Citrus Sinensis ID: 042810

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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
Protein Sequence
MDVRVNLHLEGTGSCSNNPLMCPVGNIGIVLKQRCQKVNRSPSNGQQFILRDYTRSVNRFPVIQIPANALTSPMYLFRELVTLNLDHMLCVFLHQHLAQGAFYLSSGGLTGFHLSADVEVVEIEVVEDEIERSERKEASRFVVEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLVG
Secondary Structure (PSIPRED)
ccEEEccEEEcccccccccccccccccccEEEEccccccccccccccccccccccccccccEEEcccccccccHHHHHHHHHcccccHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHccccEEEcccccHHcccccccccEEccccccHHHHHHccccccccccccccccccccHHHHHHHHcccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEEEEEccccccccccccccHHHHHHHHHcccccccccccHHEccccccccccccEEEEcHHHEccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHccccccccEEEcccHHHHHHHHHccccccccccHHHHHHHHHccHHHHccccccHHHHccccccEEEEHHHcEccccccccccccccEEEEccccccccHHHHHHHHHHccccccccccccHHcccc
Coil and Loop (DISEMBL)
MDVRVNlhlegtgscsnnplmcpvgniGIVLKQRCqkvnrspsngqqfilrdytrsvnrfpviqipanaltspmYLFRELVTLNLDHMLCVFLHQHLAQGAfylssggltgfhlsadvEVVEIEVVEDEIERSERKEASRFVVEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEeikgqttekktqlitmpchhifHASCISRWLeeqnscpmcrrqiqyEDLVG
Flexible Loop (DISEMBL)
MDVRVNLHLegtgscsnnplmCPVGNIGIVLKQRCQKvnrspsngqqfilRDYTRSVNRFPVIQIPANALTSPMYLFRELVTLNLDHMLCVFLHQHLAQGAFYLSSGGLTGFHLSADVEVVEIEVVedeierserkeasrfvvemlsrkqrrvldldfnklvkAGDNCAVCLEELIAkeeikgqttekkTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLVG
Low Complexity Region (SEG)
MDVRVNLHLEGTGSCSNNPLMCPVGNIGIVLKQRCQKVNRSPSNGQQFILRDYTRSVNRFPVIQIPANALTSPMYLFRELVTLNLDHMLCVFLHQHLAQGAFYLSSGGLTGFHLSAdvevveievvedeieRSERKEASRFVVEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLVG
Disordered region (IsUnstruct)
***********TGSCSNNPLMCPVGNIGIVLKQRCQKVNR***NGQQFILRDYTRSVNRFPVIQIPANALTSPMYLFRELVTLNLDHMLCVFLHQHLAQGAFYLSSGGLTGFHLSADVEVVEIEVVEDEI*********RFVVEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ******
Disordered Region (DISOPRED)
**VRVNL****************VGNIGIV***************************************LTSPMYLFRELVTLNLDHMLCVFLHQHLAQGAFYLSSGGLTGFHLSADVEVVEI********************EMLSRKQRRVLDL****LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQY*****
Disordered Region (DISEMBL)
MDVRVNLHLEGTGSCSNNPLMCPVGNIGIVLKQRCQKVNRSPSNGQQFILRDYTRSVNRFPVIQIPANALTSPMYLFRELVTLNLDHMLCVFLHQHLAQGAFYLSSGGLTGFHLSADVEVVEIEVVEDEIERSERKEASRFVVEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLVG
Disordered Region (DISPRO)
MDVRVNLHLEGTGSCSNNPLMCPVGNIGIVLKQRCQKVN*******QFILRDYTRSVNRFPVIQIPANALTSPMYLFRELVTLNLDHMLCVFLHQHLAQGAFYLSSGGLTGFHLSADVEVVEIEVVEDEIERSERKEASRFVVEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDVRVNLHLEGTGSCSNNPLMCPVGNIGIVLKQRCQKVNRSPSNGQQFILRDYTRSVNRFPVIQIPANALTSPMYLFRELVTLNLDHMLCVFLHQHLAQGAFYLSSGGLTGFHLSADVEVVEIEVVEDEIERSERKEASRFVVEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLVG
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	230	2.2.26 [Sep-21-2011]
P30631	161	Uncharacterized RING fing	yes	no	0.356	0.509	0.347	8e-10
Q9CY62	165	E3 ubiquitin-protein liga	yes	no	0.456	0.636	0.325	1e-09
P0CH30	338	E3 ubiquitin-protein liga	N/A	no	0.430	0.292	0.281	3e-09
Q8LPN7	328	E3 ubiquitin-protein liga	no	no	0.447	0.314	0.260	1e-08
Q9M0R6	302	Putative RING-H2 finger p	no	no	0.382	0.291	0.330	3e-08
Q9Y4L5	304	E3 ubiquitin-protein liga	yes	no	0.239	0.180	0.378	9e-08
Q8BP31	155	RING finger protein 122 O	no	no	0.260	0.387	0.394	1e-07
Q9D0C1	305	E3 ubiquitin-protein liga	no	no	0.239	0.180	0.363	2e-07
Q9H9V4	155	RING finger protein 122 O	no	no	0.260	0.387	0.394	2e-07
Q6NRX0	397	E3 ubiquitin-protein liga	N/A	no	0.321	0.186	0.305	3e-07

>sp|P30631|YOUD_CAEEL Uncharacterized RING finger protein ZK637.14 OS=Caenorhabditis elegans GN=ZK637.14 PE=4 SV=2

 Score = 63.9 bits (154), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 32/92 (34%), Positives = 49/92 (53%), Gaps = 10/92 (10%)

Query: 143 VEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEEL----------IAKEEIKGQTTEKKTQL 192
           ++  S K  R++D +     K    CA+CL+ L          + KEE+K   T   T +
Sbjct: 47  IDKKSYKALRLMDRETTDQQKEDATCAICLDNLQNNVDIPEDHVIKEELKIDPTTFGTTV 106

Query: 193 ITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ 224
           I MPC H FH  C++ WLE Q +CP CR++++
Sbjct: 107 IVMPCKHRFHYFCLTLWLEAQQTCPTCRQKVK 138

Caenorhabditis elegans (taxid: 6239)

>sp|Q9CY62|RN181_MOUSE E3 ubiquitin-protein ligase RNF181 OS=Mus musculus GN=Rnf181 PE=2 SV=1

 Score = 63.2 bits (152), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 42/129 (32%), Positives = 62/129 (48%), Gaps = 24/129 (18%)

Query: 99  QGAFYLSSGGLTGFHLSADVEVVEIEVVEDEIERSERKEASRFVVEMLSRKQRRVLDLDF 158
           +GA+  + GG + F+   D E + +   E  +       A++ VVE L R          
Sbjct: 32  RGAWSWAPGGRSLFN-RMDFEDLGLVDWEHHLP----PPAAKAVVESLPRT--------V 78

Query: 159 NKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPM 218
               KA   C VCL E  A+E +           I MPCHH+FH++CI  WL + NSCP+
Sbjct: 79  ISSAKADLKCPVCLLEFEAEETV-----------IEMPCHHLFHSNCILPWLSKTNSCPL 127

Query: 219 CRRQIQYED 227
           CR ++  +D
Sbjct: 128 CRHELPTDD 136

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.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score = 62.0 bits (149), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 36/128 (28%), Positives = 61/128 (47%), Gaps = 29/128 (22%)

Query: 111 GFHLSADV---------EVVEIEVVEDEIERSERKEASRFVVEMLS--RKQRRVLDLDFN 159
           GF L A++         E +  ++ E++  R     AS+  +E L      +  L+ +FN
Sbjct: 163 GFRLPANIGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPLVNITKSNLNSEFN 222

Query: 160 KLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMC 219
           +       CAVC+++            E+ T+   MPC H++H  C+  WLE  NSCP+C
Sbjct: 223 Q-------CAVCMDDF-----------EEGTEAKQMPCKHLYHKDCLLPWLELHNSCPVC 264

Query: 220 RRQIQYED 227
           R ++  +D
Sbjct: 265 RHELPTDD 272

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

 Score = 60.1 bits (144), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 32/123 (26%), Positives = 57/123 (46%), Gaps = 20/123 (16%)

Query: 107 GGLTGFHLSADVEVVEIEVVEDEIERSERKEASRFVVEMLS--RKQRRVLDLDFNKLVKA 164
           G    +     +E +  ++ E++  R     AS+  ++ L   +  + +L  + N+    
Sbjct: 160 GNFGDYFFGPGLEQLIQQLAENDPNRYGTPPASKSAIDALPTVKVTKDMLKSEMNQ---- 215

Query: 165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ 224
              CAVC++E     ++K            MPC H+FH  C+  WLE  NSCP+CR ++ 
Sbjct: 216 ---CAVCMDEFEDGSDVK-----------QMPCKHVFHQDCLLPWLELHNSCPVCRFELP 261

Query: 225 YED 227
            +D
Sbjct: 262 TDD 264

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

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9M0R6|ATL35_ARATH Putative RING-H2 finger protein ATL35 OS=Arabidopsis thaliana GN=ATL35 PE=3 SV=1

 Score = 58.9 bits (141), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 35/106 (33%), Positives = 48/106 (45%), Gaps = 18/106 (16%)

Query: 116 ADVEVVEIEVVEDEIERSERKE-ASRFVVEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEE 174
           A+VE    EV      R   KE    F + + S       ++   K+ K G  CA+CL E
Sbjct: 77  AEVEAASQEVFHSRARRGLEKELVESFPIFLYS-------EVKGLKIGKGGVECAICLSE 129

Query: 175 LIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCR 220
            + KE ++             PC H FHA+CI  WL  Q++CP CR
Sbjct: 130 FVDKETLRWMP----------PCSHTFHANCIDVWLSSQSTCPACR 165

Arabidopsis thaliana (taxid: 3702)

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

 Score = 57.4 bits (137), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 37/66 (56%), Gaps = 11/66 (16%)

Query: 162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR 221
           V  G  C VC E+   +EE++            +PC+H FH+SCI  WLE  ++CP+CR+
Sbjct: 222 VDMGLECPVCKEDYTVEEEVR-----------QLPCNHFFHSSCIVPWLELHDTCPVCRK 270

Query: 222 QIQYED 227
            +  ED
Sbjct: 271 SLNGED 276

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

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q8BP31|RN122_MOUSE RING finger protein 122 OS=Mus musculus GN=Rnf122 PE=2 SV=1

 Score = 56.6 bits (135), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/71 (39%), Positives = 36/71 (50%), Gaps = 11/71 (15%)

Query: 153 VLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE 212
           VL  D  KL   G  CAVCLE+   K+E+             +PC H FH  C+ +WLE 
Sbjct: 78  VLKGDAKKLQLYGQTCAVCLEDFKGKDELG-----------VLPCQHAFHRKCLVKWLEV 126

Query: 213 QNSCPMCRRQI 223
           +  CPMC + I
Sbjct: 127 RCVCPMCNKPI 137

May induce necrosis and apoptosis. May play a role in cell viability.

Mus musculus (taxid: 10090)

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

 Score = 56.6 bits (135), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 37/66 (56%), Gaps = 11/66 (16%)

Query: 162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR 221
           V  G  C VC E+   +E+++            +PC+H FH+SCI  WLE  ++CP+CR+
Sbjct: 223 VNTGLECPVCKEDYTVEEKVR-----------QLPCNHFFHSSCIVPWLELHDTCPVCRK 271

Query: 222 QIQYED 227
            +  ED
Sbjct: 272 SLNGED 277

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|Q9H9V4|RN122_HUMAN RING finger protein 122 OS=Homo sapiens GN=RNF122 PE=2 SV=2

 Score = 56.2 bits (134), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/71 (39%), Positives = 36/71 (50%), Gaps = 11/71 (15%)

Query: 153 VLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE 212
           VL  D  KL   G  CAVCLE+   K+E+             +PC H FH  C+ +WLE 
Sbjct: 78  VLKGDAKKLQLYGQTCAVCLEDFKGKDELG-----------VLPCQHAFHRKCLVKWLEV 126

Query: 213 QNSCPMCRRQI 223
           +  CPMC + I
Sbjct: 127 RCVCPMCNKPI 137

May induce necrosis and apoptosis. May play a role in cell viability.

Homo sapiens (taxid: 9606)

>sp|Q6NRX0|RN149_XENLA E3 ubiquitin-protein ligase RNF149 OS=Xenopus laevis GN=rnf149 PE=2 SV=1

 Score = 55.8 bits (133), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/95 (30%), Positives = 47/95 (49%), Gaps = 21/95 (22%)

Query: 132 RSERKEASRFVVEML---SRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEK 188
           +S RKE  + + ++     +K  + +D+D        +NCAVC+E    K+ ++      
Sbjct: 232 QSNRKETKKAISQLQLHRVKKGEKGIDID-------AENCAVCIENYKTKDLVR------ 278

Query: 189 KTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQI 223
                 +PC HIFH  CI  WL E  +CPMC+  +
Sbjct: 279 -----ILPCKHIFHRLCIDPWLIEHRTCPMCKLDV 308

Xenopus laevis (taxid: 8355)

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	230
255585222	227	conserved hypothetical protein [Ricinus	0.882	0.894	0.285	2e-13
224146442	223	predicted protein [Populus trichocarpa]	0.652	0.672	0.306	6e-12
224083886	257	predicted protein [Populus trichocarpa]	0.886	0.793	0.238	4e-10
296412639	291	hypothetical protein [Tuber melanosporum	0.317	0.250	0.366	2e-09
255572321	246	zinc finger protein, putative [Ricinus c	0.443	0.414	0.304	2e-09
255585224	155	zinc finger protein, putative [Ricinus c	0.378	0.561	0.359	2e-08
118489091	296	unknown [Populus trichocarpa x Populus d	0.465	0.361	0.285	3e-08
17557013	161	Protein ZK637.14 [Caenorhabditis elegans	0.356	0.509	0.347	5e-08
251829631	340	zinc finger protein [Carica papaya]	0.478	0.323	0.305	5e-08
66359194	493	ring domain protein [Cryptosporidium par	0.478	0.223	0.346	6e-08

>gi|255585222|ref|XP_002533313.1| conserved hypothetical protein [Ricinus communis] gi|223526857|gb|EEF29070.1| conserved hypothetical protein [Ricinus communis]

 Score = 82.0 bits (201), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 110/245 (44%), Gaps = 42/245 (17%)

Query: 1   MDVRVNLHLEGTGSCSNNPLMCPVGNIGIVLKQRCQKVNRSPSNGQQFILRDYTRSVNRF 60
           M   VNL L GT   +      PV  + +    + +++ R+P  GQ    + Y+   +  
Sbjct: 1   MSRTVNLIL-GTKPSTTQEQENPVFCLELRFHYKYKRLFRNP-EGQVREAQSYSAPPSS- 57

Query: 61  PVIQIPANALTSPMYLFRE----LVTLNLDHMLCVFLHQHLAQGAFYLSSGGLTGFHLSA 116
            + Q+  +AL+       +    L +LN+DH L +FL   +A    +L S    GFH  A
Sbjct: 58  ALFQLQPSALSHSFTCHAQIHELLSSLNVDHELRLFLAPEIAT---FLMSLSRPGFHAVA 114

Query: 117 DVEVVEIEVVE------------------DEIERSERKEASRFVVEMLSRKQRRVLDLDF 158
           D+EVV  E ++                   E     R+  SR  +E L +++      + 
Sbjct: 115 DIEVVHEEFLDAQEPLPMMMMLDGVMMMDGEDVNEPRRGVSRSTLEKLKKERFSAAAAEA 174

Query: 159 NKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPM 218
             +    D+CA+CLEE   +            +LI MPC HIFH +CI RWL+ Q +CP 
Sbjct: 175 GGI---SDDCAICLEEFGGE-----------VKLIKMPCAHIFHENCIFRWLKNQKTCPT 220

Query: 219 CRRQI 223
           CRR++
Sbjct: 221 CRREV 225

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224146442|ref|XP_002326009.1| predicted protein [Populus trichocarpa] gi|222862884|gb|EEF00391.1| predicted protein [Populus trichocarpa]

 Score = 77.0 bits (188), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 53/173 (30%), Positives = 80/173 (46%), Gaps = 23/173 (13%)

Query: 62  VIQIPANALTSPM----YLFRELVTLNLDHMLCVFLHQHLAQGAFYLSSGGLTGFHLSAD 117
           V ++P   +  P     YL + +   N D  LCV L   +A  A++L  G   GF++SA 
Sbjct: 64  VFEVPIQEVAVPASFIHYLAQRISGFNFDASLCVDLASLIASHAYHLE-GHCRGFYVSAH 122

Query: 118 VEVVEI---EVVEDEIE---RSERKEASRFVVEMLSRKQRRVLDLDFNKLVKAGDNCAVC 171
           V++V++   EV   EI     SE     R   E + +K+R +          +G  C VC
Sbjct: 123 VDLVDVDVNEVAASEIRPILDSEGFTLPRGASETVLKKER-LCKKQGGADSSSGSTCVVC 181

Query: 172 LEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ 224
           LE+                +L  +PC H+FH  CI RWL    SCP+CR +++
Sbjct: 182 LEDF-----------SSSVKLTKLPCSHVFHDKCIFRWLLYSKSCPICRTEVE 223

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224083886|ref|XP_002307159.1| predicted protein [Populus trichocarpa] gi|222856608|gb|EEE94155.1| predicted protein [Populus trichocarpa]

 Score = 70.9 bits (172), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 59/247 (23%), Positives = 103/247 (41%), Gaps = 43/247 (17%)

Query: 4   RVNLHLEGTGSCSNNPLMCPVGNIGIVLKQRCQKVNRSPSNGQQFILRDYTRSVNRF--P 61
           + NL +  T S SN+P  CP+ +   + +   +   ++P+   + +L D     +    P
Sbjct: 17  QCNLAVSITVSPSNDPF-CPICHDSFIEELEARNP-QNPNPLSESVLNDPFDPFSSLFPP 74

Query: 62  VIQIPANALTSPMYLFRELVTLNLDHMLCVFLHQHL-------------------AQGAF 102
           + QI  N  + P +  R  ++         FL  HL                    QG  
Sbjct: 75  LFQISGN-FSHPEFQIRPELSDQNAFNPFDFLRSHLQNLHSGGARVQFVIENNGGEQGGL 133

Query: 103 YLSSGGLTGFHLSADVEVVEIEVVEDEIERSERKEASRFVVEMLS--RKQRRVLDLDFNK 160
               G    + + + +E +  ++ E++  R     AS+  +E L   +    ++  + N 
Sbjct: 134 RFPGGNFGDYFIGSGLEQLIQQLAENDPNRYGTPPASKTAIEALPTMKVTEEMMKSEMN- 192

Query: 161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCR 220
                + CAVC +E  + EE+KG           MPC H+FH  CI  WL+  NSCP+CR
Sbjct: 193 -----NQCAVCKDEFESGEEVKG-----------MPCKHVFHEDCIMPWLKMHNSCPVCR 236

Query: 221 RQIQYED 227
            ++  +D
Sbjct: 237 YELPADD 243

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296412639|ref|XP_002836030.1| hypothetical protein [Tuber melanosporum Mel28] gi|295629830|emb|CAZ80187.1| unnamed protein product [Tuber melanosporum]

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/90 (36%), Positives = 50/90 (55%), Gaps = 17/90 (18%)

Query: 138 ASRFVVEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPC 197
           ASR  +E L + +        +++V  GD+CA+C E+L+  EE+             +PC
Sbjct: 157 ASREAIESLPKVKVT------HQMVLDGDDCAICKEDLVINEEVS-----------QLPC 199

Query: 198 HHIFHASCISRWLEEQNSCPMCRRQIQYED 227
            H +H  C+SRWLEE ++CP+CR  I  ED
Sbjct: 200 KHCYHFQCVSRWLEEHDTCPICRHPITPED 229

Source: Tuber melanosporum Mel28

Species: Tuber melanosporum

Genus: Tuber

Family: Tuberaceae

Order: Pezizales

Class: Pezizomycetes

Phylum: Ascomycota

Superkingdom: Eukaryota

>gi|255572321|ref|XP_002527099.1| zinc finger protein, putative [Ricinus communis] gi|223533522|gb|EEF35262.1| zinc finger protein, putative [Ricinus communis]

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 42/138 (30%), Positives = 63/138 (45%), Gaps = 36/138 (26%)

