5899999999999999999999998765443

>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=98.23  E-value=1.1e-07  Score=71.16  Aligned_cols=47  Identities=19%  Similarity=0.492  Sum_probs=37.4

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccC--------CCcCcccc
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH--------NSCPVCRQ  227 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~--------~sCP~CR~  227 (309)
                      ....|+||++++...+.+..++|+|.||.+||..|++..        -.||.|..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            346899999999776666777899999999999999732        25998643

>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=92.70  E-value=0.022  Score=36.53  Aligned_cols=44  Identities=32%  Similarity=0.639  Sum_probs=30.1

Q ss_pred             cccccccccccCCceEEccccceeccccchhhhccCC----CcCcccc
Q 021640          184 HCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN----SCPVCRQ  227 (309)
Q Consensus       184 ~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~----sCP~CR~  227 (309)
                      .|.||...-..+.-+.--.|...||..|+.+-+....    .||.|+.
T Consensus         2 ~C~vC~~~~~~~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            5889976543332233334899999999999876433    4999974

>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=92.28  E-value=0.078  Score=36.25  Aligned_cols=45  Identities=31%  Similarity=0.632  Sum_probs=30.1

Q ss_pred             cccccccccccccCCceEEccccceeccccchhhhccCC----CcCcccccc
Q 021640          182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN----SCPVCRQEL  229 (309)
Q Consensus       182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~----sCP~CR~~l  229 (309)
                      ...|.||.+   .++-+.--.|...||..|+.+.|....    .||.|+...
T Consensus         7 c~~C~~C~~---~~~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   55 (70)
T d1fp0a1           7 ATICRVCQK---PGDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   55 (70)
T ss_dssp             SSCCSSSCS---SSCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCCCCC---cCEEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcC
Confidence            346777753   333333334999999999999886443    499996543

>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=89.54  E-value=0.088  Score=35.14  Aligned_cols=47  Identities=19%  Similarity=0.509  Sum_probs=32.7

Q ss_pred             ccccccccccccccCCceE-Eccccceeccccchhhhc-----cCCCcCcccc
Q 021640          181 SDSHCPVCQDKFELGSEAR-QMPCNHIYHSDCIVPWLV-----QHNSCPVCRQ  227 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~-~lpC~H~fh~~Ci~~Wl~-----~~~sCP~CR~  227 (309)
                      ....|.||......++..+ --.|+..||..|+..-..     ..-.||.|+.
T Consensus         5 ~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~   57 (64)
T d1we9a_           5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcC
Confidence            3568999998776655433 334999999999964322     2346999975

>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=88.11  E-value=0.17  Score=35.86  Aligned_cols=49  Identities=22%  Similarity=0.565  Sum_probs=31.9

Q ss_pred             cccccccccccccC-CceE-Eccccceeccccchhhhcc--------CCCcCccccccc
Q 021640          182 DSHCPVCQDKFELG-SEAR-QMPCNHIYHSDCIVPWLVQ--------HNSCPVCRQELP  230 (309)
Q Consensus       182 ~~~C~IC~~~~~~~-~~~~-~lpC~H~fh~~Ci~~Wl~~--------~~sCP~CR~~l~  230 (309)
                      ...|.||....... ..++ .--|...||..|+.+.+..        .-.||.|.....
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~~   74 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMK   74 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHC
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchHh
Confidence            46799998654322 2222 2238899999999876531        225999976543

>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=87.21  E-value=0.19  Score=33.12  Aligned_cols=45  Identities=31%  Similarity=0.593  Sum_probs=30.6

Q ss_pred             ccccccccccccccCCceEEccccceeccccchhhhccC----CCcCccccc
Q 021640          181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH----NSCPVCRQE  228 (309)
Q Consensus       181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~----~sCP~CR~~  228 (309)
                      ....|.||.+.   ++-+.--.|.-.||..||...+...    -.||.|+..
T Consensus         8 ~~~~C~~C~~~---g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~   56 (61)
T d1mm2a_           8 HMEFCRVCKDG---GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCP   56 (61)
T ss_dssp             SCSSCTTTCCC---SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTT
T ss_pred             CcCCCcCCCCC---CeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCc
Confidence            34579999742   3333333489999999998776542    249999754

>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=81.31  E-value=0.17  Score=35.65  Aligned_cols=33  Identities=24%  Similarity=0.785  Sum_probs=25.3

Q ss_pred             ccccccccccccccccCCceEEcc---ccceeccccchhh
Q 021640          179 LRSDSHCPVCQDKFELGSEARQMP---CNHIYHSDCIVPW  215 (309)
Q Consensus       179 ~~~~~~C~IC~~~~~~~~~~~~lp---C~H~fh~~Ci~~W  215 (309)
                      ...+..|.|| +.|...   .++|   |+-+||..|+.+.
T Consensus        12 v~~D~mC~vC-~v~t~~---~l~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          12 VVNDEMCDVC-EVWTAE---SLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCSCCCTTT-CCCCSS---CCSSCSSSSSCCCHHHHHHH
T ss_pred             CCcCcccccc-Cccccc---ceecceeecchhhHHHHHHh
Confidence            4467889999 666554   3456   7899999999876