Query: 109 LTGFHLSADVEVVE----------------------IEVVEDEIERSERKEASRFVVEML 146
           L  FH+ ADVE V                       +E +ED +   E        + ML
Sbjct: 122 LLDFHVVADVEFVSEECHDMQEVVRILAMVEDGLFSMESLEDHLGAEEPIRGYGVSIPML 181

Query: 147 SRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCI 206
            + +    +  F    ++GD+C +CLEE+               +LI +PC+HIFH  CI
Sbjct: 182 EKLKN---ERHFAAAGQSGDDCPICLEEIC-----------DGVELIKVPCNHIFHEKCI 227

Query: 207 SRWLEEQNSCPMCRRQIQ 224
            RWLE +NSCP+CR +++
Sbjct: 228 FRWLENRNSCPICRYEVK 245

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255585224|ref|XP_002533314.1| zinc finger protein, putative [Ricinus communis] gi|223526858|gb|EEF29071.1| zinc finger protein, putative [Ricinus communis]

 Score = 65.5 bits (158), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 37/103 (35%), Positives = 53/103 (51%), Gaps = 16/103 (15%)

Query: 123 IEVVEDEIERSERKEASRFVVEMLSR-KQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEI 181
           IE +ED +   E        + ML + K  R     F    ++GD+C +CLEE+      
Sbjct: 67  IESLEDHLGAEEPIRGHGVSIPMLEKLKNGR----HFAATGRSGDDCPICLEEIC----- 117

Query: 182 KGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ 224
                    +LI MPC+HIFH  CI RWLE +NSCP+C  +++
Sbjct: 118 ------DGVELIKMPCNHIFHERCIFRWLENRNSCPICLYEVK 154

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118489091|gb|ABK96352.1| unknown [Populus trichocarpa x Populus deltoides]

 Score = 64.7 bits (156), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 36/126 (28%), Positives = 61/126 (48%), Gaps = 19/126 (15%)

Query: 104 LSSGGLTGFHLSADVEVVEIEVVEDEIERSERKEASRFVVEMLSRKQRRVLDLDFNKLVK 163
              G    + + + +E +  ++ E++  R     AS+  +E L     +V +    +++K
Sbjct: 144 FPDGNFGDYFIGSGLEQLIQQLAENDPNRYGTPPASKKAIEAL--PTMKVTE----EMMK 197

Query: 164 A--GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR 221
           +   + CAVC +E    EE+KG           MPC H+FH  CI  WL   NSCP+CR 
Sbjct: 198 SEMNNQCAVCKDEFEGGEEVKG-----------MPCKHVFHEDCIIPWLNMHNSCPVCRY 246

Query: 222 QIQYED 227
           ++  +D
Sbjct: 247 ELPTDD 252

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|17557013|ref|NP_498962.1| Protein ZK637.14 [Caenorhabditis elegans] gi|418354|sp|P30631.2|YOUD_CAEEL RecName: Full=Uncharacterized RING finger protein ZK637.14 gi|3881662|emb|CAA77447.1| Protein ZK637.14 [Caenorhabditis elegans]

 Score = 63.9 bits (154), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 32/92 (34%), Positives = 49/92 (53%), Gaps = 10/92 (10%)

Query: 143 VEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEEL----------IAKEEIKGQTTEKKTQL 192
           ++  S K  R++D +     K    CA+CL+ L          + KEE+K   T   T +
Sbjct: 47  IDKKSYKALRLMDRETTDQQKEDATCAICLDNLQNNVDIPEDHVIKEELKIDPTTFGTTV 106

Query: 193 ITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ 224
           I MPC H FH  C++ WLE Q +CP CR++++
Sbjct: 107 IVMPCKHRFHYFCLTLWLEAQQTCPTCRQKVK 138

Source: Caenorhabditis elegans

Species: Caenorhabditis elegans

Genus: Caenorhabditis

Family: Rhabditidae

Order: Rhabditida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

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

 Score = 63.9 bits (154), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 40/131 (30%), Positives = 61/131 (46%), Gaps = 21/131 (16%)

Query: 100 GAFYLSSG-GLTGFHLSADVEVVEIEVVEDEIERSERKEASRFVVEMLSRKQ--RRVLDL 156
           GAF L     L  + L   +E +  ++ E++  R     AS+  +E L   +  + + D 
Sbjct: 135 GAFRLPGSLNLGDYFLGPGLEQLIQQLAENDPNRHGTPPASKSAIEALPTIKIFQEMPDS 194

Query: 157 DFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSC 216
           D ++       CAVC +     EE K            MPC HI+H+ CI  WLE  NSC
Sbjct: 195 DSSQ-------CAVCKDSFALAEEAK-----------QMPCKHIYHSQCILPWLELHNSC 236

Query: 217 PMCRRQIQYED 227
           P+CR ++  +D
Sbjct: 237 PVCRYELPTDD 247

Source: Carica papaya

Species: Carica papaya

Genus: Carica

Family: Caricaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|66359194|ref|XP_626775.1| ring domain protein [Cryptosporidium parvum Iowa II] gi|46228373|gb|EAK89272.1| ring domain protein [Cryptosporidium parvum Iowa II]

 Score = 63.5 bits (153), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 43/124 (34%), Positives = 64/124 (51%), Gaps = 14/124 (11%)

Query: 109 LTGFHLSADVEVVEIEV-----VEDEIERSERKEASRFVVEMLSRKQRRVLDLDFNKLVK 163
           LTG  LS  VE +E  +      ED   R     AS  VVE L R+   V + +  ++  
Sbjct: 190 LTGSTLSNLVESMENALAVALSTEDPNNRFGSPPASTQVVEQLPRE--TVTEDNIVRIKM 247

Query: 164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQI 223
            G  C VC +E    +E+ G + +++       CHHIFHA+C+  WL + NSCP+CR ++
Sbjct: 248 CGP-CVVCQDEYSIGDEVMGLSRDEEV------CHHIFHANCLLPWLNQHNSCPVCRFEL 300

Query: 224 QYED 227
             +D
Sbjct: 301 PTDD 304

Source: Cryptosporidium parvum Iowa II

Species: Cryptosporidium parvum

Genus: Cryptosporidium

Family: Cryptosporidiidae

Order: Eucoccidiorida

Class: Coccidia

Phylum: Apicomplexa

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	230
WB|WBGene00014031	161	ZK637.14 [Caenorhabditis elega	0.356	0.509	0.347	3.5e-11
MGI|MGI:1913760	165	Rnf181 "ring finger protein 18	0.234	0.327	0.430	4.1e-10
FB|FBgn0038627	147	CG7694 [Drosophila melanogaste	0.330	0.517	0.373	1.1e-09
RGD|1359698	165	Rnf181 "ring finger protein 18	0.234	0.327	0.415	1.1e-09
UNIPROTKB|Q6AXU4	165	Rnf181 "E3 ubiquitin-protein l	0.234	0.327	0.415	1.1e-09
UNIPROTKB|C9J1C6	139	RNF181 "E3 ubiquitin-protein l	0.178	0.294	0.512	1.8e-09
UNIPROTKB|Q9P0P0	153	RNF181 "E3 ubiquitin-protein l	0.178	0.267	0.512	1.8e-09
UNIPROTKB|Q3T0W3	153	RNF181 "E3 ubiquitin-protein l	0.178	0.267	0.487	2.2e-09
UNIPROTKB|F1SVB7	153	RNF181 "Uncharacterized protei	0.178	0.267	0.487	2.9e-09
UNIPROTKB|F1Q2J1	155	RNF122 "Uncharacterized protei	0.260	0.387	0.408	8.2e-09

WB|WBGene00014031 ZK637.14 [Caenorhabditis elegans (taxid:6239)]

 Score = 154 (59.3 bits), Expect = 3.5e-11, P = 3.5e-11
 Identities = 32/92 (34%), Positives = 49/92 (53%)

Query:   143 VEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEEL----------IAKEEIKGQTTEKKTQL 192
             ++  S K  R++D +     K    CA+CL+ L          + KEE+K   T   T +
Sbjct:    47 IDKKSYKALRLMDRETTDQQKEDATCAICLDNLQNNVDIPEDHVIKEELKIDPTTFGTTV 106

Query:   193 ITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ 224
             I MPC H FH  C++ WLE Q +CP CR++++
Sbjct:   107 IVMPCKHRFHYFCLTLWLEAQQTCPTCRQKVK 138

GO:0008270 "zinc ion binding" evidence=IEA

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

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

MGI|MGI:1913760 Rnf181 "ring finger protein 181" [Mus musculus (taxid:10090)]

 Score = 144 (55.7 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 28/65 (43%), Positives = 38/65 (58%)

Query:   163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQ 222
             KA   C VCL E  A+E +           I MPCHH+FH++CI  WL + NSCP+CR +
Sbjct:    83 KADLKCPVCLLEFEAEETV-----------IEMPCHHLFHSNCILPWLSKTNSCPLCRHE 131

Query:   223 IQYED 227
             +  +D
Sbjct:   132 LPTDD 136

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

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

 Score = 140 (54.3 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 34/91 (37%), Positives = 55/91 (60%)

Query:   143 VEMLSRKQRRVLDLDFNKLVKA---GD-NCAVCLEELIAKEEIKGQTTEKKTQLITMPCH 198
             +E+    +R +L+L  +++VK+   GD  C+VC E   A+E   GQ    K +++  PC 
Sbjct:    41 IEVPEASKRAILELPVHEIVKSDEGGDLECSVCKEP--AEE---GQ----KYRIL--PCK 89

Query:   199 HIFHASCISRWLEEQNSCPMCRRQIQYEDLV 229
             H FH  CI  WL++ NSCP+CR +++ +D V
Sbjct:    90 HEFHEECILLWLKKTNSCPLCRYELETDDPV 120

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

RGD|1359698 Rnf181 "ring finger protein 181" [Rattus norvegicus (taxid:10116)]

 Score = 140 (54.3 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 27/65 (41%), Positives = 38/65 (58%)

Query:   163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQ 222
             KA   C VCL E            E++  +I MPCHH+FH++CI  WL + NSCP+CR +
Sbjct:    83 KAELKCPVCLLEF-----------EEEETVIEMPCHHLFHSNCILPWLSKTNSCPLCRHE 131

Query:   223 IQYED 227
             +  +D
Sbjct:   132 LPTDD 136

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

UNIPROTKB|Q6AXU4 Rnf181 "E3 ubiquitin-protein ligase RNF181" [Rattus norvegicus (taxid:10116)]

 Score = 140 (54.3 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 27/65 (41%), Positives = 38/65 (58%)

Query:   163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQ 222
             KA   C VCL E            E++  +I MPCHH+FH++CI  WL + NSCP+CR +
Sbjct:    83 KAELKCPVCLLEF-----------EEEETVIEMPCHHLFHSNCILPWLSKTNSCPLCRHE 131

Query:   223 IQYED 227
             +  +D
Sbjct:   132 LPTDD 136

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|C9J1C6 RNF181 "E3 ubiquitin-protein ligase RNF181" [Homo sapiens (taxid:9606)]

 Score = 138 (53.6 bits), Expect = 1.8e-09, P = 1.8e-09
 Identities = 21/41 (51%), Positives = 30/41 (73%)

Query:   187 EKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYED 227
             E++   I MPCHH+FH+SCI  WL + NSCP+CR ++  +D
Sbjct:    84 EEEETAIEMPCHHLFHSSCILPWLSKTNSCPLCRYELPTDD 124

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q9P0P0 RNF181 "E3 ubiquitin-protein ligase RNF181" [Homo sapiens (taxid:9606)]

 Score = 138 (53.6 bits), Expect = 1.8e-09, P = 1.8e-09
 Identities = 21/41 (51%), Positives = 30/41 (73%)

Query:   187 EKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYED 227
             E++   I MPCHH+FH+SCI  WL + NSCP+CR ++  +D
Sbjct:    84 EEEETAIEMPCHHLFHSSCILPWLSKTNSCPLCRYELPTDD 124

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=IEA

UNIPROTKB|Q3T0W3 RNF181 "E3 ubiquitin-protein ligase RNF181" [Bos taurus (taxid:9913)]

 Score = 137 (53.3 bits), Expect = 2.2e-09, P = 2.2e-09
 Identities = 20/41 (48%), Positives = 30/41 (73%)

Query:   187 EKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYED 227
             E++   I MPCHH+FH++CI  WL + NSCP+CR ++  +D
Sbjct:    84 EEEETAIEMPCHHLFHSNCILPWLSKTNSCPLCRHELPTDD 124

GO:0016567 "protein ubiquitination" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1SVB7 RNF181 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 136 (52.9 bits), Expect = 2.9e-09, P = 2.9e-09
 Identities = 20/41 (48%), Positives = 29/41 (70%)

Query:   187 EKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYED 227
             E++   I MPCHH+FH+ CI  WL + NSCP+CR ++  +D
Sbjct:    84 EEEETAIEMPCHHLFHSGCILPWLSKTNSCPLCRHELPTDD 124

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1Q2J1 RNF122 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 132 (51.5 bits), Expect = 8.2e-09, P = 8.2e-09
 Identities = 29/71 (40%), Positives = 37/71 (52%)

Query:   153 VLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE 212
             VL  D  KL   G  CAVCLE+   K+E+ G           +PC H FH  C+ +WLE 
Sbjct:    78 VLKGDAKKLQLYGQTCAVCLEDFKGKDEL-G----------VLPCQHAFHRKCLVKWLEV 126

Query:   213 QNSCPMCRRQI 223
             +  CPMC + I
Sbjct:   127 RCVCPMCNKPI 137

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	230
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	1e-14
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	1e-13
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	1e-10
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	3e-09
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	3e-09
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	5e-08
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	9e-08
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	7e-07
smart00184	40	smart00184, RING, Ring finger	7e-07
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	4e-06
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	1e-05
pfam05883	135	pfam05883, Baculo_RING, Baculovirus U-box/Ring-lik	8e-04
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	0.004

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

 Score = 65.9 bits (161), Expect = 1e-14
 Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 166 DNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCR 220
           D CA+C               +    ++   C H FH  CISRWL+ +N+CP+CR
Sbjct: 20  DVCAICRNHFDGTCPECKSPGDDCP-VVWGECGHAFHLHCISRWLKTRNTCPLCR 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|222279 pfam13639, zf-RING_2, Ring finger domain

 Score = 62.8 bits (153), Expect = 1e-13
 Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 11/56 (19%)

Query: 166 DNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR 221
           D C +CL+E    EE+           + +PC H+FH  C+ +WL   N+CP+CR 
Sbjct: 1   DECPICLDEFEPGEEV-----------VVLPCGHVFHKECLDKWLRSSNTCPLCRA 45

Length = 46

>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 = 56.0 bits (135), Expect = 1e-10
 Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 2/64 (3%)

Query: 166 DNCAVCLEELIAK--EEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQI 223
           D CA+C   ++    E   G T   +  ++   C+H FH  CI RWL+ +  CP+ R+  
Sbjct: 21  DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTW 80

Query: 224 QYED 227
              D
Sbjct: 81  VLAD 84

Length = 88

>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 = 50.9 bits (122), Expect = 3e-09
 Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 14/57 (24%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE-QNSCPMCRRQI 223
           C +CLEE              +  ++ +PC H+F  SCI +WL+  +N+CP+CR  I
Sbjct: 2   CPICLEEF-------------REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 55.7 bits (134), Expect = 3e-09
 Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 2/58 (3%)

Query: 165 GDN-CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR 221
            D  C +C++E+   +          T    +PC HI H  C+  WLE Q +CP+CRR
Sbjct: 286 SDRTCTICMDEMFHPDHEPLPRGLDMTPK-RLPCGHILHLHCLKNWLERQQTCPICRR 342

Length = 491

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

 Score = 52.3 bits (125), Expect = 5e-08
 Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 12/60 (20%)

Query: 165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWL-EEQNSCPMCRRQI 223
           G  CA+C+   I           K  +L  +PC H FH  C+ +WL    N CP+CR  I
Sbjct: 323 GVECAICMSNFI-----------KNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAI 371

Length = 374

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

 Score = 47.9 bits (114), Expect = 9e-08
 Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 3/34 (8%)

Query: 197 CHHIFHASCISRWLEEQNS---CPMCRRQIQYED 227
           C H FH  CI +WL  + S   CPMCR+   + +
Sbjct: 52  CKHNFHMHCILKWLATETSKGLCPMCRQTFVFAE 85

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

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

 Score = 44.4 bits (105), Expect = 7e-07
 Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 13/54 (24%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR 221
           C +CL+ L             +  ++  PC H+F   CI R+L++++ CP+CR 
Sbjct: 5   CPICLDLL-------------RDPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 44.4 bits (105), Expect = 7e-07
 Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 14/53 (26%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN-SCPMC 219
           C +CLEE +                + +PC H F  SCI +WLE  N +CP+C
Sbjct: 1   CPICLEEYL-------------KDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40

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

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

 Score = 42.1 bits (99), Expect = 4e-06
 Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 14/53 (26%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLE-EQNSCPMC 219
           C +CLEE              K  +  +PC H+F + CI  WLE    +CP+C
Sbjct: 1   CPICLEEP-------------KDPVTILPCGHLFCSKCILSWLESGNVTCPLC 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 = 44.4 bits (105), Expect = 1e-05
 Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 6/56 (10%)

Query: 165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCR 220
              CA+C+E++  KE IK          I   C+H+F   CI  W +E+N+CP+CR
Sbjct: 174 DKECAICMEKVYDKE-IK-----NMYFGILSNCNHVFCIECIDIWKKEKNTCPVCR 223

Length = 238

>gnl|CDD|218794 pfam05883, Baculo_RING, Baculovirus U-box/Ring-like domain

 Score = 38.0 bits (89), Expect = 8e-04
 Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 18/64 (28%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCH------HIFHASCISRWLEEQNSCPMCRR 221
           CA+CL+ +    +  G        ++ +          +FHA C  RW  E+   P   R
Sbjct: 29  CAICLDRIN---DNDG--------VVAVTDGGTLNLEKMFHAECDKRWKRERKRDPF-NR 76

Query: 222 QIQY 225
            I+Y
Sbjct: 77  NIKY 80

This family consists of several Baculovirus proteins of around 130 residues in length. 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. Length = 135

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

 Score = 37.7 bits (87), Expect = 0.004
 Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 2/31 (6%)

Query: 197  CHHIFHASCISRWLEEQNS--CPMCRRQIQY 225
            C + FH  C+ +W        CP+CR +I +
Sbjct: 1494 CKNKFHTRCLYKWFASSARSNCPLCRSEITF 1524

Length = 1525

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	230
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.64
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.61
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	99.47
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.47
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.47
PHA02929	238	N1R/p28-like protein; Provisional	99.38
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.27
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.27
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.2
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.18
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.1
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.07
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	99.05
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.05
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.03
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.0
PHA02926	242	zinc finger-like protein; Provisional	98.98
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.96
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.94
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.91
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.9
PF14634	44	zf-RING_5: zinc-RING finger domain	98.88
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.88
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.84
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.83
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.77
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.59
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.55
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.52
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.47
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.45
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.34
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.33
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.29
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.19
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.14
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.13
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.11
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.1
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.07
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	97.86
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.81
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.79
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.74
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.74
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.74
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.48
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.4
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.38
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.32
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.3
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.19
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	96.9
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	96.72
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.61
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.55
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	96.31
COG5152	259	Uncharacterized conserved protein, contains RING a	96.28
PF14369	35	zf-RING_3: zinc-finger	96.24
KOG2660	331	consensus Locus-specific chromosome binding protei	96.21
KOG3039	303	consensus Uncharacterized conserved protein [Funct	96.2
PHA03096	284	p28-like protein; Provisional	96.17
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.08
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	96.07
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	96.06
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	96.06
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	95.99
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	95.96
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.77
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	95.7
PHA02862	156	5L protein; Provisional	95.67
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	95.64
KOG1002	791	consensus Nucleotide excision repair protein RAD16	95.48
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	95.46
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	95.44
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	95.39
COG5236	493	Uncharacterized conserved protein, contains RING Z	95.23
PHA02825	162	LAP/PHD finger-like protein; Provisional	95.17
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	94.99
PF04641	260	Rtf2: Rtf2 RING-finger	94.92
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	94.45
COG5222	427	Uncharacterized conserved protein, contains RING Z	94.22
KOG1940	276	consensus Zn-finger protein [General function pred	94.22
KOG1001	674	consensus Helicase-like transcription factor HLTF/	93.93
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	93.61
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	93.03
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	92.65
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	92.32
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	92.14
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	91.75
COG5175	480	MOT2 Transcriptional repressor [Transcription]	91.68
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	91.47
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	90.25
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	89.27
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	88.81
KOG0298	1394	consensus DEAD box-containing helicase-like transc	88.13
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	87.75
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	87.74
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	87.05
KOG3899	381	consensus Uncharacterized conserved protein [Funct	86.82
KOG3053	293	consensus Uncharacterized conserved protein [Funct	85.51
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	84.99
KOG3002	299	consensus Zn finger protein [General function pred	83.77
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	83.37
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	81.95
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	81.81
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	81.62
KOG1609	323	consensus Protein involved in mRNA turnover and st	81.18
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	80.42

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

Probab=99.64  E-value=1.3e-16  Score=142.18  Aligned_cols=78  Identities=31%  Similarity=0.715  Sum_probs=64.1

Q ss_pred             ccccccHHHHHhccccccchhhhhhhhcccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC
Q 042810          134 ERKEASRFVVEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ  213 (230)
Q Consensus       134 ~~~~~s~~~i~~l~~~~~~~~~~~~~~~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~  213 (230)
                      +..++.++.+++++...+...+    +.... ..|+||+|+|..           |+.++.|||+|.||..||++||.+.
T Consensus       203 ~~~r~~k~~l~~~p~~~f~~~~----~~~~~-~~CaIClEdY~~-----------GdklRiLPC~H~FH~~CIDpWL~~~  266 (348)
T KOG4628|consen  203 RRNRLIKRLLKKLPVRTFTKGD----DEDAT-DTCAICLEDYEK-----------GDKLRILPCSHKFHVNCIDPWLTQT  266 (348)
T ss_pred             hhhhhHHHHHhhCCcEEecccc----ccCCC-ceEEEeeccccc-----------CCeeeEecCCCchhhccchhhHhhc
Confidence            5567888999999998885422    22222 599999999998           9999999999999999999999887


Q ss_pred             Cc-ccccccCccccC
Q 042810          214 NS-CPMCRRQIQYED  227 (230)
Q Consensus       214 ~t-CP~CR~~i~~~~  227 (230)
                      ++ ||+||+++.+..
T Consensus       267 r~~CPvCK~di~~~~  281 (348)
T KOG4628|consen  267 RTFCPVCKRDIRTDS  281 (348)
T ss_pred             CccCCCCCCcCCCCC
Confidence            55 999999886653

>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=99.61  E-value=2e-16  Score=101.25  Aligned_cols=44  Identities=50%  Similarity=1.294  Sum_probs=40.0

Q ss_pred             CccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccc
Q 042810          166 DNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCR  220 (230)
Q Consensus       166 ~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR  220 (230)
                      ++|+||++++..           ++.++.++|||.||.+||.+|++++++||+||
T Consensus         1 d~C~IC~~~~~~-----------~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFED-----------GEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHT-----------TSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcC-----------CCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence            479999999988           78899999999999999999999999999998

...

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

Probab=99.47  E-value=3.1e-15  Score=127.66  Aligned_cols=152  Identities=18%  Similarity=0.345  Sum_probs=110.5

Q ss_pred             ccccCCCceeecCCCCCC-ChHHHHHHHHhcCCCcceeeeehhhcccCceeeccCCeeeEEEechhHHHHHHHHHHHHHh
Q 042810           54 TRSVNRFPVIQIPANALT-SPMYLFRELVTLNLDHMLCVFLHQHLAQGAFYLSSGGLTGFHLSADVEVVEIEVVEDEIER  132 (230)
Q Consensus        54 ~~~~~s~~~~~i~~~~~~-~~~~l~~lL~~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~l~~~v~~v~~~~~~~~~~~  132 (230)
                      ++.+++++.+.-+.+... .-+|+..+...+++ +..+..+....-+.++++.++|+.-..+.+|+..+..+.+...+..
T Consensus       133 pRlVYkwFl~lyklSy~~g~vGyl~im~~~~g~-n~~F~~~~~~~md~gi~~lfyglYyGvlgRdfa~icsd~mAs~iGf  211 (328)
T KOG1734|consen  133 PRLVYKWFLFLYKLSYLLGVVGYLAIMFAQFGL-NFTFFYLKTTYMDFGISFLFYGLYYGVLGRDFAEICSDYMASTIGF  211 (328)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhce-eeEEeecchhHhhhhHHHHHHHHHHHhhhhHHHHHHHHHHHHHhcc
Confidence            444555543333332222 44777777777777 4455566666668888888888888889999999888888777777


Q ss_pred             hccccccHHHHHhccccccchhhhhhhhcccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHh--h
Q 042810          133 SERKEASRFVVEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRW--L  210 (230)
Q Consensus       133 ~~~~~~s~~~i~~l~~~~~~~~~~~~~~~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~W--l  210 (230)
                      +.+.+.+        +.-.            ++..|+||-..+..+.++++.    -++..+|.|+|+||+.||+.|  +
T Consensus       212 Ys~~glP--------tkhl------------~d~vCaVCg~~~~~s~~eegv----ienty~LsCnHvFHEfCIrGWciv  267 (328)
T KOG1734|consen  212 YSPSGLP--------TKHL------------SDSVCAVCGQQIDVSVDEEGV----IENTYKLSCNHVFHEFCIRGWCIV  267 (328)
T ss_pred             cCCCCCC--------CCCC------------CcchhHhhcchheeecchhhh----hhhheeeecccchHHHhhhhheee
Confidence            6664443        2222            378999999888775554443    467889999999999999999  4


Q ss_pred             ccCCcccccccCccccCCCC
Q 042810          211 EEQNSCPMCRRQIQYEDLVG  230 (230)
Q Consensus       211 ~~~~tCP~CR~~i~~~~l~~  230 (230)
                      .++++||.|+.++..+.+++
T Consensus       268 GKkqtCPYCKekVdl~rmfs  287 (328)
T KOG1734|consen  268 GKKQTCPYCKEKVDLKRMFS  287 (328)
T ss_pred             cCCCCCchHHHHhhHhhhcc
Confidence            68999999999998887753

>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=99.47  E-value=2.1e-14  Score=101.80  Aligned_cols=59  Identities=41%  Similarity=0.843  Sum_probs=42.1

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccc
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCR  220 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR  220 (230)
                      ....++.|+||++.+.+....... ......+...+|||.||..||.+|++++++||+||
T Consensus        15 ~~~~~d~C~IC~~~l~~~~~~~~~-~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   15 WDIADDNCAICREPLEDPCPECQA-PQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             ESSCCSBETTTTSBTTSTTCCHHH-CTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             ecCcCCcccccChhhhChhhhhcC-CccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            333466799999999653321111 11245566778999999999999999999999998

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 ....

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

Probab=99.47  E-value=1.3e-14  Score=128.75  Aligned_cols=84  Identities=25%  Similarity=0.675  Sum_probs=60.3

Q ss_pred             cccccHHHHHhccccccchhhhhhhhcccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCC
Q 042810          135 RKEASRFVVEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN  214 (230)
Q Consensus       135 ~~~~s~~~i~~l~~~~~~~~~~~~~~~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~  214 (230)
                      ...+.++..+.++.+..+       +...+|..|.||||++-..+...-+ -..+..+++|||||.||.+|++-|+++++
T Consensus       264 ~~r~~kdl~~~~~t~t~e-------ql~n~D~~C~ICmde~~h~~~~~~~-~~~~~~pKrLpCGHilHl~CLknW~ERqQ  335 (491)
T COG5243         264 FRRATKDLNAMYPTATEE-------QLTNSDRTCTICMDEMFHPDHEPLP-RGLDMTPKRLPCGHILHLHCLKNWLERQQ  335 (491)
T ss_pred             HHHHhhHHHhhcchhhhh-------hhcCCCCeEEEecccccCCCCccCc-ccccCCcccccccceeeHHHHHHHHHhcc
Confidence            345566666666665553       3456789999999995442221111 12245688999999999999999999999


Q ss_pred             cccccccCcccc
Q 042810          215 SCPMCRRQIQYE  226 (230)
Q Consensus       215 tCP~CR~~i~~~  226 (230)
                      |||+||.++-.+
T Consensus       336 TCPICr~p~ifd  347 (491)
T COG5243         336 TCPICRRPVIFD  347 (491)
T ss_pred             CCCcccCccccc
Confidence            999999996443

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.38  E-value=2.9e-13  Score=115.88  Aligned_cols=79  Identities=25%  Similarity=0.543  Sum_probs=55.7

Q ss_pred             ccccHHHHHhccccccchhhhhhhhcccCCCccccCchhhhhhhhhhccccccCcee-EEeCCCCccchhhHHHhhccCC
Q 042810          136 KEASRFVVEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQL-ITMPCHHIFHASCISRWLEEQN  214 (230)
Q Consensus       136 ~~~s~~~i~~l~~~~~~~~~~~~~~~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v-~~LpC~H~FH~~CI~~Wl~~~~  214 (230)
                      .+.++..++.+|....+..   .......+.+|+||++.+.+.+       ...... ...+|+|.||..||.+|++++.
T Consensus       148 ~~~~~~~i~~lp~vl~~~e---~~~~~~~~~eC~ICle~~~~~~-------~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~  217 (238)
T PHA02929        148 GKNYKKFLKTIPSVLSEYE---KLYNRSKDKECAICMEKVYDKE-------IKNMYFGILSNCNHVFCIECIDIWKKEKN  217 (238)
T ss_pred             cchhHHHHHhcchhhhhhh---hhhcCCCCCCCccCCcccccCc-------cccccceecCCCCCcccHHHHHHHHhcCC
Confidence            4557888888888765321   1123345789999999976510       001112 3346999999999999999999


Q ss_pred             cccccccCcc
Q 042810          215 SCPMCRRQIQ  224 (230)
Q Consensus       215 tCP~CR~~i~  224 (230)
                      +||+||.++.
T Consensus       218 tCPlCR~~~~  227 (238)
T PHA02929        218 TCPVCRTPFI  227 (238)
T ss_pred             CCCCCCCEee
Confidence            9999999774

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

Probab=99.27  E-value=2.2e-12  Score=112.02  Aligned_cols=54  Identities=37%  Similarity=0.957  Sum_probs=47.6

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhc-cCCcccccccCccc
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLE-EQNSCPMCRRQIQY  225 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~-~~~tCP~CR~~i~~  225 (230)
                      +...+-+|+|||++|--           +++.+.+||.|.||..|++.|+. -++.||+||.++++
T Consensus       319 ea~~GveCaICms~fiK-----------~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         319 EADKGVECAICMSNFIK-----------NDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             hcCCCceEEEEhhhhcc-----------cceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            33446899999999954           88899999999999999999987 78899999999875

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

Probab=99.27  E-value=1.9e-12  Score=93.31  Aligned_cols=64  Identities=27%  Similarity=0.612  Sum_probs=47.7

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc---CCcccccccCccccC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE---QNSCPMCRRQIQYED  227 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~---~~tCP~CR~~i~~~~  227 (230)
                      ..++.|+||+..|....+....++ .+..++...|+|.||..||.+|+.+   +++||+||+++..++
T Consensus        19 ~~dd~CgICr~~fdg~Cp~Ck~Pg-d~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k~   85 (85)
T PF12861_consen   19 ANDDVCGICRMPFDGCCPDCKFPG-DDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKFKE   85 (85)
T ss_pred             CCCCceeeEecccccCCCCccCCC-CCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeeeCC
Confidence            458999999999986443222222 2334555569999999999999985   468999999987654

>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=99.20  E-value=6.5e-12  Score=82.42  Aligned_cols=46  Identities=33%  Similarity=1.000  Sum_probs=40.0

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCc-cchhhHHHhhccCCcccccccCcc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHI-FHASCISRWLEEQNSCPMCRRQIQ  224 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~Wl~~~~tCP~CR~~i~  224 (230)
                      +..|.||++....              +..+||||. ||..|+.+|++++.+||+||++|.
T Consensus         2 ~~~C~iC~~~~~~--------------~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRD--------------VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSS--------------EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCCc--------------eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            4689999998654              889999999 999999999999999999999885

...

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.18  E-value=8.7e-12  Score=103.03  Aligned_cols=53  Identities=26%  Similarity=0.758  Sum_probs=44.4

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc----------------CCcccccccCcccc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE----------------QNSCPMCRRQIQYE  226 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~----------------~~tCP~CR~~i~~~  226 (230)
                      .++.+|+||++.+.+              ++.++|||.||..||.+|+..                +.+||+||..+...
T Consensus        16 ~~~~~CpICld~~~d--------------PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~   81 (193)
T PLN03208         16 GGDFDCNICLDQVRD--------------PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEA   81 (193)
T ss_pred             CCccCCccCCCcCCC--------------cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChh
Confidence            357899999998765              677899999999999999842                34799999999887


Q ss_pred             CCC
Q 042810          227 DLV  229 (230)
Q Consensus       227 ~l~  229 (230)
                      +++
T Consensus        82 ~Lv   84 (193)
T PLN03208         82 TLV   84 (193)
T ss_pred             cEE
Confidence            764

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

Probab=99.10  E-value=5e-11  Score=103.15  Aligned_cols=53  Identities=38%  Similarity=0.873  Sum_probs=47.5

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      .....|.+|+|..+.              +..+||||+||-.||..|...+..||+||..+...+++
T Consensus       237 ~a~~kC~LCLe~~~~--------------pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskvi  289 (293)
T KOG0317|consen  237 EATRKCSLCLENRSN--------------PSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKVI  289 (293)
T ss_pred             CCCCceEEEecCCCC--------------CCcCcCcchHHHHHHHHHHccccCCCcccccCCCccee
Confidence            346899999998654              88899999999999999999999999999999988875

>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=99.07  E-value=7.3e-11  Score=73.43  Aligned_cols=39  Identities=41%  Similarity=1.134  Sum_probs=32.8

Q ss_pred             cccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCccccc
Q 042810          168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMC  219 (230)
Q Consensus       168 C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~C  219 (230)
                      |+||++.+.+             .++.++|||.||..|+.+|++.+.+||+|
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            8999998743             34788999999999999999999999998

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

Probab=99.05  E-value=7e-11  Score=83.40  Aligned_cols=67  Identities=27%  Similarity=0.530  Sum_probs=48.6

Q ss_pred             cccCCCccccCchhhhhhhhhhccc-cccCc-eeEEeCCCCccchhhHHHhhccCCcccccccCccccC
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQT-TEKKT-QLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYED  227 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~-~~~~~-~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~  227 (230)
                      .+..-+.|+||...+..-+.+.... ...++ .+..--|+|.||..||.+||.+++.||++|+++...+
T Consensus        16 wdi~id~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~~   84 (88)
T COG5194          16 WDIPIDVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLAD   84 (88)
T ss_pred             cccccchhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEec
Confidence            3334678999999887755433321 11233 4444559999999999999999999999999876543

>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=99.05  E-value=1.4e-10  Score=72.84  Aligned_cols=44  Identities=45%  Similarity=1.250  Sum_probs=36.0

Q ss_pred             ccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc-CCcccccccCc
Q 042810          167 NCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE-QNSCPMCRRQI  223 (230)
Q Consensus       167 ~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~-~~tCP~CR~~i  223 (230)
                      .|+||++.+..             .....+|+|.||..|+..|++. +..||+||..+
T Consensus         1 ~C~iC~~~~~~-------------~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFRE-------------PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhhC-------------ceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            49999998733             2444559999999999999987 77899999864

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

Probab=99.03  E-value=9.4e-11  Score=111.95  Aligned_cols=56  Identities=39%  Similarity=0.909  Sum_probs=46.3

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccc
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQY  225 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~  225 (230)
                      ....++.|+||+|.+...+         +..+++|||+|+||..|+..|++++++||+||..+..
T Consensus       287 ~~~~~~~C~IC~e~l~~~~---------~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~~  342 (543)
T KOG0802|consen  287 LALSDELCIICLEELHSGH---------NITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLYD  342 (543)
T ss_pred             hhhcCCeeeeechhhcccc---------ccccceeecccchHHHHHHHHHHHhCcCCcchhhhhc
Confidence            3345889999999997711         2348899999999999999999999999999995543

>smart00504 Ubox Modified RING finger domain

Probab=99.00  E-value=2.2e-10  Score=78.19  Aligned_cols=50  Identities=22%  Similarity=0.508  Sum_probs=44.8

Q ss_pred             CccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccCCC
Q 042810          166 DNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       166 ~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      -.|+||.+.+.+              ++.+||||+|+..||.+|++.+.+||+|+..+..++++
T Consensus         2 ~~Cpi~~~~~~~--------------Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~   51 (63)
T smart00504        2 FLCPISLEVMKD--------------PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLI   51 (63)
T ss_pred             cCCcCCCCcCCC--------------CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhce
Confidence            369999999866              67889999999999999999889999999999888775

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=98.98  E-value=2e-10  Score=96.30  Aligned_cols=57  Identities=30%  Similarity=0.814  Sum_probs=39.9

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEe-CCCCccchhhHHHhhccC------CcccccccCcc
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITM-PCHHIFHASCISRWLEEQ------NSCPMCRRQIQ  224 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~Wl~~~------~tCP~CR~~i~  224 (230)
                      .+.+.+|+||+|..-....      .+...-..| +|+|.||..||..|.+.+      ++||+||..+.
T Consensus       167 ~SkE~eCgICmE~I~eK~~------~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        167 VSKEKECGICYEVVYSKRL------ENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             ccCCCCCccCccccccccc------cccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            3457899999998644100      002223455 599999999999998753      46999999764

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

Probab=98.96  E-value=2.1e-10  Score=93.00  Aligned_cols=54  Identities=28%  Similarity=0.747  Sum_probs=45.8

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccCCC
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      ....|+|||+.+..            ..+.-..|||+||..||+.-++..+.||+||+.|..++++
T Consensus       130 ~~~~CPiCl~~~se------------k~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~~~  183 (187)
T KOG0320|consen  130 GTYKCPICLDSVSE------------KVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQFH  183 (187)
T ss_pred             cccCCCceecchhh------------ccccccccchhHHHHHHHHHHHhCCCCCCcccccchhhhe
Confidence            35789999999855            1234467999999999999999999999999999988775

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

Probab=98.94  E-value=4.5e-10  Score=71.12  Aligned_cols=38  Identities=39%  Similarity=1.002  Sum_probs=30.1

Q ss_pred             cccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC----Cccccc
Q 042810          168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ----NSCPMC  219 (230)
Q Consensus       168 C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~----~tCP~C  219 (230)
                      |+||++.|.+              ++.|+|||.|+..||.+|.+..    ..||.|
T Consensus         1 CpiC~~~~~~--------------Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKD--------------PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SS--------------EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCC--------------ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            8999999977              8999999999999999998754    369987

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

Probab=98.91  E-value=1.2e-10  Score=81.58  Aligned_cols=66  Identities=27%  Similarity=0.602  Sum_probs=47.6

Q ss_pred             hcccCCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhcc---CCcccccccCccccC
Q 042810          160 KLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEE---QNSCPMCRRQIQYED  227 (230)
Q Consensus       160 ~~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~---~~tCP~CR~~i~~~~  227 (230)
                      .....+++|.||.-.|...+....-++  ++-+.++- |.|.||..||..|+..   +..||+||+++..+|
T Consensus        15 tW~~~~e~CGiCRm~Fdg~Cp~Ck~Pg--DdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~~e   84 (84)
T KOG1493|consen   15 TWDAPDETCGICRMPFDGCCPDCKLPG--DDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQFKE   84 (84)
T ss_pred             EEcCCCCccceEecccCCcCCCCcCCC--CCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEecC
Confidence            456678899999999977443332222  33333444 9999999999999975   457999999886553

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

Probab=98.90  E-value=4.9e-10  Score=94.42  Aligned_cols=53  Identities=25%  Similarity=0.746  Sum_probs=45.4

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc---CCcccccccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE---QNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~---~~tCP~CR~~i~~~~l~  229 (230)
                      ...-+|-||+|.-++              +++..|||.||-.||.+||..   ++.||+||..|..++++
T Consensus        45 ~~~FdCNICLd~akd--------------PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vv  100 (230)
T KOG0823|consen   45 GGFFDCNICLDLAKD--------------PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVV  100 (230)
T ss_pred             CCceeeeeeccccCC--------------CEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEE
Confidence            446789999998544              888899999999999999975   35799999999998875

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.88  E-value=1.1e-09  Score=69.99  Aligned_cols=44  Identities=27%  Similarity=0.814  Sum_probs=37.9

Q ss_pred             ccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCccccccc
Q 042810          167 NCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR  221 (230)
Q Consensus       167 ~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~  221 (230)
                      .|+||++.|.+           ......++|||+||..|+..+......||+||+
T Consensus         1 ~C~~C~~~~~~-----------~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSE-----------ERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccC-----------CCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            48999999944           556888899999999999999866779999985

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

Probab=98.88  E-value=8.8e-10  Score=81.53  Aligned_cols=67  Identities=28%  Similarity=0.577  Sum_probs=50.9

Q ss_pred             hcccCCCccccCchhhhhhhhhhccc---cccCceeEEeCCCCccchhhHHHhhccCCcccccccCcccc
Q 042810          160 KLVKAGDNCAVCLEELIAKEEIKGQT---TEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYE  226 (230)
Q Consensus       160 ~~~~~~~~C~ICle~~~~~~~~~~~~---~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~  226 (230)
                      ..+-.-+.|+||...+-+.+-+....   .+....+...-|+|.||..||.+||++++.||+|.+++..+
T Consensus        41 aWDi~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~~q  110 (114)
T KOG2930|consen   41 AWDIVVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWVFQ  110 (114)
T ss_pred             eeeeeechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcceeEe
Confidence            44556789999999988866433322   23334555666999999999999999999999999887544

>smart00184 RING Ring finger

Probab=98.84  E-value=1.5e-09  Score=65.74  Aligned_cols=38  Identities=50%  Similarity=1.304  Sum_probs=32.5

Q ss_pred             cccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhc-cCCccccc
Q 042810          168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLE-EQNSCPMC  219 (230)
Q Consensus       168 C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~-~~~tCP~C  219 (230)
                      |+||++....              ...++|+|.||..|++.|++ .+.+||+|
T Consensus         1 C~iC~~~~~~--------------~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELKD--------------PVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCCC--------------cEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            7899887433              78889999999999999998 66789987

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)

>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=98.83  E-value=1.4e-09  Score=68.13  Aligned_cols=39  Identities=41%  Similarity=1.164  Sum_probs=33.0

Q ss_pred             cccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhc--cCCccccc
Q 042810          168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLE--EQNSCPMC  219 (230)
Q Consensus       168 C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~--~~~tCP~C  219 (230)
                      |+||++.+..             ....++|||.||.+|+.+|++  ....||+|
T Consensus         1 C~iC~~~~~~-------------~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFED-------------PVILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSS-------------EEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccC-------------CCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            8999998855             235789999999999999998  55689998

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 ....

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.77  E-value=3.8e-09  Score=96.66  Aligned_cols=53  Identities=30%  Similarity=0.671  Sum_probs=45.6

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccCC
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDL  228 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l  228 (230)
                      .+....|+||++.|..              ++.++|||.||..||..|+..+..||+||..+...++
T Consensus        23 Le~~l~C~IC~d~~~~--------------PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~L   75 (397)
T TIGR00599        23 LDTSLRCHICKDFFDV--------------PVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKL   75 (397)
T ss_pred             cccccCCCcCchhhhC--------------ccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccccC
Confidence            3456799999999866              6678999999999999999988899999998876554

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

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

Probab=98.59  E-value=2.5e-08  Score=63.35  Aligned_cols=39  Identities=26%  Similarity=0.855  Sum_probs=23.2

Q ss_pred             cccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC----Cccc
Q 042810          168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ----NSCP  217 (230)
Q Consensus       168 C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~----~tCP  217 (230)
                      |+||.| |...          ...+++|+|||+|+.+|+.+|+++.    -.||
T Consensus         1 CpIc~e-~~~~----------~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTE----------ENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TT----------SS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCC----------CCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 7441          5567889999999999999999753    2576

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

Probab=98.55  E-value=2e-08  Score=86.18  Aligned_cols=53  Identities=32%  Similarity=0.764  Sum_probs=44.5

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHH-hhccCC-cccccccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISR-WLEEQN-SCPMCRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~-Wl~~~~-tCP~CR~~i~~~~l~  229 (230)
                      ..+..|+||++....              +..+||||+||-.||.. |-.++- .||+||+.+..++++
T Consensus       213 ~~d~kC~lC~e~~~~--------------ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~vi  267 (271)
T COG5574         213 LADYKCFLCLEEPEV--------------PSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKVI  267 (271)
T ss_pred             ccccceeeeecccCC--------------cccccccchhhHHHHHHHHHhhccccCchhhhhccchhhh
Confidence            347889999998655              88899999999999999 976665 499999998877653

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

Probab=98.52  E-value=5.5e-08  Score=68.79  Aligned_cols=51  Identities=27%  Similarity=0.537  Sum_probs=41.5

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc-CCcccccccCccccCCC
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE-QNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~-~~tCP~CR~~i~~~~l~  229 (230)
                      ...|+|+.+-|.+              ++.+|+||+|.+.||..|+++ ..+||+|+.++..++++
T Consensus         4 ~f~CpIt~~lM~d--------------PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~   55 (73)
T PF04564_consen    4 EFLCPITGELMRD--------------PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLI   55 (73)
T ss_dssp             GGB-TTTSSB-SS--------------EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSE
T ss_pred             ccCCcCcCcHhhC--------------ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccce
Confidence            3579999999877              889999999999999999998 88999999999988774

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 ....

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

Probab=98.47  E-value=3.8e-08  Score=87.04  Aligned_cols=51  Identities=29%  Similarity=0.696  Sum_probs=46.1

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccCC
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDL  228 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l  228 (230)
                      .-..|.||.|.|..              +..+||+|.||.-||+..|..+..||.|+.++.+.+|
T Consensus        22 ~lLRC~IC~eyf~i--------------p~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~L   72 (442)
T KOG0287|consen   22 DLLRCGICFEYFNI--------------PMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDL   72 (442)
T ss_pred             HHHHHhHHHHHhcC--------------ceeccccchHHHHHHHHHhccCCCCCceecccchhhh
Confidence            35689999999988              8889999999999999999999999999999887654

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

Probab=98.45  E-value=6.2e-08  Score=89.85  Aligned_cols=51  Identities=35%  Similarity=0.804  Sum_probs=42.6

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc-----CCcccccccCccccCCC
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE-----QNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~-----~~tCP~CR~~i~~~~l~  229 (230)
                      +..|+||++....              +..+.|||+||..||-+.+..     ...||+||..|..+||.
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            7899999998655              666779999999999987754     35899999999988763

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

Probab=98.34  E-value=2.3e-07  Score=60.59  Aligned_cols=42  Identities=26%  Similarity=0.893  Sum_probs=32.4

Q ss_pred             ccccCchhhhhhhhhhccccccCceeEEeCCC-----CccchhhHHHhhccC--Ccccccc
Q 042810          167 NCAVCLEELIAKEEIKGQTTEKKTQLITMPCH-----HIFHASCISRWLEEQ--NSCPMCR  220 (230)
Q Consensus       167 ~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~-----H~FH~~CI~~Wl~~~--~tCP~CR  220 (230)
                      .|.||++ ..+           ++.+...||.     |.+|..|+.+|+..+  .+||+|+
T Consensus         1 ~CrIC~~-~~~-----------~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHD-EGD-----------EGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCC-CCC-----------CCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4899998 222           4446678985     899999999999654  4899995

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

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

Probab=98.33  E-value=2.1e-07  Score=91.38  Aligned_cols=57  Identities=25%  Similarity=0.739  Sum_probs=42.9

Q ss_pred             hcccCCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhcc--CCcccccccCcc
Q 042810          160 KLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEE--QNSCPMCRRQIQ  224 (230)
Q Consensus       160 ~~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~--~~tCP~CR~~i~  224 (230)
                      ...++-++|+||+..+..-++        .-.-++-| |.|-||..|+..|++.  +++||+||.+++
T Consensus      1464 ~~fsG~eECaICYsvL~~vdr--------~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1464 EKFSGHEECAICYSVLDMVDR--------SLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             hhcCCcchhhHHHHHHHHHhc--------cCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            456678899999998875221        11122334 9999999999999986  468999999876

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

Probab=98.29  E-value=1.5e-07  Score=86.75  Aligned_cols=63  Identities=24%  Similarity=0.748  Sum_probs=43.2

Q ss_pred             cCCCccccCchhhhhhh---hhhccccccCceeEEeCCCCccchhhHHHhhc-cCCcccccccCccc
Q 042810          163 KAGDNCAVCLEELIAKE---EIKGQTTEKKTQLITMPCHHIFHASCISRWLE-EQNSCPMCRRQIQY  225 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~---~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~-~~~tCP~CR~~i~~  225 (230)
                      .....|+|||.+...-.   ++..........-...||.|+||..|+.+|.. .+-.||+||.+++.
T Consensus       569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            34678999999875511   00000011112344579999999999999998 56699999999864

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

Probab=98.19  E-value=2.9e-07  Score=64.62  Aligned_cols=53  Identities=25%  Similarity=0.718  Sum_probs=24.1

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEe--CCCCccchhhHHHhhcc----C-------CcccccccCccc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITM--PCHHIFHASCISRWLEE----Q-------NSCPMCRRQIQY  225 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~L--pC~H~FH~~CI~~Wl~~----~-------~tCP~CR~~i~~  225 (230)
                      +..|+||++.+.+.++        ...+..-  .|++.||..|+.+||..    +       .+||.|+++|.-
T Consensus         2 ~~~C~IC~~~~~~~~~--------~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~   67 (70)
T PF11793_consen    2 ELECGICYSYRLDDGE--------IPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW   67 (70)
T ss_dssp             --S-SSS--SS-TT-------------B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred             CCCCCcCCcEecCCCC--------cCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence            4579999998753110        1112222  49999999999999863    1       259999998864

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

Probab=98.14  E-value=1.5e-06  Score=79.63  Aligned_cols=51  Identities=37%  Similarity=0.907  Sum_probs=40.2

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCcc
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ  224 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~  224 (230)
                      ..+-.+|+||+|.+.++          -..+..+.|.|.||..|+..|-  -.+||+||.-..
T Consensus       172 ~tELPTCpVCLERMD~s----------~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~  222 (493)
T KOG0804|consen  172 LTELPTCPVCLERMDSS----------TTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS  222 (493)
T ss_pred             cccCCCcchhHhhcCcc----------ccceeeeecccccchHHHhhcc--cCcChhhhhhcC
Confidence            34578999999999652          2336667799999999999994  568999998554

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

Probab=98.13  E-value=8.6e-07  Score=76.05  Aligned_cols=47  Identities=34%  Similarity=0.818  Sum_probs=39.9

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCccccccc
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR  221 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~  221 (230)
                      ...+...|+||++.|..              +..+||+|.||..|+..|....-.||.||.
T Consensus         9 ~~~~~~~C~iC~~~~~~--------------p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen    9 VLQEELTCPICLEYFRE--------------PVLLPCGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             hccccccChhhHHHhhc--------------CccccccchHhHHHHHHhcCCCcCCcccCC
Confidence            33457899999999977              488999999999999999875568999993

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

Probab=98.11  E-value=9.6e-07  Score=76.89  Aligned_cols=47  Identities=30%  Similarity=0.567  Sum_probs=42.0

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQY  225 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~  225 (230)
                      -..|-||-+.+..              +...+|||.||.-||+..|..+.-||+||.+..+
T Consensus        25 ~lrC~IC~~~i~i--------------p~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~e   71 (391)
T COG5432          25 MLRCRICDCRISI--------------PCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCE   71 (391)
T ss_pred             HHHhhhhhheeec--------------ceecccccchhHHHHHHHhcCCCCCccccccHHh
Confidence            5689999999877              7778899999999999999999999999987644

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

Probab=98.10  E-value=1.2e-06  Score=78.37  Aligned_cols=48  Identities=31%  Similarity=0.909  Sum_probs=41.5

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCc-cchhhHHHhhccCCcccccccCcc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHI-FHASCISRWLEEQNSCPMCRRQIQ  224 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~Wl~~~~tCP~CR~~i~  224 (230)
                      +...+|.||+.+-.+              ..+|||.|. .|.+|.+.---+++.||+||++|.
T Consensus       288 ~~gkeCVIClse~rd--------------t~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~  336 (349)
T KOG4265|consen  288 ESGKECVICLSESRD--------------TVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIE  336 (349)
T ss_pred             cCCCeeEEEecCCcc--------------eEEecchhhehhHhHHHHHHHhhcCCCccccchH
Confidence            447899999998665              899999999 999999887557889999999874

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

Probab=98.07  E-value=1.4e-06  Score=59.47  Aligned_cols=49  Identities=29%  Similarity=0.693  Sum_probs=25.6

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccCC
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDL  228 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l  228 (230)
                      -..|++|.+.+..             .+....|.|+||..||.+-+..  .||+|+.+--.+|+
T Consensus         7 lLrCs~C~~~l~~-------------pv~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD~   55 (65)
T PF14835_consen    7 LLRCSICFDILKE-------------PVCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQDI   55 (65)
T ss_dssp             TTS-SSS-S--SS--------------B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS-
T ss_pred             hcCCcHHHHHhcC-------------CceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHHH
Confidence            4579999999855             2344559999999999997664  49999998877775

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

Probab=97.86  E-value=3.5e-05  Score=69.12  Aligned_cols=54  Identities=11%  Similarity=-0.041  Sum_probs=39.6

Q ss_pred             eeeccccccccc-CceeEEEeecccccCCCceeecCCCCCC--ChHHHHHHHHhcCC
Q 042810           32 KQRCQKVNRSPS-NGQQFILRDYTRSVNRFPVIQIPANALT--SPMYLFRELVTLNL   85 (230)
Q Consensus        32 ~~~~~~~~~~~~-~g~~~~~~~~~~~~~s~~~~~i~~~~~~--~~~~l~~lL~~~~~   85 (230)
                      .-..|.++|+++ ++..+.+++...-.+-....|-|+.+..  +..-+..++++++.
T Consensus       173 ~~~~~~~~~~l~~~~~~t~l~e~v~d~~~~~r~~~~~~g~~~v~~s~~d~LIsr~g~  229 (355)
T KOG1571|consen  173 RGGFRETERVLPLGTRLTALGELVRDGYCGVRVQPPMQGPLYVTKSAADRLISREGD  229 (355)
T ss_pred             eecccceEEeeccccceeeeehheecCCCceEecCCccCcceeeccchhhHHHhhcc
Confidence            445678888888 8889999998777766677777777754  22237777887776

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

Probab=97.81  E-value=2.3e-06  Score=77.44  Aligned_cols=56  Identities=25%  Similarity=0.767  Sum_probs=45.2

Q ss_pred             hhhcccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc--CCcccccccCccccC
Q 042810          158 FNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE--QNSCPMCRRQIQYED  227 (230)
Q Consensus       158 ~~~~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~--~~tCP~CR~~i~~~~  227 (230)
                      +.+..+.-+.|-||-|.              ...++.-||||..|..|+..|...  .++||.||.+|..-+
T Consensus       362 YceMgsTFeLCKICaen--------------dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte  419 (563)
T KOG1785|consen  362 YCEMGSTFELCKICAEN--------------DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTE  419 (563)
T ss_pred             HHHccchHHHHHHhhcc--------------CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEecccc
Confidence            44556667889999997              344888899999999999999753  589999999986544

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

Probab=97.79  E-value=8.2e-06  Score=73.60  Aligned_cols=54  Identities=30%  Similarity=0.850  Sum_probs=38.8

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhh--cc-----CCcccccccCc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWL--EE-----QNSCPMCRRQI  223 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl--~~-----~~tCP~CR~~i  223 (230)
                      ..+.+|+||++..-+..       .....-..+| |.|.||..||+.|-  ++     ...||.||...
T Consensus       159 s~~k~CGICme~i~ek~-------~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s  220 (344)
T KOG1039|consen  159 SSEKECGICMETINEKA-------ASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPS  220 (344)
T ss_pred             cccccceehhhhccccc-------hhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcc
Confidence            45889999999875521       0011233456 99999999999996  33     46899999854

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

Probab=97.74  E-value=6.7e-06  Score=79.69  Aligned_cols=51  Identities=25%  Similarity=0.610  Sum_probs=43.0

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhc-cCCcccccccCccccCC
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLE-EQNSCPMCRRQIQYEDL  228 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~-~~~tCP~CR~~i~~~~l  228 (230)
                      +-..|++|-..+.+              .+...|+|+||..||.+-+. +++.||.|.+.+..-|+
T Consensus       642 ~~LkCs~Cn~R~Kd--------------~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv  693 (698)
T KOG0978|consen  642 ELLKCSVCNTRWKD--------------AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDV  693 (698)
T ss_pred             hceeCCCccCchhh--------------HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccc
Confidence            45689999988877              55556999999999999987 56789999999987775

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

Probab=97.74  E-value=6.4e-06  Score=79.86  Aligned_cols=50  Identities=20%  Similarity=0.501  Sum_probs=41.1

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQY  225 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~  225 (230)
                      ...|++|+..+.+           +......+|+|.||..||..|-+..++||+||..+..
T Consensus       123 ~~~CP~Ci~s~~D-----------qL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~  172 (1134)
T KOG0825|consen  123 ENQCPNCLKSCND-----------QLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGE  172 (1134)
T ss_pred             hhhhhHHHHHHHH-----------HhhccccccccccHHHHhhhhhhhcccCchhhhhhhe
Confidence            4567777777766           5555667899999999999999999999999997643

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

Probab=97.74  E-value=3.8e-06  Score=55.37  Aligned_cols=46  Identities=28%  Similarity=0.725  Sum_probs=35.3

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCc-cchhhHHH-hhccCCcccccccCcc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHI-FHASCISR-WLEEQNSCPMCRRQIQ  224 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~-Wl~~~~tCP~CR~~i~  224 (230)
                      +++|.||+|.-.+              .+.--|||. .|.+|-.+ |-..+..||+||++|.
T Consensus         7 ~dECTICye~pvd--------------sVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    7 SDECTICYEHPVD--------------SVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             ccceeeeccCcch--------------HHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            4789999998544              334459999 88898655 4447889999999874

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

Probab=97.48  E-value=3.9e-05  Score=69.75  Aligned_cols=52  Identities=27%  Similarity=0.922  Sum_probs=40.7

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc--CCcccccccCccc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE--QNSCPMCRRQIQY  225 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~--~~tCP~CR~~i~~  225 (230)
                      ..+|+||++.+...         ....+..+.|||.|...||..||.+  +..||.|..+-..
T Consensus         4 g~tcpiclds~~~~---------g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katk   57 (463)
T KOG1645|consen    4 GTTCPICLDSYTTA---------GNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATK   57 (463)
T ss_pred             cccCceeeeeeeec---------CceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHH
Confidence            56899999998772         2455666779999999999999963  3479999875443

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

Probab=97.40  E-value=2.1e-05  Score=70.28  Aligned_cols=49  Identities=33%  Similarity=0.686  Sum_probs=39.5

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhcc-CCcccccccCccc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEE-QNSCPMCRRQIQY  225 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~-~~tCP~CR~~i~~  225 (230)
                      ..+..|+||++.+.-              .+..+ |.|.||..||..-++. .++||.||+.+..
T Consensus        41 ~~~v~c~icl~llk~--------------tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S   91 (381)
T KOG0311|consen   41 DIQVICPICLSLLKK--------------TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS   91 (381)
T ss_pred             hhhhccHHHHHHHHh--------------hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence            347789999999866              44445 9999999999888875 5789999997644

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

Probab=97.38  E-value=7e-05  Score=69.09  Aligned_cols=54  Identities=24%  Similarity=0.656  Sum_probs=45.3

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEE-eCCCCccchhhHHHhhccCCcccccccCccccCCC
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLIT-MPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~-LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      .+.+..|++|...+.+              +.. ..|||.||..|+..|+..+..||.|+..+...+.+
T Consensus        18 ~~~~l~C~~C~~vl~~--------------p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~   72 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRD--------------PVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEEL   72 (391)
T ss_pred             CcccccCccccccccC--------------CCCCCCCCCcccccccchhhccCcCCcccccccchhhcc
Confidence            3457899999999866              444 57999999999999999999999999988766554

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

Probab=97.32  E-value=5e-05  Score=68.74  Aligned_cols=47  Identities=40%  Similarity=0.904  Sum_probs=39.1

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC--Cccccccc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ--NSCPMCRR  221 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~--~tCP~CR~  221 (230)
                      +.-|..|-+.+-.          +.+..--|||.|+||..|+...|.++  ++||-||+
T Consensus       365 ~L~Cg~CGe~~Gl----------k~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  365 ELYCGLCGESIGL----------KNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             hhhhhhhhhhhcC----------CcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            6679999887744          36678889999999999999999754  68999994

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

Probab=97.30  E-value=0.00013  Score=67.07  Aligned_cols=49  Identities=31%  Similarity=0.817  Sum_probs=42.5

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQY  225 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~  225 (230)
                      ..+-.|.||+..+..              ++.+||||.||..||.+-+.+...||.||..+..
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            457799999888755              7788999999999999988888899999998753

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

Probab=97.19  E-value=6.6e-05  Score=65.83  Aligned_cols=52  Identities=31%  Similarity=0.862  Sum_probs=42.7

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc-----------------------CCcccccc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE-----------------------QNSCPMCR  220 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~-----------------------~~tCP~CR  220 (230)
                      ....|.||+--|.+           ++...+.+|-|.||..|+.+.|..                       +..||+||
T Consensus       114 p~gqCvICLygfa~-----------~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcr  182 (368)
T KOG4445|consen  114 PNGQCVICLYGFAS-----------SPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCR  182 (368)
T ss_pred             CCCceEEEEEeecC-----------CCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhh
Confidence            46689999999988           777899999999999999887621                       23599999


Q ss_pred             cCcccc
Q 042810          221 RQIQYE  226 (230)
Q Consensus       221 ~~i~~~  226 (230)
                      ..|..+
T Consensus       183 e~i~~e  188 (368)
T KOG4445|consen  183 ERIKIE  188 (368)
T ss_pred             hhcccc
Confidence            988654

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

Probab=96.90  E-value=0.0005  Score=70.78  Aligned_cols=52  Identities=38%  Similarity=0.896  Sum_probs=41.2

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC----------CcccccccCcc
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ----------NSCPMCRRQIQ  224 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~----------~tCP~CR~~i~  224 (230)
                      .+.|+.|-||+.+-..           ....++|.|+|+||..|.+.-|+++          -+||+|+.+|.
T Consensus      3483 QD~DDmCmICFTE~L~-----------AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3483 QDADDMCMICFTEALS-----------AAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             cccCceEEEEehhhhC-----------CCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            3458899999887655           6668899999999999997755432          26999998874

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

Probab=96.72  E-value=0.0012  Score=44.39  Aligned_cols=42  Identities=19%  Similarity=0.565  Sum_probs=27.5

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc--CCcccc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE--QNSCPM  218 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~--~~tCP~  218 (230)
                      ....|+|.+..|.+             .++...|+|+|-+..|.+|+++  ...||+
T Consensus        10 ~~~~CPiT~~~~~~-------------PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFED-------------PVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-SS-------------EEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhhC-------------CcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            46789999999855             3555579999999999999943  457998

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

Probab=96.61  E-value=0.0013  Score=59.14  Aligned_cols=50  Identities=22%  Similarity=0.531  Sum_probs=42.7

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccc
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQY  225 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~  225 (230)
                      +.+++.|+||.-.-..              .+..||+|.-|.+||.+-+...+.|=.|+..+..
T Consensus       419 ~sEd~lCpICyA~pi~--------------Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  419 DSEDNLCPICYAGPIN--------------AVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             CcccccCcceecccch--------------hhccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            3568999999876333              6678999999999999999999999999998764

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

Probab=96.55  E-value=0.0012  Score=42.76  Aligned_cols=46  Identities=30%  Similarity=0.614  Sum_probs=22.2

Q ss_pred             cccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhc-cCCcccccccCc
Q 042810          168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLE-EQNSCPMCRRQI  223 (230)
Q Consensus       168 C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~-~~~tCP~CR~~i  223 (230)
                      |++|.+++..          ++....--+|++.++..|...-++ ....||-||++-
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            7899998833          122232234899999999988876 478999999863

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=96.31  E-value=0.0023  Score=42.41  Aligned_cols=38  Identities=26%  Similarity=0.717  Sum_probs=31.0

Q ss_pred             CceeEEeCCCCccchhhHHHhhccCCcccccccCccccCC
Q 042810          189 KTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDL  228 (230)
Q Consensus       189 ~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l  228 (230)
                      +..-.++||+|+.+..|..-|  +-+-||+|-+++...+.
T Consensus        17 ~~~~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~~~~~   54 (55)
T PF14447_consen   17 GTKGTVLPCGHLICDNCFPGE--RYNGCPFCGTPFEFDDP   54 (55)
T ss_pred             ccccccccccceeeccccChh--hccCCCCCCCcccCCCC
Confidence            444677899999999997765  67789999999987764

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

Probab=96.28  E-value=0.0014  Score=54.56  Aligned_cols=44  Identities=20%  Similarity=0.571  Sum_probs=38.7

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccC
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQ  222 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~  222 (230)
                      .-.|.||.++|++              ++...|||.||..|.-.-++...+|-+|-+.
T Consensus       196 PF~C~iCKkdy~s--------------pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~  239 (259)
T COG5152         196 PFLCGICKKDYES--------------PVVTECGHSFCSLCAIRKYQKGDECGVCGKA  239 (259)
T ss_pred             ceeehhchhhccc--------------hhhhhcchhHHHHHHHHHhccCCcceecchh
Confidence            4489999999987              7788899999999998888888899999664

>PF14369 zf-RING_3: zinc-finger

Probab=96.24  E-value=0.0029  Score=38.24  Aligned_cols=29  Identities=21%  Similarity=0.222  Sum_probs=21.0

Q ss_pred             eEEEEEeeeeccCCCCccccccccceeeee
Q 042810            4 RVNLHLEGTGSCSNNPLMCPVGNIGIVLKQ   33 (230)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   33 (230)
                      .||-.|+.......++ .||.||.|||+++
T Consensus         7 ~C~~~V~~~~~~~~~~-~CP~C~~gFvEei   35 (35)
T PF14369_consen    7 QCNRFVRIAPSPDSDV-ACPRCHGGFVEEI   35 (35)
T ss_pred             cCCCEeEeCcCCCCCc-CCcCCCCcEeEeC
Confidence            3556666665555555 4999999999985

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

Probab=96.21  E-value=0.00071  Score=60.18  Aligned_cols=48  Identities=38%  Similarity=0.755  Sum_probs=39.5

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhccCCcccccccCcc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEEQNSCPMCRRQIQ  224 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~~~tCP~CR~~i~  224 (230)
                      ..--+|.+|...|-+              .-.+. |-|.||..||-..|...++||.|...|-
T Consensus        13 n~~itC~LC~GYliD--------------ATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih   61 (331)
T KOG2660|consen   13 NPHITCRLCGGYLID--------------ATTITECLHTFCKSCIVKYLEESKYCPTCDIVIH   61 (331)
T ss_pred             ccceehhhccceeec--------------chhHHHHHHHHHHHHHHHHHHHhccCCccceecc
Confidence            345689999988866              33444 9999999999999999999999987663

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.20  E-value=0.0037  Score=53.68  Aligned_cols=56  Identities=18%  Similarity=0.446  Sum_probs=47.9

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEe-CCCCccchhhHHHhhccCCcccccccCccccCCCC
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITM-PCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLVG  230 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~~  230 (230)
                      ....|+||.+.+..           ......| ||||+|+.+|+...++.-..||+|-.++..+|+|+
T Consensus       220 ~ryiCpvtrd~LtN-----------t~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~  276 (303)
T KOG3039|consen  220 KRYICPVTRDTLTN-----------TTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIG  276 (303)
T ss_pred             cceecccchhhhcC-----------ccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEe
Confidence            45689999999876           4445555 69999999999999888889999999999999874

>PHA03096 p28-like protein; Provisional

Probab=96.17  E-value=0.0023  Score=56.60  Aligned_cols=49  Identities=33%  Similarity=0.589  Sum_probs=34.0

Q ss_pred             CccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhcc---CCccccccc
Q 042810          166 DNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEE---QNSCPMCRR  221 (230)
Q Consensus       166 ~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~---~~tCP~CR~  221 (230)
                      ..|.||++.......       ....-..|+ |.|.||..||+.|-..   +.+||.||.
T Consensus       179 k~c~ic~e~~~~k~~-------~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYI-------IKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhcc-------ccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            689999999876221       133345577 9999999999999643   234555543

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

Probab=96.08  E-value=0.0011  Score=58.20  Aligned_cols=42  Identities=31%  Similarity=0.770  Sum_probs=34.3

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCc-cchhhHHHhhccCCcccccccCcc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHI-FHASCISRWLEEQNSCPMCRRQIQ  224 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~Wl~~~~tCP~CR~~i~  224 (230)
                      +..|+|||+.-.+              ...|+|||. -|.+|-...    +.||+||+.|.
T Consensus       300 ~~LC~ICmDaP~D--------------CvfLeCGHmVtCt~CGkrm----~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAPRD--------------CVFLECGHMVTCTKCGKRM----NECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCCcc--------------eEEeecCcEEeehhhcccc----ccCchHHHHHH
Confidence            6789999998555              889999998 788887653    48999998763

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

Probab=96.07  E-value=0.0027  Score=51.99  Aligned_cols=64  Identities=25%  Similarity=0.634  Sum_probs=41.1

Q ss_pred             cCCCccccCchhhhhhhhhhccc----------cccCceeEEeCCCCccchhhHHHhhcc----CC-------ccccccc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQT----------TEKKTQLITMPCHHIFHASCISRWLEE----QN-------SCPMCRR  221 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~----------~~~~~~v~~LpC~H~FH~~CI~~Wl~~----~~-------tCP~CR~  221 (230)
                      ++..+|.+|...|.+.++..+.-          ..+.+..--..||.-||.-|+..||+.    ++       .||.|..
T Consensus       146 kd~lE~df~a~a~Lekdd~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~  225 (234)
T KOG3268|consen  146 KDQLECDFCAAAFLEKDDELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSD  225 (234)
T ss_pred             cceeeeCccHHHhcCcchhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCC
Confidence            44566777776666654433321          111223334569999999999999862    22       5999999


Q ss_pred             Ccccc
Q 042810          222 QIQYE  226 (230)
Q Consensus       222 ~i~~~  226 (230)
                      ++..+
T Consensus       226 PialK  230 (234)
T KOG3268|consen  226 PIALK  230 (234)
T ss_pred             cceee
Confidence            88654

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

Probab=96.06  E-value=0.0048  Score=53.75  Aligned_cols=51  Identities=24%  Similarity=0.506  Sum_probs=38.5

Q ss_pred             hcccCCCccccCchhhhhhhhhhccccccCceeEEe-CCCCccchhhHHHhhcc--CCcccccccCcc
Q 042810          160 KLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITM-PCHHIFHASCISRWLEE--QNSCPMCRRQIQ  224 (230)
Q Consensus       160 ~~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~Wl~~--~~tCP~CR~~i~  224 (230)
                      ...+.+.+|++|-+.-..              +..+ +|+|+||..||..=+..  .-+||.|..++.
T Consensus       234 s~~t~~~~C~~Cg~~Pti--------------P~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  234 STGTSDTECPVCGEPPTI--------------PHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             ccccCCceeeccCCCCCC--------------CeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            344568899999986322              4444 59999999999886543  468999988775

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

Probab=96.06  E-value=0.0037  Score=40.27  Aligned_cols=40  Identities=35%  Similarity=0.977  Sum_probs=25.6

Q ss_pred             cccCchhhhhhhhhhccccccCceeEEeCCC--C---ccchhhHHHhhcc--CCccccc
Q 042810          168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCH--H---IFHASCISRWLEE--QNSCPMC  219 (230)
Q Consensus       168 C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~--H---~FH~~CI~~Wl~~--~~tCP~C  219 (230)
                      |-||++.-.+           .. ....||+  =   ..|.+|+.+|+..  +.+|++|
T Consensus         1 CrIC~~~~~~-----------~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEE-----------DE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SS-----------SS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCC-----------CC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            6688887543           22 4556854  3   6899999999974  4679987

>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=95.99  E-value=0.0055  Score=45.54  Aligned_cols=35  Identities=31%  Similarity=0.804  Sum_probs=27.9

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHH
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCIS  207 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~  207 (230)
                      ..+++..|++|...+..            ......||||+||..|++
T Consensus        74 ~i~~~~~C~vC~k~l~~------------~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   74 VITESTKCSVCGKPLGN------------SVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             EECCCCCccCcCCcCCC------------ceEEEeCCCeEEeccccc
Confidence            34567889999998733            447778999999999985

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=95.96  E-value=0.0036  Score=49.08  Aligned_cols=36  Identities=19%  Similarity=0.585  Sum_probs=30.0

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCC------CccchhhHHHhhc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCH------HIFHASCISRWLE  211 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~------H~FH~~CI~~Wl~  211 (230)
                      .-+|.||++.+..           ...++.++||      |+||.+|+.+|-+
T Consensus        26 ~~EC~IC~~~I~~-----------~~GvV~vt~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   26 TVECQICFDRIDN-----------NDGVVYVTDGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             Ceeehhhhhhhhc-----------CCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence            5689999999866           4568888887      8999999999943

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.

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

Probab=95.77  E-value=0.0036  Score=57.29  Aligned_cols=46  Identities=26%  Similarity=0.683  Sum_probs=36.6

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc--------CCcccccc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE--------QNSCPMCR  220 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~--------~~tCP~CR  220 (230)
                      .--.|.||+++..-           ....+.+||+|+||..|.+..+..        .-.||-+.
T Consensus       183 slf~C~ICf~e~~G-----------~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~  236 (445)
T KOG1814|consen  183 SLFDCCICFEEQMG-----------QHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPK  236 (445)
T ss_pred             hcccceeeehhhcC-----------cceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence            35689999998754           578999999999999999999853        23587654

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

Probab=95.70  E-value=0.0052  Score=60.71  Aligned_cols=49  Identities=27%  Similarity=0.792  Sum_probs=36.1

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEe-CCCCccchhhHHHhhccC-------Cccccccc
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITM-PCHHIFHASCISRWLEEQ-------NSCPMCRR  221 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~Wl~~~-------~tCP~CR~  221 (230)
                      .....+|.||.+.+..           ...+..- .|-|+||..||..|-++.       -.||-|..
T Consensus       188 ~~~~yeCmIC~e~I~~-----------t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs  244 (950)
T KOG1952|consen  188 SNRKYECMICTERIKR-----------TAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS  244 (950)
T ss_pred             hcCceEEEEeeeeccc-----------cCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence            3457799999999865           3333333 389999999999997532       15999983

>PHA02862 5L protein; Provisional

Probab=95.67  E-value=0.0046  Score=49.01  Aligned_cols=47  Identities=19%  Similarity=0.650  Sum_probs=34.2

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCC-----CccchhhHHHhhcc--CCcccccccCcccc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCH-----HIFHASCISRWLEE--QNSCPMCRRQIQYE  226 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~-----H~FH~~CI~~Wl~~--~~tCP~CR~~i~~~  226 (230)
                      ++.|-||.++-.+             .  .-||.     ..-|+.|+.+|+..  +.+||+|+.+..-+
T Consensus         2 ~diCWIC~~~~~e-------------~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik   55 (156)
T PHA02862          2 SDICWICNDVCDE-------------R--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK   55 (156)
T ss_pred             CCEEEEecCcCCC-------------C--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence            4679999997322             1  24654     56899999999974  45899999876543

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

Probab=95.64  E-value=0.0039  Score=54.81  Aligned_cols=45  Identities=20%  Similarity=0.514  Sum_probs=39.5

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQI  223 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i  223 (230)
                      ...|-||...|..              +++..|+|.||..|...=+++...|++|-+..
T Consensus       241 Pf~c~icr~~f~~--------------pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t  285 (313)
T KOG1813|consen  241 PFKCFICRKYFYR--------------PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQT  285 (313)
T ss_pred             Ccccccccccccc--------------chhhcCCceeehhhhccccccCCcceeccccc
Confidence            4569999999977              78889999999999988888889999997754

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

Probab=95.48  E-value=0.0051  Score=58.05  Aligned_cols=52  Identities=27%  Similarity=0.671  Sum_probs=40.4

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc-----CCcccccccCcccc
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE-----QNSCPMCRRQIQYE  226 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~-----~~tCP~CR~~i~~~  226 (230)
                      +..+...|.+|-+.-++              .+...|.|.||+.||.+++..     .-+||.|-..+.-+
T Consensus       532 enk~~~~C~lc~d~aed--------------~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD  588 (791)
T KOG1002|consen  532 ENKGEVECGLCHDPAED--------------YIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID  588 (791)
T ss_pred             cccCceeecccCChhhh--------------hHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence            44557799999997555              677789999999999888642     35899998766543

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

Probab=95.46  E-value=0.0043  Score=50.10  Aligned_cols=32  Identities=34%  Similarity=0.799  Sum_probs=28.1

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccch
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHA  203 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~  203 (230)
                      ..++..+|.||+|+++.           ++.+.+|||--+||+
T Consensus       173 L~ddkGECvICLEdL~~-----------GdtIARLPCLCIYHK  204 (205)
T KOG0801|consen  173 LKDDKGECVICLEDLEA-----------GDTIARLPCLCIYHK  204 (205)
T ss_pred             hcccCCcEEEEhhhccC-----------CCceeccceEEEeec
Confidence            34557799999999998           999999999999996

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

Probab=95.44  E-value=0.0089  Score=50.75  Aligned_cols=48  Identities=27%  Similarity=0.697  Sum_probs=38.6

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc--------CCcccccccCc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE--------QNSCPMCRRQI  223 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~--------~~tCP~CR~~i  223 (230)
                      -...|..|-..+..           ++.+ +|-|-|+||-+|+++|-..        .-.||-|..+|
T Consensus        49 Y~pNC~LC~t~La~-----------gdt~-RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~ei  104 (299)
T KOG3970|consen   49 YNPNCRLCNTPLAS-----------GDTT-RLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEI  104 (299)
T ss_pred             CCCCCceeCCcccc-----------Ccce-eehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCcc
Confidence            36789999998876           5555 4679999999999999653        23699999877

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

Probab=95.39  E-value=0.0013  Score=59.75  Aligned_cols=52  Identities=27%  Similarity=0.668  Sum_probs=43.9

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQY  225 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~  225 (230)
                      ....|+||.+.+...          -+++..+-|||.+|.+|+..||.++..||.||++++.
T Consensus       195 lv~sl~I~~~slK~~----------y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~  246 (465)
T KOG0827|consen  195 LVGSLSICFESLKQN----------YDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPK  246 (465)
T ss_pred             HHhhhHhhHHHHHHH----------HHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhh
Confidence            367899999998771          1456667899999999999999999999999998864

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

Probab=95.23  E-value=0.0086  Score=53.85  Aligned_cols=51  Identities=27%  Similarity=0.623  Sum_probs=39.4

Q ss_pred             hcccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHh--hccCCcccccccCcc
Q 042810          160 KLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRW--LEEQNSCPMCRRQIQ  224 (230)
Q Consensus       160 ~~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~W--l~~~~tCP~CR~~i~  224 (230)
                      +.+++...|-||.+.+.              ...++||+|..|-.|-.+-  |=.+..||+||.++.
T Consensus        56 dtDEen~~C~ICA~~~T--------------Ys~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e  108 (493)
T COG5236          56 DTDEENMNCQICAGSTT--------------YSARYPCGHQICHACAVRLRALYMQKGCPLCRTETE  108 (493)
T ss_pred             ccccccceeEEecCCce--------------EEEeccCCchHHHHHHHHHHHHHhccCCCccccccc
Confidence            34456778999998743              3788999999999998654  345778999998763

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=95.17  E-value=0.014  Score=46.97  Aligned_cols=48  Identities=25%  Similarity=0.675  Sum_probs=34.0

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCC--CC---ccchhhHHHhhccC--CcccccccCccc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPC--HH---IFHASCISRWLEEQ--NSCPMCRRQIQY  225 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC--~H---~FH~~CI~~Wl~~~--~tCP~CR~~i~~  225 (230)
                      ..+..|-||.++-.+             .  .-||  ..   .-|..|+.+|+..+  .+|++|+.+..-
T Consensus         6 ~~~~~CRIC~~~~~~-------------~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i   60 (162)
T PHA02825          6 LMDKCCWICKDEYDV-------------V--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNI   60 (162)
T ss_pred             CCCCeeEecCCCCCC-------------c--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEE
Confidence            347789999886311             1  2364  44   46999999999754  579999987643

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

Probab=94.99  E-value=0.012  Score=52.07  Aligned_cols=50  Identities=24%  Similarity=0.638  Sum_probs=38.9

Q ss_pred             CccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc-CCcccccccCc
Q 042810          166 DNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE-QNSCPMCRRQI  223 (230)
Q Consensus       166 ~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~-~~tCP~CR~~i  223 (230)
                      ..|-||-++|+..+        +...++.|.|||.|+..|+..-+.. ...||.||...
T Consensus         4 ~~c~~c~~~~s~~~--------~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSED--------GDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccC--------cccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            57999999998732        1345777779999999999776654 35799999974

>PF04641 Rtf2: Rtf2 RING-finger

Probab=94.92  E-value=0.02  Score=49.93  Aligned_cols=55  Identities=22%  Similarity=0.546  Sum_probs=43.3

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCce-eEEeCCCCccchhhHHHhhccCCcccccccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQ-LITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~-v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      ...-.|||...+|..           ... +...||||+|-..++.+- .....||+|-.++..+|+|
T Consensus       111 ~~~~~CPvt~~~~~~-----------~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~f~~~DiI  166 (260)
T PF04641_consen  111 EGRFICPVTGKEFNG-----------KHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKPFTEEDII  166 (260)
T ss_pred             CceeECCCCCcccCC-----------ceeEEEEcCCCCEeeHHHHHhh-cccccccccCCccccCCEE
Confidence            456789999998844           333 444589999999999996 3356899999999988876

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

Probab=94.45  E-value=0.03  Score=55.60  Aligned_cols=43  Identities=23%  Similarity=0.770  Sum_probs=33.3

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQI  223 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i  223 (230)
                      ...|..|--.++.             ..+---|||.||.+|+.   +....||-|+.+.
T Consensus       840 ~skCs~C~~~Ldl-------------P~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  840 VSKCSACEGTLDL-------------PFVHFLCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeeecccCCcccc-------------ceeeeecccHHHHHhhc---cCcccCCccchhh
Confidence            4689999888744             24445699999999998   4567899998743

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

Probab=94.22  E-value=0.024  Score=50.08  Aligned_cols=47  Identities=30%  Similarity=0.721  Sum_probs=35.9

Q ss_pred             CccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhh-ccCCccccc-ccCcccc
Q 042810          166 DNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWL-EEQNSCPMC-RRQIQYE  226 (230)
Q Consensus       166 ~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl-~~~~tCP~C-R~~i~~~  226 (230)
                      ..|+.|..-+..              +.+.| |+|.||..||..-| .....||.| |++|-.+
T Consensus       275 LkCplc~~Llrn--------------p~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdvlld  324 (427)
T COG5222         275 LKCPLCHCLLRN--------------PMKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLD  324 (427)
T ss_pred             ccCcchhhhhhC--------------cccCccccchHHHHHHhhhhhhccccCCCcccccchhh
Confidence            689999887755              55667 99999999998765 456789999 4454443

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

Probab=94.22  E-value=0.022  Score=50.06  Aligned_cols=47  Identities=28%  Similarity=0.679  Sum_probs=38.9

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCccccccc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR  221 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~  221 (230)
                      ...|+||.+.+-..          ...+..++|||..|..|........-+||+|.+
T Consensus       158 ~~ncPic~e~l~~s----------~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  158 EFNCPICKEYLFLS----------FEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             cCCCchhHHHhccc----------cccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence            34499999988662          556788999999999999988776789999987

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

Probab=93.93  E-value=0.013  Score=57.56  Aligned_cols=49  Identities=24%  Similarity=0.749  Sum_probs=39.7

Q ss_pred             CccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC--CcccccccCccccCCC
Q 042810          166 DNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ--NSCPMCRRQIQYEDLV  229 (230)
Q Consensus       166 ~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~--~tCP~CR~~i~~~~l~  229 (230)
                      ..|.||++ ...              ....+|+|.||..|+..-+...  ..||.||..+..++++
T Consensus       455 ~~c~ic~~-~~~--------------~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~  505 (674)
T KOG1001|consen  455 HWCHICCD-LDS--------------FFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLL  505 (674)
T ss_pred             cccccccc-ccc--------------ceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHh
Confidence            78999999 322              6778899999999998877543  3699999998887765

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

Probab=93.61  E-value=0.052  Score=49.52  Aligned_cols=31  Identities=26%  Similarity=0.901  Sum_probs=23.2

Q ss_pred             CCCccchhhHHHhhccC-------------CcccccccCccccC
Q 042810          197 CHHIFHASCISRWLEEQ-------------NSCPMCRRQIQYED  227 (230)
Q Consensus       197 C~H~FH~~CI~~Wl~~~-------------~tCP~CR~~i~~~~  227 (230)
                      |.-..|.+|+-+|+..+             -+||+||+++.--|
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilD  354 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILD  354 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeee
Confidence            44566889999998643             26999999886544

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

>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=93.03  E-value=0.034  Score=35.11  Aligned_cols=24  Identities=25%  Similarity=0.956  Sum_probs=16.0

Q ss_pred             CCCCccchhhHHHhhccCC--ccccc
Q 042810          196 PCHHIFHASCISRWLEEQN--SCPMC  219 (230)
Q Consensus       196 pC~H~FH~~CI~~Wl~~~~--tCP~C  219 (230)
                      .|+=.+|..|+..+++.+.  .||.|
T Consensus        18 ~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen   18 DCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             ccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            3888899999999998765  79987

; PDB: 3NW0_A 2CT0_A.

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

Probab=92.65  E-value=0.051  Score=34.94  Aligned_cols=33  Identities=21%  Similarity=0.742  Sum_probs=23.4

Q ss_pred             EeCCC-CccchhhHHHhhccCCcccccccCcccc
Q 042810          194 TMPCH-HIFHASCISRWLEEQNSCPMCRRQIQYE  226 (230)
Q Consensus       194 ~LpC~-H~FH~~CI~~Wl~~~~tCP~CR~~i~~~  226 (230)
                      .+.|+ |..|..|+...+.+...||+|..+++++
T Consensus        15 Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen   15 LIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK   48 (50)
T ss_dssp             EEE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred             eeeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence            34575 9999999999999999999999998764

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.

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

Probab=92.32  E-value=0.085  Score=52.72  Aligned_cols=38  Identities=29%  Similarity=0.775  Sum_probs=30.1

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhh
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWL  210 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl  210 (230)
                      ..+.++.|.+|.-.+..            ..-.+-||||.||.+|+-+-.
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            45678999999988865            345667999999999997653

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

Probab=92.14  E-value=0.051  Score=48.57  Aligned_cols=52  Identities=19%  Similarity=0.441  Sum_probs=40.3

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhccCCcccccccCccccCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEEQNSCPMCRRQIQYEDL  228 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l  228 (230)
                      .+.+.|+||+.....              ...+. -|-+||-.||.+.+.+.++||+=..+..-+++
T Consensus       298 ~~~~~CpvClk~r~N--------------ptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~v~~l  350 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQN--------------PTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPASVDHL  350 (357)
T ss_pred             CccccChhHHhccCC--------------CceEEecceEEeHHHHHHHHHhcCCCCccCCcchHHHH
Confidence            457899999987543              44444 69999999999999999999987666554443

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

Probab=91.75  E-value=0.097  Score=44.26  Aligned_cols=39  Identities=28%  Similarity=0.820  Sum_probs=29.7

Q ss_pred             cccCchhhhhhhhhhccccccCceeEEeCCCCc-cchhhHHHhhccCCcccccccCcc
Q 042810          168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHI-FHASCISRWLEEQNSCPMCRRQIQ  224 (230)
Q Consensus       168 C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~Wl~~~~tCP~CR~~i~  224 (230)
                      |-.|.+.              ...+..+||.|. +|..|=..    -++||+|+....
T Consensus       161 Cr~C~~~--------------~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~  200 (207)
T KOG1100|consen  161 CRKCGER--------------EATVLLLPCRHLCLCGICDES----LRICPICRSPKT  200 (207)
T ss_pred             ceecCcC--------------CceEEeecccceEeccccccc----CccCCCCcChhh
Confidence            7777775              444888999988 88899754    456999998653

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=91.68  E-value=0.086  Score=47.44  Aligned_cols=55  Identities=24%  Similarity=0.594  Sum_probs=38.1

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhc-cCCcccccccCccccC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLE-EQNSCPMCRRQIQYED  227 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~-~~~tCP~CR~~i~~~~  227 (230)
                      ++++-|+.|+|.+...          +..-.--|||-..|+.|....-+ ....||-||+....+.
T Consensus        12 deed~cplcie~mdit----------dknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~den   67 (480)
T COG5175          12 DEEDYCPLCIEPMDIT----------DKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDEN   67 (480)
T ss_pred             cccccCcccccccccc----------cCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccc
Confidence            3455699999998662          33344457999999988655422 3468999999766554

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

Probab=91.47  E-value=0.07  Score=47.43  Aligned_cols=33  Identities=27%  Similarity=0.791  Sum_probs=24.9

Q ss_pred             eeEEeCCCCccchhhHHHhhccCCcccccccCccc
Q 042810          191 QLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQY  225 (230)
Q Consensus       191 ~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~  225 (230)
                      .-+.+||+|+||.+|...  ..-+.||.|-.+|..
T Consensus       103 YGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~Vqr  135 (389)
T KOG2932|consen  103 YGRMIPCKHVFCLECARS--DSDKICPLCDDRVQR  135 (389)
T ss_pred             eecccccchhhhhhhhhc--CccccCcCcccHHHH
Confidence            356689999999999754  334589999776643

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

Probab=90.25  E-value=0.11  Score=51.28  Aligned_cols=30  Identities=27%  Similarity=0.721  Sum_probs=25.7

Q ss_pred             CceeEEeCCCCccchhhHHHhhccCCcccc
Q 042810          189 KTQLITMPCHHIFHASCISRWLEEQNSCPM  218 (230)
Q Consensus       189 ~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~  218 (230)
                      +.......|+|+.|..|...|++....||.
T Consensus      1040 gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1040 GSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             ccchhhccccccccHHHHHHHHhcCCcCCC
Confidence            344566779999999999999999999984

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

Probab=89.27  E-value=0.25  Score=45.30  Aligned_cols=48  Identities=19%  Similarity=0.389  Sum_probs=37.4

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC---CcccccccCc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ---NSCPMCRRQI  223 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~---~tCP~CR~~i  223 (230)
                      --.|||=.+.-.+           ...+..|.|||+...+-+++.-+..   -.||.|=.+.
T Consensus       334 vF~CPVlKeqtsd-----------eNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~  384 (394)
T KOG2817|consen  334 VFICPVLKEQTSD-----------ENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ  384 (394)
T ss_pred             eeecccchhhccC-----------CCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence            4578987776555           6779999999999999999976543   3699995543

>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]

Probab=88.81  E-value=0.15  Score=43.78  Aligned_cols=49  Identities=24%  Similarity=0.676  Sum_probs=34.5

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhccC-Cccc--cccc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEEQ-NSCP--MCRR  221 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~~-~tCP--~CR~  221 (230)
                      .+..||||..+--.         .+.-.+-.-| |-|..|..|+++-+.+. ..||  -|.+
T Consensus         9 ~d~~CPvCksDrYL---------nPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~k   61 (314)
T COG5220           9 EDRRCPVCKSDRYL---------NPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGK   61 (314)
T ss_pred             hcccCCcccccccc---------CCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHH
Confidence            36689999765433         1123333447 99999999999998764 5899  7754

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

Probab=88.13  E-value=0.14  Score=53.14  Aligned_cols=45  Identities=27%  Similarity=0.592  Sum_probs=37.2

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCccccccc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR  221 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~  221 (230)
                      .--.|.||++.+..           .  -....|||.+|..|...|+..+..||+|+.
T Consensus      1152 ~~~~c~ic~dil~~-----------~--~~I~~cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRN-----------Q--GGIAGCGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred             cccchHHHHHHHHh-----------c--CCeeeechhHhhhHHHHHHHHhccCcchhh
Confidence            34589999999865           1  223459999999999999999999999974

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

Probab=87.75  E-value=0.22  Score=49.50  Aligned_cols=57  Identities=23%  Similarity=0.690  Sum_probs=41.2

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeCCC-----CccchhhHHHhhcc--CCcccccccCccccCCCC
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCH-----HIFHASCISRWLEE--QNSCPMCRRQIQYEDLVG  230 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~-----H~FH~~CI~~Wl~~--~~tCP~CR~~i~~~~l~~  230 (230)
                      .+++..|-||..+=..            +.+-.=||+     ...|+.|+-+|++-  ...|-+|..++.-+++.+
T Consensus         9 N~d~~~CRICr~e~~~------------d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~IY~   72 (1175)
T COG5183           9 NEDKRSCRICRTEDIR------------DDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDIYK   72 (1175)
T ss_pred             CccchhceeecCCCCC------------CCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeeecc
Confidence            3456899999886433            223344665     34899999999974  457999999998887653

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

Probab=87.74  E-value=0.22  Score=48.28  Aligned_cols=44  Identities=23%  Similarity=0.661  Sum_probs=33.0

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCccccccc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR  221 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~  221 (230)
                      -..|.||+..|...          .-.++.+-|||+.|.+|+..-.  +.+|| |+.
T Consensus        11 ~l~c~ic~n~f~~~----------~~~Pvsl~cghtic~~c~~~ly--n~scp-~~~   54 (861)
T KOG3161|consen   11 LLLCDICLNLFVVQ----------RLEPVSLQCGHTICGHCVQLLY--NASCP-TKR   54 (861)
T ss_pred             HhhchHHHHHHHHH----------hcCcccccccchHHHHHHHhHh--hccCC-CCc
Confidence            34699998888762          4456778899999999998764  45788 543

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=87.05  E-value=0.83  Score=30.28  Aligned_cols=43  Identities=23%  Similarity=0.681  Sum_probs=33.0

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhccCCcccc--cccC
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEEQNSCPM--CRRQ  222 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~~~tCP~--CR~~  222 (230)
                      ...|.+|-+.|.+           ++.+++-| ||=.+|+.|...    ...|-.  |...
T Consensus         5 ~~~C~~Cg~~~~~-----------~dDiVvCp~CgapyHR~C~~~----~g~C~~~~c~~~   50 (54)
T PF14446_consen    5 GCKCPVCGKKFKD-----------GDDIVVCPECGAPYHRDCWEK----AGGCINYSCGTG   50 (54)
T ss_pred             CccChhhCCcccC-----------CCCEEECCCCCCcccHHHHhh----CCceEeccCCCC
Confidence            5689999999987           66688888 999999999644    455654  5443

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.82  E-value=0.26  Score=43.58  Aligned_cols=31  Identities=26%  Similarity=0.779  Sum_probs=22.9

Q ss_pred             CCCccchhhHHHhhc-------------cCCcccccccCccccC
Q 042810          197 CHHIFHASCISRWLE-------------EQNSCPMCRRQIQYED  227 (230)
Q Consensus       197 C~H~FH~~CI~~Wl~-------------~~~tCP~CR~~i~~~~  227 (230)
                      |....|..|+.+|+.             .+-+||+||+++.-.|
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~d  368 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRD  368 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEee
Confidence            455677889999874             3457999999876544

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=85.51  E-value=0.22  Score=43.21  Aligned_cols=50  Identities=30%  Similarity=0.771  Sum_probs=34.6

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCcee-EEeCC-----CCccchhhHHHhhccCC--------cccccccCc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQL-ITMPC-----HHIFHASCISRWLEEQN--------SCPMCRRQI  223 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v-~~LpC-----~H~FH~~CI~~Wl~~~~--------tCP~CR~~i  223 (230)
                      +.+.-|=||+..=++           .... -+-||     .|.-|..|+..|+..++        +||-|+.+-
T Consensus        18 e~eR~CWiCF~TdeD-----------n~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY   81 (293)
T KOG3053|consen   18 ELERCCWICFATDED-----------NRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY   81 (293)
T ss_pred             ccceeEEEEeccCcc-----------cchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence            346788999986443           2212 33465     38899999999996443        599998753

>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=84.99  E-value=0.54  Score=37.96  Aligned_cols=13  Identities=23%  Similarity=0.669  Sum_probs=9.9

Q ss_pred             CCccccCchhhhh
Q 042810          165 GDNCAVCLEELIA  177 (230)
Q Consensus       165 ~~~C~ICle~~~~  177 (230)
                      +..|+||||.-..
T Consensus         2 d~~CpICme~PHN   14 (162)
T PF07800_consen    2 DVTCPICMEHPHN   14 (162)
T ss_pred             CccCceeccCCCc
Confidence            5689999997433

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.

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

Probab=83.77  E-value=0.68  Score=41.33  Aligned_cols=45  Identities=29%  Similarity=0.606  Sum_probs=32.9

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCcc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ  224 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~  224 (230)
                      +-.+|+||.+.+..             .+.+-+=||.-|..|=.   +..+.||.||.++.
T Consensus        47 ~lleCPvC~~~l~~-------------Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   47 DLLDCPVCFNPLSP-------------PIFQCDNGHLACSSCRT---KVSNKCPTCRLPIG   91 (299)
T ss_pred             hhccCchhhccCcc-------------cceecCCCcEehhhhhh---hhcccCCccccccc
Confidence            45689999998855             23332237888888865   45788999999886

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

Probab=83.37  E-value=0.67  Score=36.40  Aligned_cols=51  Identities=18%  Similarity=0.468  Sum_probs=36.4

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeC---CCCccchhhHHHhhc---cCCcccccccCccccC
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP---CHHIFHASCISRWLE---EQNSCPMCRRQIQYED  227 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp---C~H~FH~~CI~~Wl~---~~~tCP~CR~~i~~~~  227 (230)
                      .--+|-||.|.-.+             +--.-|   ||-..|..|.....+   ....||+|+..+....
T Consensus        79 ~lYeCnIC~etS~e-------------e~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~  135 (140)
T PF05290_consen   79 KLYECNICKETSAE-------------ERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS  135 (140)
T ss_pred             CceeccCcccccch-------------hhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence            45689999997544             122223   999999998866444   4578999999886543

>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=81.95  E-value=0.45  Score=30.89  Aligned_cols=42  Identities=19%  Similarity=0.604  Sum_probs=18.7

Q ss_pred             ccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC-----CcccccccC
Q 042810          167 NCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ-----NSCPMCRRQ  222 (230)
Q Consensus       167 ~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~-----~tCP~CR~~  222 (230)
                      .|+|-...+..             .++-..|.|.-+.+ +..|+...     =.||+|.++
T Consensus         4 ~CPls~~~i~~-------------P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    4 RCPLSFQRIRI-------------PVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             B-TTTSSB-SS-------------EEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eCCCCCCEEEe-------------CccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            57777776633             34444599986544 45666432     269999864

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 entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.

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

Probab=81.81  E-value=0.7  Score=44.55  Aligned_cols=47  Identities=36%  Similarity=0.966  Sum_probs=38.5

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYED  227 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~  227 (230)
                      +..+.|.||+.+. .              .+..+|.   |..|...|+..+..||+|+..+..++
T Consensus       477 ~~~~~~~~~~~~~-~--------------~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~  523 (543)
T KOG0802|consen  477 EPNDVCAICYQEM-S--------------ARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDD  523 (543)
T ss_pred             cccCcchHHHHHH-H--------------hcccccc---chhHHHhhhhhccccCCCchhhhccc
Confidence            4577899999987 3              4556677   89999999999999999998776655

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

Probab=81.62  E-value=0.32  Score=47.73  Aligned_cols=47  Identities=28%  Similarity=0.750  Sum_probs=37.6

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC---CcccccccCccc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ---NSCPMCRRQIQY  225 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~---~tCP~CR~~i~~  225 (230)
                      ..+|+||...+..              ...+.|.|.|+..|+..-|..+   ..||+|+..+..
T Consensus        21 ~lEc~ic~~~~~~--------------p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK   70 (684)
T KOG4362|consen   21 ILECPICLEHVKE--------------PSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEK   70 (684)
T ss_pred             hccCCceeEEeec--------------cchhhhhHHHHhhhhhceeeccCccccchhhhhhhhh
Confidence            5689999999866              4677899999999997766544   479999976643

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

Probab=81.18  E-value=0.61  Score=41.06  Aligned_cols=50  Identities=28%  Similarity=0.743  Sum_probs=35.6

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCC-----CccchhhHHHhhc--cCCcccccccCcc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCH-----HIFHASCISRWLE--EQNSCPMCRRQIQ  224 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~-----H~FH~~CI~~Wl~--~~~tCP~CR~~i~  224 (230)
                      +..|-||.++....          .......||.     +..|..|+..|+.  ....|.+|.....
T Consensus        78 ~~~cRIc~~~~~~~----------~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~  134 (323)
T KOG1609|consen   78 GPICRICHEEDEES----------NGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI  134 (323)
T ss_pred             CCcEEEEecccccc----------cccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence            57899999976541          1114556764     5579999999997  4567999987543

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

Probab=80.42  E-value=0.62  Score=43.03  Aligned_cols=39  Identities=21%  Similarity=0.583  Sum_probs=27.2

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE  212 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~  212 (230)
                      ...+|.||+.+....          .+.-....|+|.||.+|..+-++.
T Consensus       145 ~~~~C~iC~~e~~~~----------~~~f~~~~C~H~fC~~C~k~~iev  183 (384)
T KOG1812|consen  145 PKEECGICFVEDPEA----------EDMFSVLKCGHRFCKDCVKQHIEV  183 (384)
T ss_pred             ccccCccCccccccH----------hhhHHHhcccchhhhHHhHHHhhh
Confidence            467899999444331          122334569999999999988764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	230
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		1e-07
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		4e-05
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		7e-05
1u6g_B	108	Crystal Structure Of The Cand1-Cul1-Roc1 Complex Le		7e-05
4a0k_B	117	Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp		7e-05
3dpl_R	106	Structural Insights Into Nedd8 Activation Of Cullin		7e-05
4a0c_D	98	Structure Of The Cand1-Cul4b-Rbx1 Complex Length =		9e-05
3dqv_R	106	Structural Insights Into Nedd8 Activation Of Cullin		9e-05
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		1e-04
1ldj_B	90	Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiqu		1e-04
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		1e-04
2lgv_A	100	Rbx1 Length = 100		2e-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 = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 11/66 (16%)
Query: 162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR 221
           V +G  C VC E+    E ++            +PC+H+FH SCI  WLE+ +SCP+CR+
Sbjct: 12  VGSGLECPVCKEDYALGESVR-----------QLPCNHLFHDSCIVPWLEQHDSCPVCRK 60
Query: 222 QIQYED 227
            +  ++
Sbjct: 61  SLTGQN 66

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 23/57 (40%), Positives = 29/57 (50%), Gaps = 12/57 (21%)
Query: 165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEEQNSCPMCR 220
           G  CAVCL EL   EE +            +P C H FHA C+  WL   ++CP+CR
Sbjct: 5   GVECAVCLAELEDGEEAR-----------FLPRCGHGFHAECVDMWLGSHSTCPLCR 50

>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 = 43.9 bits (102), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 6/46 (13%)
Query: 175 LIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCR 220
           +   E +KG    +      +PCHH FH  C+S WL++  +CP+CR
Sbjct: 45  ICCSEYVKGDVATE------LPCHHYFHKPCVSIWLQKSGTCPVCR 84

>pdb|1U6G|B Chain B, Crystal Structure Of The Cand1-Cul1-Roc1 Complex Length = 108

Iteration: 1
 Score = 43.9 bits (102), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 166 DNCAVC----LEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR 221
           DNCA+C    ++  I  +  +   T ++  +    C+H FH  CISRWL+ +  CP+  R
Sbjct: 40  DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 99
Query: 222 QIQYE 226
           + +++
Sbjct: 100 EWEFQ 104

>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic Site Containing Dna-Duplex Length = 117

Iteration: 1
 Score = 43.9 bits (102), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 166 DNCAVC----LEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR 221
           DNCA+C    ++  I  +  +   T ++  +    C+H FH  CISRWL+ +  CP+  R
Sbjct: 49  DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 108
Query: 222 QIQYE 226
           + +++
Sbjct: 109 EWEFQ 113

>pdb|3DPL|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring Ligases: Conformational Control Of Conjugation. Length = 106

Iteration: 1
 Score = 43.9 bits (102), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 166 DNCAVC----LEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR 221
           DNCA+C    ++  I  +  +   T ++  +    C+H FH  CISRWL+ +  CP+  R
Sbjct: 38  DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 97
Query: 222 QIQYE 226
           + +++
Sbjct: 98  EWEFQ 102

>pdb|4A0C|D Chain D, Structure Of The Cand1-Cul4b-Rbx1 Complex Length = 98

Iteration: 1
 Score = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 166 DNCAVC----LEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR 221
           DNCA+C    ++  I  +  +   T ++  +    C+H FH  CISRWL+ +  CP+  R
Sbjct: 30  DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 89
Query: 222 QIQYE 226
           + +++
Sbjct: 90  EWEFQ 94

>pdb|3DQV|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring Ligases: Conformational Control Of Conjugation Length = 106

Iteration: 1
 Score = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 4/65 (6%)
Query: 166 DNCAVCLEEL----IAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR 221
           DNCA+C   +    I  +  +   T ++  +    C+H FH  CISRWL+ +  CP+  R
Sbjct: 38  DNCAICRNHIXDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 97
Query: 222 QIQYE 226
           + +++
Sbjct: 98  EWEFQ 102

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 15/34 (44%), Positives = 23/34 (67%)
Query: 187 EKKTQLITMPCHHIFHASCISRWLEEQNSCPMCR 220
           E +  L  +PC+H FHA C+ +WL+   +CP+CR
Sbjct: 34  ESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICR 67

>pdb|1LDJ|B Chain B, Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiquitin Ligase Complex Length = 90

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 166 DNCAVC----LEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR 221
           DNCA+C    ++  I  +  +   T ++  +    C+H FH  CISRWL+ +  CP+  R
Sbjct: 22  DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 81
Query: 222 QIQYE 226
           + +++
Sbjct: 82  EWEFQ 86

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/85 (31%), Positives = 40/85 (47%), Gaps = 18/85 (21%)
Query: 147 SRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCI 206
           S    +V +L+ ++L      CAVCLE+   ++E           L   PC H FH  C+
Sbjct: 3   SGSSGKVKELNLHEL------CAVCLEDFKPRDE-----------LGICPCKHAFHRKCL 45
Query: 207 SRWLEEQNSCPMCRRQI-QYEDLVG 230
            +WLE +  CP+C   + Q   L G
Sbjct: 46  IKWLEVRKVCPLCNMPVLQLAQLSG 70

>pdb|2LGV|A Chain A, Rbx1 Length = 100

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 166 DNCAVC----LEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR 221
           DNCA+C    ++  I  +  +   T ++  +    C+H FH  CISRWL+ +  CP+  R
Sbjct: 32  DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 91
Query: 222 QIQYE 226
           + +++
Sbjct: 92  EWEFQ 96

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	230
2ect_A	78	Ring finger protein 126; metal binding protein, st	2e-18
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	3e-18
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	2e-16
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	1e-15
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	2e-15
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	4e-15
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	6e-15
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	8e-15
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	5e-14
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	6e-14
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	2e-13
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	2e-13
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	1e-12
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	1e-12
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	1e-12
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	7e-11
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	1e-10
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	1e-10
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	2e-09
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	3e-08
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	5e-08
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	5e-08
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	7e-08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-07
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-06
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	2e-07
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	2e-07
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	3e-06
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	4e-06
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	5e-06
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	1e-05
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	3e-05
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	3e-05
1z6u_A	150	NP95-like ring finger protein isoform B; structura	4e-05
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	5e-05
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	5e-05
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	5e-05
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	9e-05
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	2e-04
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	2e-04
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	2e-04
3nw0_A	238	Non-structural maintenance of chromosomes element	3e-04
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	4e-04
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	4e-04
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	5e-04
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	6e-04

>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 = 75.9 bits (187), Expect = 2e-18
 Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 11/68 (16%)

Query: 160 KLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMC 219
           + V +G  C VC E+    E ++            +PC+H+FH SCI  WLE+ +SCP+C
Sbjct: 10  EHVGSGLECPVCKEDYALGESVR-----------QLPCNHLFHDSCIVPWLEQHDSCPVC 58

Query: 220 RRQIQYED 227
           R+ +  ++
Sbjct: 59  RKSLTGQN 66

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

 Score = 75.5 bits (186), Expect = 3e-18
 Identities = 22/97 (22%), Positives = 37/97 (38%), Gaps = 15/97 (15%)

Query: 127 EDEIERSERKEASRFVVEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTT 186
                      AS+  ++ L      ++  D +  V     C +C  E +  +       
Sbjct: 6   HHHSHMVANPPASKESIDAL---PEILVTED-HGAVGQEMCCPICCSEYVKGDVAT---- 57

Query: 187 EKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQI 223
                   +PCHH FH  C+S WL++  +CP+CR   
Sbjct: 58  -------ELPCHHYFHKPCVSIWLQKSGTCPVCRCMF 87

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

 Score = 70.6 bits (173), Expect = 2e-16
 Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 11/64 (17%)

Query: 160 KLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMC 219
           K +   + CAVCLE+   ++E+              PC H FH  C+ +WLE +  CP+C
Sbjct: 10  KELNLHELCAVCLEDFKPRDELG-----------ICPCKHAFHRKCLIKWLEVRKVCPLC 58

Query: 220 RRQI 223
              +
Sbjct: 59  NMPV 62

>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 = 68.2 bits (167), Expect = 1e-15
 Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 11/60 (18%)

Query: 164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQI 223
             + C +CL  L   E+++            +PC H+FH  C+ +WL     CP+CR  I
Sbjct: 13  TEEKCTICLSILEEGEDVR-----------RLPCMHLFHQVCVDQWLITNKKCPICRVDI 61

>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 = 67.3 bits (165), Expect = 2e-15
 Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 10/58 (17%)

Query: 166 DNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQI 223
             C +CLE++     +             +PC H+ H +C    L+E   CP+C    
Sbjct: 6   SGCPICLEDIHTSRVV----------AHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPS 53

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

 Score = 67.0 bits (164), Expect = 4e-15
 Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 11/65 (16%)

Query: 159 NKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPM 218
           N        C VC+ +  +++ ++            +PC+H FHA C+ +WL+   +CP+
Sbjct: 17  NNHQSEQTLCVVCMCDFESRQLLR-----------VLPCNHEFHAKCVDKWLKANRTCPI 65

Query: 219 CRRQI 223
           CR   
Sbjct: 66  CRADS 70

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

 Score = 66.3 bits (162), Expect = 6e-15
 Identities = 14/63 (22%), Positives = 26/63 (41%), Gaps = 15/63 (23%)

Query: 165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ 224
            + C +C++                   + +PC H F   CI +W +   +CP+CR Q+ 
Sbjct: 15  EEECCICMDG---------------RADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMT 59

Query: 225 YED 227
             +
Sbjct: 60  GAN 62

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

 Score = 65.9 bits (161), Expect = 8e-15
 Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 13/62 (20%)

Query: 164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQI 223
             + C +CLE+                  + +PC H F   CI+RW+ +  +CP+C+  +
Sbjct: 4   VAERCPICLEDP-------------SNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPV 50

Query: 224 QY 225
           + 
Sbjct: 51  ES 52

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

 Score = 63.8 bits (155), Expect = 5e-14
 Identities = 13/57 (22%), Positives = 29/57 (50%), Gaps = 7/57 (12%)

Query: 167 NCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQI 223
           +C +C++          +  +    +++  C H+F + C+   L+  N+CP CR++I
Sbjct: 17  SCPICMDGYS-------EIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66

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

 Score = 63.8 bits (155), Expect = 6e-14
 Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 166 DNCAVCLEELIAK-EEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ 224
           D CA+C  +++      + +  ++   ++   C+H FH  C+S W+++ N CP+C++   
Sbjct: 16  DTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWV 75

Query: 225 YEDL 228
            + +
Sbjct: 76  VQRI 79

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

 Score = 62.6 bits (152), Expect = 2e-13
 Identities = 13/62 (20%), Positives = 31/62 (50%), Gaps = 7/62 (11%)

Query: 167 NCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYE 226
           +C +C++          +  +    +++  C H+F + C+   L+  N+CP CR++I ++
Sbjct: 12  SCPICMDGYS-------EIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 64

Query: 227 DL 228
             
Sbjct: 65  RY 66

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

 Score = 61.7 bits (150), Expect = 2e-13
 Identities = 13/62 (20%), Positives = 31/62 (50%), Gaps = 7/62 (11%)

Query: 167 NCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYE 226
           +C +C++          +  +    +++  C H+F + C+   L+  N+CP CR++I ++
Sbjct: 5   SCPICMDGYS-------EIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 57

Query: 227 DL 228
             
Sbjct: 58  RY 59

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

 Score = 59.9 bits (146), Expect = 1e-12
 Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 12/63 (19%)

Query: 162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEEQNSCPMCR 220
           +  G  CAVCL EL   EE +            +P C H FHA C+  WL   ++CP+CR
Sbjct: 2   MDDGVECAVCLAELEDGEEAR-----------FLPRCGHGFHAECVDMWLGSHSTCPLCR 50

Query: 221 RQI 223
             +
Sbjct: 51  LTV 53

>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 = 61.4 bits (148), Expect = 1e-12
 Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 4/65 (6%)

Query: 166 DNCAVCLEELIA----KEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR 221
           DNCA+C   ++      +  +   T ++  +    C+H FH  CISRWL+ +  CP+  R
Sbjct: 38  DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 97

Query: 222 QIQYE 226
           + +++
Sbjct: 98  EWEFQ 102

>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 = 61.4 bits (148), Expect = 1e-12
 Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 4/65 (6%)

Query: 166 DNCAVCLEELIA----KEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR 221
           DNCA+C   ++      +  +   T ++  +    C+H FH  CISRWL+ +  CP+  R
Sbjct: 49  DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 108

Query: 222 QIQYE 226
           + +++
Sbjct: 109 EWEFQ 113

>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 = 56.8 bits (136), Expect = 7e-11
 Identities = 15/65 (23%), Positives = 24/65 (36%), Gaps = 9/65 (13%)

Query: 166 DNCAVCLEELIAKEEIKGQTTEKKTQLITM----PCHHIFHASCISRWLEEQN-----SC 216
           ++C +C+E+L         T  K    + +     C H FH  C+       N      C
Sbjct: 26  EDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQC 85

Query: 217 PMCRR 221
           P C+ 
Sbjct: 86  PSCKT 90

>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 = 1e-10
 Identities = 17/57 (29%), Positives = 20/57 (35%), Gaps = 13/57 (22%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ 224
           C++C   LI                IT  C H F  SCI R     N CP C   + 
Sbjct: 18  CSICKGYLI------------DATTIT-ECLHTFCKSCIVRHFYYSNRCPKCNIVVH 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 = 1e-10
 Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 14/62 (22%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYED 227
           CA+CL+                   +++PC H+F   C+         C +CR++I  + 
Sbjct: 18  CAICLQTC--------------VHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDF 63

Query: 228 LV 229
           L 
Sbjct: 64  LD 65

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens} Length = 100

 Score = 52.2 bits (125), Expect = 2e-09
 Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 14/63 (22%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN-SCPMCRRQIQYE 226
           C +C+E+L             +   +   C  +   SCI RWL EQ   CP CR  +Q  
Sbjct: 25  CFICMEKL-------------RDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLR 71

Query: 227 DLV 229
           +LV
Sbjct: 72  ELV 74

>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 = 3e-08
 Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 15/73 (20%)

Query: 158 FNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN-SC 216
           + ++      C +C E                  +   PC H+   SC++ W E +   C
Sbjct: 325 YCEMGSTFQLCKICAEND--------------KDVKIEPCGHLMCTSCLTSWQESEGQGC 370

Query: 217 PMCRRQIQYEDLV 229
           P CR +I+  + +
Sbjct: 371 PFCRCEIKGTEPI 383

>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 = 48.7 bits (116), Expect = 5e-08
 Identities = 15/57 (26%), Positives = 21/57 (36%), Gaps = 13/57 (22%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ 224
           C +C    I                  + C H F  +CI R+LE    CP+C  Q+ 
Sbjct: 18  CVLCGGYFIDA-------------TTIIECLHSFCKTCIVRYLETSKYCPICDVQVH 61

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

 Score = 49.7 bits (118), Expect = 5e-08
 Identities = 20/98 (20%), Positives = 44/98 (44%), Gaps = 15/98 (15%)

Query: 128 DEIERSERKEASRFVVEMLSRKQRRV-LDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTT 186
           + I +++ KE  +   E    + ++  +    N +++    C +C E             
Sbjct: 26  EAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYF----------- 74

Query: 187 EKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ 224
               + +T+ C H F + CI+ W++ +  CP+CR+ I+
Sbjct: 75  ---IEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIK 109

>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 = 47.6 bits (113), Expect = 7e-08
 Identities = 11/63 (17%), Positives = 20/63 (31%), Gaps = 15/63 (23%)

Query: 166 DNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNS--CPMCRRQI 223
             C +C   LI  +  +              C    H  C++++ +      CP C    
Sbjct: 16  KICNICHSLLIQGQSCE-------------TCGIRMHLPCVAKYFQSNAEPRCPHCNDYW 62

Query: 224 QYE 226
            +E
Sbjct: 63  PHE 65

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

 Score = 48.2 bits (114), Expect = 1e-07
 Identities = 13/58 (22%), Positives = 29/58 (50%), Gaps = 7/58 (12%)

Query: 167 NCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ 224
           +C +C++          +  +    +++  C H+F + C+   L+  N+CP CR++I 
Sbjct: 9   SCPICMDGYS-------EIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN 59

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

 Score = 44.8 bits (105), Expect = 2e-06
 Identities = 11/62 (17%), Positives = 26/62 (41%)

Query: 167 NCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYE 226
                        +   +  +    +++  C H+F + C+   L+  N+CP CR++I ++
Sbjct: 67  YIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 126

Query: 227 DL 228
             
Sbjct: 127 RY 128

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

 Score = 47.1 bits (112), Expect = 2e-07
 Identities = 11/37 (29%), Positives = 17/37 (45%)

Query: 193 ITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLV 229
           I   C H + + CI ++L  +  CP C   +   DL 
Sbjct: 37  IIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLK 73

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

 Score = 46.4 bits (110), Expect = 2e-07
 Identities = 9/57 (15%), Positives = 14/57 (24%), Gaps = 14/57 (24%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ 224
           C +C +                   +   C H F  SC          C +C +   
Sbjct: 18  CFICRQAF--------------QNPVVTKCRHYFCESCALEHFRATPRCYICDQPTG 60

>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 = 44.2 bits (104), Expect = 3e-06
 Identities = 24/118 (20%), Positives = 36/118 (30%), Gaps = 21/118 (17%)

Query: 108 GLTGFHLSADVEVVEIEVVEDEIERSERKEASRFVVEMLSRKQRRVLDLDFNKLVKAGDN 167
           G   + L+A    +   + ED+       E    + +   R         F   V+    
Sbjct: 1   GSEPYSLTAQQSSL---IREDKSNAKLWNEVLASLKD---RPASGSPFQLFLSKVEETFQ 54

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ-NSCPMCRRQIQ 224
           C  C E +               + IT  C H     C+ R    Q  SCP CR  + 
Sbjct: 55  CICCQELV--------------FRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLG 98

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

 Score = 42.4 bits (100), Expect = 4e-06
 Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 17/64 (26%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN---SCPMCRRQIQ 224
           C +CL+ L               + +T+ C H F   CI++  E       CP+C+  ++
Sbjct: 23  CPICLDIL--------------QKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVR 68

Query: 225 YEDL 228
              +
Sbjct: 69  KNAI 72

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

 Score = 45.6 bits (107), Expect = 5e-06
 Identities = 11/67 (16%), Positives = 21/67 (31%), Gaps = 17/67 (25%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNS-----------C 216
           C +C    +   E+   + +         C    HA C+  W +               C
Sbjct: 311 CNICFAYRLDGGEVPLVSCDNAK------CVLKCHAVCLEEWFKTLMDGKTFLEVSFGQC 364

Query: 217 PMCRRQI 223
           P C+ ++
Sbjct: 365 PFCKAKL 371

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

 Score = 40.9 bits (96), Expect = 1e-05
 Identities = 9/37 (24%), Positives = 15/37 (40%), Gaps = 1/37 (2%)

Query: 193 ITMPCHHIFHASCISRWLEEQN-SCPMCRRQIQYEDL 228
               C H F  SC++  L   +  C  C+  I  + +
Sbjct: 29  KQTECGHRFCESCMAALLSSSSPKCTACQESIVKDKV 65

>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 = 41.2 bits (97), Expect = 3e-05
 Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 17/65 (26%)

Query: 167 NCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN---SCPMCRRQI 223
            C +CLE +               + ++  C HIF   C+ + L ++     CP+C+  I
Sbjct: 23  ECPICLELI--------------KEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDI 68

Query: 224 QYEDL 228
               L
Sbjct: 69  TKRSL 73

>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 = 41.1 bits (96), Expect = 3e-05
 Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 1/38 (2%)

Query: 193 ITMPCHHIFHASCISRWLEEQNS-CPMCRRQIQYEDLV 229
           +   C H+F   CI R L+   S CP CR      DL 
Sbjct: 37  VETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE 74

>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 = 41.5 bits (97), Expect = 4e-05
 Identities = 15/58 (25%), Positives = 20/58 (34%), Gaps = 15/58 (25%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN-SCPMCRRQIQ 224
           C  C E +               Q +T  C H     C+ R  + Q  SCP CR  + 
Sbjct: 81  CVCCQELV--------------YQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLG 124

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

 Score = 40.7 bits (95), Expect = 5e-05
 Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 15/58 (25%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN-SCPMCRRQIQ 224
           C +C+E L               + +T+PC+H     C    +E+ +  CP CRR++ 
Sbjct: 18  CGICMEIL--------------VEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVS 61

>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 = 40.7 bits (95), Expect = 5e-05
 Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 15/61 (24%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYED 227
           C+ C   L             +  +    C HIF ++C+S  +     CP+C      +D
Sbjct: 25  CSRCTNIL-------------REPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQD 69

Query: 228 L 228
           L
Sbjct: 70  L 70

>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* Length = 63

 Score = 39.4 bits (92), Expect = 5e-05
 Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 13/61 (21%)

Query: 165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFH-ASCISRWLEEQNSCPMCRRQI 223
              C++C +              +   +I     H+     C  R  +   SCP+C+++I
Sbjct: 7   LKPCSLCEKR------------PRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEI 54

Query: 224 Q 224
           Q
Sbjct: 55  Q 55

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

 Score = 38.9 bits (90), Expect = 9e-05
 Identities = 13/66 (19%), Positives = 21/66 (31%), Gaps = 11/66 (16%)

Query: 165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN-SCPMCRRQI 223
              C +C+E L   +                 C +     C  R   ++N  CP CR+  
Sbjct: 11  PVECPLCMEPLEIDDIN----------FFPCTCGYQICRFCWHRIRTDENGLCPACRKPY 60

Query: 224 QYEDLV 229
             +  V
Sbjct: 61  PEDPAV 66

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

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 20/68 (29%)

Query: 167 NCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN------SCPMCR 220
            C +CLE L               + ++  C+H F  +CI+   E         +CP+CR
Sbjct: 21  TCPICLELL--------------KEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCR 66

Query: 221 RQIQYEDL 228
               + +L
Sbjct: 67  VPYPFGNL 74

>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 Length = 64

 Score = 37.5 bits (87), Expect = 2e-04
 Identities = 12/67 (17%), Positives = 24/67 (35%), Gaps = 13/67 (19%)

Query: 159 NKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFH-ASCISRWLEEQNSCP 217
           +  + A + C +C                K   ++     H+    +C  +  +    CP
Sbjct: 2   SLPLNAIEPCVICQGR------------PKNGCIVHGKTGHLMACFTCAKKLKKRNKPCP 49

Query: 218 MCRRQIQ 224
           +CR+ IQ
Sbjct: 50  VCRQPIQ 56

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

 Score = 37.8 bits (88), Expect = 2e-04
 Identities = 11/62 (17%), Positives = 21/62 (33%), Gaps = 15/62 (24%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN--SCPMCRRQIQY 225
           C +C + +                ++   C + +   CI   L E +  +CP C +    
Sbjct: 18  CLICKDIM-------------TDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS 64

Query: 226 ED 227
            D
Sbjct: 65  PD 66

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

 Score = 39.7 bits (92), Expect = 3e-04
 Identities = 14/87 (16%), Positives = 28/87 (32%), Gaps = 18/87 (20%)

Query: 145 MLSRKQRRVLDLDFNKLVKAGDN---CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIF 201
             +   R +L+++        D    C +C   LI  +  +              C    
Sbjct: 157 EFTLHGRAILEMEQYIRETYPDAVKICNICHSLLIQGQSCET-------------CGIRM 203

Query: 202 HASCISRWLEEQNS--CPMCRRQIQYE 226
           H  C++++ +      CP C     +E
Sbjct: 204 HLPCVAKYFQSNAEPRCPHCNDYWPHE 230

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens} Length = 79

 Score = 37.2 bits (87), Expect = 4e-04
 Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 21/69 (30%)

Query: 167 NCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN-------SCPMC 219
            C +CLE L              T+ +++ C H    +CI+   +E         SCP+C
Sbjct: 14  TCPICLELL--------------TEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVC 59

Query: 220 RRQIQYEDL 228
                +E L
Sbjct: 60  GISYSFEHL 68

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 85

 Score = 37.2 bits (87), Expect = 4e-04
 Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 20/68 (29%)

Query: 167 NCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN------SCPMCR 220
            C +CLE L              TQ +++ C H F  +C++   ++        SCP+CR
Sbjct: 21  TCPICLELL--------------TQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCR 66

Query: 221 RQIQYEDL 228
              Q E++
Sbjct: 67  ISYQPENI 74

>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 = 37.5 bits (87), Expect = 5e-04
 Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 15/76 (19%)

Query: 155 DLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN 214
           D++F+  +++   C +CL  L               + +  PC H F  +CI + + +  
Sbjct: 8   DVEFDPPLESKYECPICLMAL--------------REAVQTPCGHRFCKACIIKSIRDAG 53

Query: 215 S-CPMCRRQIQYEDLV 229
             CP+    +    L 
Sbjct: 54  HKCPVDNEILLENQLF 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 = 38.0 bits (88), Expect = 6e-04
 Identities = 18/61 (29%), Positives = 24/61 (39%), Gaps = 14/61 (22%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN-SCPMCRRQIQYE 226
           C +CL+ L            K T      C H F A CI   L   N  CP CR+++  +
Sbjct: 57  CPICLDML------------KNTMTTK-ECLHRFCADCIITALRSGNKECPTCRKKLVSK 103

Query: 227 D 227
            
Sbjct: 104 R 104

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	230
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.71
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.65
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.62
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.61
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.6
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.59
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.57
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.54
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.52
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.52
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.51
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.51
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.49
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.47
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.46
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.46
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.45
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.44
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.43
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.42
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.4
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.4
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.39
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.38
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.37
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.37
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.36
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.36
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.35
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.34
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.34
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.33
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.29
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.28
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.27
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.27
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.26
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.26
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.24
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.23
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.22
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.22
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.21
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.18
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.17
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.16
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.15
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.15
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.14
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.13
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.11
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.11
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.1
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.09
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.07
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.07
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.06
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.97
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.95
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.92
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.85
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.84
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.84
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.82
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.77
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.73
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.73
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.64
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.6
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.53
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.27
3nw0_A	238	Non-structural maintenance of chromosomes element	98.0
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	95.55
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	94.75
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	94.54
1we9_A	64	PHD finger family protein; structural genomics, PH	90.17
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	89.38
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	88.88
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	88.09
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	87.84
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	87.46
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	87.15
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	87.12
2yt5_A	66	Metal-response element-binding transcription facto	85.94
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	84.42
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	84.03
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	83.45
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	83.32
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	82.47
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	81.88
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	81.61
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	80.2

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

Probab=99.71  E-value=7.8e-18  Score=122.98  Aligned_cols=78  Identities=27%  Similarity=0.583  Sum_probs=65.7

Q ss_pred             hccccccHHHHHhccccccchhhhhhhhcccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc
Q 042810          133 SERKEASRFVVEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE  212 (230)
Q Consensus       133 ~~~~~~s~~~i~~l~~~~~~~~~~~~~~~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~  212 (230)
                      ...++++++.++.|+...+...    ......+..|+||++.|..           ++.++.+||+|.||..||.+|++.
T Consensus        12 ~~~~~~s~~~i~~lp~~~~~~~----~~~~~~~~~C~IC~~~~~~-----------~~~~~~l~C~H~Fh~~Ci~~wl~~   76 (91)
T 2l0b_A           12 VANPPASKESIDALPEILVTED----HGAVGQEMCCPICCSEYVK-----------GDVATELPCHHYFHKPCVSIWLQK   76 (91)
T ss_dssp             SCCCCCCHHHHHTSCEEECCTT----CSSSSSCSEETTTTEECCT-----------TCEEEEETTTEEEEHHHHHHHHTT
T ss_pred             cCCCCCCHHHHHhCCCeeeccc----ccccCCCCCCcccChhhcC-----------CCcEEecCCCChHHHHHHHHHHHc
Confidence            3457899999999998877431    1234567889999999977           778899999999999999999999


Q ss_pred             CCcccccccCccc
Q 042810          213 QNSCPMCRRQIQY  225 (230)
Q Consensus       213 ~~tCP~CR~~i~~  225 (230)
                      +.+||+||+.+..
T Consensus        77 ~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           77 SGTCPVCRCMFPP   89 (91)
T ss_dssp             TCBCTTTCCBSSC
T ss_pred             CCcCcCcCccCCC
Confidence            9999999998864

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

Probab=99.65  E-value=1.1e-17  Score=117.48  Aligned_cols=68  Identities=28%  Similarity=0.684  Sum_probs=54.6

Q ss_pred             HHhccccccchhhhhhhhcccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccC
Q 042810          143 VEMLSRKQRRVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQ  222 (230)
Q Consensus       143 i~~l~~~~~~~~~~~~~~~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~  222 (230)
                      ++.++..++..     .....++..|+||++.+..           ++.++.+||+|.||..||.+|++.+.+||+||++
T Consensus         6 i~~lp~~~~~~-----~~~~~~~~~C~IC~~~~~~-----------~~~~~~l~C~H~fh~~Ci~~w~~~~~~CP~Cr~~   69 (75)
T 1x4j_A            6 SGQLPSYRFNP-----NNHQSEQTLCVVCMCDFES-----------RQLLRVLPCNHEFHAKCVDKWLKANRTCPICRAD   69 (75)
T ss_dssp             CSSCCCEEBCS-----SSCSSSCCEETTTTEECCB-----------TCEEEEETTTEEEETTHHHHHHHHCSSCTTTCCC
T ss_pred             HhhCCcEEecC-----ccccCCCCCCeECCcccCC-----------CCeEEEECCCCHhHHHHHHHHHHcCCcCcCcCCc
Confidence            34556555521     2334567899999999977           7778999999999999999999999999999999


Q ss_pred             cccc
Q 042810          223 IQYE  226 (230)
Q Consensus       223 i~~~  226 (230)
                      +...
T Consensus        70 ~~~~   73 (75)
T 1x4j_A           70 SGPS   73 (75)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

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

Probab=99.62  E-value=9.1e-17  Score=114.91  Aligned_cols=67  Identities=22%  Similarity=0.602  Sum_probs=49.8

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhccCCcccccccCccccC
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEEQNSCPMCRRQIQYED  227 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~  227 (230)
                      .+.+++.|+||++.|.+...+.......++.++.++ |+|.||.+||.+|++++++||+||+++..++
T Consensus        11 ~~~~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~   78 (81)
T 2ecl_A           11 WDVECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQR   78 (81)
T ss_dssp             CSCCCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEEE
T ss_pred             ecCCCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchhh
Confidence            344578899999999663222222222245566665 9999999999999999999999999987665

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

Probab=99.61  E-value=3.2e-16  Score=103.30  Aligned_cols=51  Identities=41%  Similarity=0.957  Sum_probs=45.7

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhccCCcccccccCcc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEEQNSCPMCRRQIQ  224 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~~~tCP~CR~~i~  224 (230)
                      +++..|+||++.+..           ++.+..+| |||.||..||.+|++++.+||+||+++.
T Consensus         3 ~~~~~C~IC~~~~~~-----------~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELED-----------GEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCT-----------TSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCcCccCCccccC-----------CCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            346789999999977           77788898 9999999999999999999999999874

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

Probab=99.60  E-value=4.3e-16  Score=109.99  Aligned_cols=57  Identities=39%  Similarity=0.964  Sum_probs=50.5

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccCCC
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      ...+..|+||++.|..           ...++.+||+|.||..||.+|++.+.+||+||+++..+++.
T Consensus        12 ~~~~~~C~IC~~~~~~-----------~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   68 (78)
T 2ect_A           12 VGSGLECPVCKEDYAL-----------GESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTA   68 (78)
T ss_dssp             SSSSCCCTTTTSCCCT-----------TSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCCCSCSC
T ss_pred             CCCCCCCeeCCccccC-----------CCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccCCcccC
Confidence            3457899999999977           66788899999999999999999999999999999887764

>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=99.59  E-value=5.2e-16  Score=107.03  Aligned_cols=55  Identities=31%  Similarity=0.873  Sum_probs=48.1

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCcccc
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYE  226 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~  226 (230)
                      ....+..|+||++.+..           +..++.+||||.||..||.+|++++.+||+||+.+...
T Consensus        10 ~~~~~~~C~IC~~~~~~-----------~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           10 EEDTEEKCTICLSILEE-----------GEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             STTCCCSBTTTTBCCCS-----------SSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             cCCCCCCCeeCCccccC-----------CCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            34457889999999866           67788999999999999999999999999999988654

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

Probab=99.57  E-value=1e-15  Score=106.95  Aligned_cols=55  Identities=35%  Similarity=0.855  Sum_probs=48.0

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCcccc
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYE  226 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~  226 (230)
                      ....+..|+||++.+..           ...+..+||+|.||..||.+|++.+.+||+||+++..-
T Consensus        11 ~~~~~~~C~IC~~~~~~-----------~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (74)
T 2ep4_A           11 ELNLHELCAVCLEDFKP-----------RDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQL   65 (74)
T ss_dssp             CCCCSCBCSSSCCBCCS-----------SSCEEEETTTEEEEHHHHHHHHHHCSBCTTTCCBCSSC
T ss_pred             cCCCCCCCcCCCcccCC-----------CCcEEEcCCCCEecHHHHHHHHHcCCcCCCcCcccccc
Confidence            34457899999999977           67788899999999999999999999999999988653

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

Probab=99.54  E-value=2.8e-15  Score=103.65  Aligned_cols=60  Identities=22%  Similarity=0.650  Sum_probs=49.5

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      +++..|+||++.+....       ..++.++.++|||.||..||.+|++.+.+||+||+++..+++.
T Consensus         8 ~~~~~C~IC~~~~~~~~-------~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   67 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIV-------QNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYH   67 (71)
T ss_dssp             TTCCBCTTTCCBHHHHH-------TTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCCCSCC
T ss_pred             CCCCCCcccChhhhccc-------cccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccChhhee
Confidence            45778999999997621       0134567889999999999999999999999999999888764

>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=99.52  E-value=4.8e-15  Score=97.47  Aligned_cols=51  Identities=27%  Similarity=0.802  Sum_probs=44.1

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCcc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ  224 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~  224 (230)
                      .+..|+||++.+...          +..++.++|+|.||..||.+|++.+.+||+||+++.
T Consensus         4 ~~~~C~IC~~~~~~~----------~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTS----------RVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTT----------TSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCC----------CcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            467899999998551          445788899999999999999999999999999875

>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=99.52  E-value=3.7e-15  Score=112.00  Aligned_cols=67  Identities=28%  Similarity=0.595  Sum_probs=49.3

Q ss_pred             cccCCCccccCchhhhhhhhhhc----cccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccC
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKG----QTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYED  227 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~----~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~  227 (230)
                      .+.+++.|+||++.|...+.+..    .....+..++.++|+|.||..||.+||+++.+||+||+++..++
T Consensus        33 ~d~~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~~~~  103 (106)
T 3dpl_R           33 WDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQK  103 (106)
T ss_dssp             ESSCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCCEEE
T ss_pred             cCCCCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcCCcCcCCCCcceeec
Confidence            34568899999999976322111    01112345777899999999999999999999999999976543

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

Probab=99.51  E-value=5.8e-15  Score=99.79  Aligned_cols=59  Identities=24%  Similarity=0.657  Sum_probs=48.5

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccCCC
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      ++..|+||++.+....+       .++.+..++|||.||..||.+|++++.+||+||+++..+++.
T Consensus         2 ~~~~C~IC~~~~~~~~~-------~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   60 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQ-------NGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYH   60 (64)
T ss_dssp             CCCBCTTTCCBHHHHHH-------TTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTTTCEE
T ss_pred             CCCCCCccChhhhCccc-------cCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCcccee
Confidence            35689999999976211       134568889999999999999999999999999999887753

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

Probab=99.51  E-value=6.3e-15  Score=101.05  Aligned_cols=58  Identities=22%  Similarity=0.655  Sum_probs=46.9

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccc
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQY  225 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~  225 (230)
                      ...++..|+||++.+....       ..+..++.++|||.||..||..|++.+.+||+||+++..
T Consensus        11 ~~~~~~~C~IC~~~~~~~~-------~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           11 RPSGTVSCPICMDGYSEIV-------QNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             CTTCCCCCTTTCCCHHHHT-------TTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCCCcccCccccccc-------cccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            3455788999999997621       013445788999999999999999999999999999865

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

Probab=99.49  E-value=5.2e-15  Score=102.74  Aligned_cols=53  Identities=26%  Similarity=0.632  Sum_probs=46.4

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      .++..|+||++.+..              .+.+||||.||..||..|+..+.+||+||..+..+++.
T Consensus        13 ~~~~~C~IC~~~~~~--------------~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   65 (71)
T 2d8t_A           13 LTVPECAICLQTCVH--------------PVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDFLD   65 (71)
T ss_dssp             SSCCBCSSSSSBCSS--------------EEEETTTEEEEHHHHHHCTTCSSBCSSSCCBCCHHHHS
T ss_pred             CCCCCCccCCcccCC--------------CEEccCCCHHHHHHHHHHHHCCCcCcCcCchhCHhhcc
Confidence            456789999999865              67889999999999999999999999999999876553

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

Probab=99.47  E-value=1.4e-14  Score=100.79  Aligned_cols=54  Identities=30%  Similarity=0.576  Sum_probs=46.8

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEe-CCCCccchhhHHHhhccCCcccccccCccccCCC
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITM-PCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      .+++..|+||++.+.+              ++.+ +|||.||..||..|++.+.+||+||+.+..++++
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            3446789999999855              5565 8999999999999999999999999999988875

>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=99.46  E-value=4.4e-15  Score=113.36  Aligned_cols=68  Identities=28%  Similarity=0.581  Sum_probs=3.4

Q ss_pred             hcccCCCccccCchhhhhhhhhhccc----cccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccC
Q 042810          160 KLVKAGDNCAVCLEELIAKEEIKGQT----TEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYED  227 (230)
Q Consensus       160 ~~~~~~~~C~ICle~~~~~~~~~~~~----~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~  227 (230)
                      ..+..++.|+||++.|...+......    ......+..++|+|.||..||.+||+++++||+||+++..++
T Consensus        43 ~wd~~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~~~k  114 (117)
T 4a0k_B           43 AWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQK  114 (117)
T ss_dssp             EECCCC------------------------------------------------------------------
T ss_pred             eecCCCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeeeeec
Confidence            44556889999999997743221110    111234455689999999999999999999999999976554

>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=99.46  E-value=3.3e-14  Score=107.30  Aligned_cols=63  Identities=19%  Similarity=0.456  Sum_probs=43.8

Q ss_pred             CCCccccCchhhhhhhhhhcc---c-cccCceeEEeCCCCccchhhHHHhh-----ccCCcccccccCcccc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQ---T-TEKKTQLITMPCHHIFHASCISRWL-----EEQNSCPMCRRQIQYE  226 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~---~-~~~~~~v~~LpC~H~FH~~CI~~Wl-----~~~~tCP~CR~~i~~~  226 (230)
                      .++.|+||++.|...+.....   . ......++.++|+|.||..||.+|+     +.+.+||+||+.+..+
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            356899999999662210000   0 0112344578899999999999999     4577999999987543

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

Probab=99.45  E-value=2.1e-14  Score=98.21  Aligned_cols=54  Identities=24%  Similarity=0.517  Sum_probs=46.0

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhc-cCCcccccccCccccCCC
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLE-EQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~-~~~tCP~CR~~i~~~~l~  229 (230)
                      ..++..|+||++.+..              ++.++|||.||..||.+|++ .+.+||+||+++..++++
T Consensus        12 ~~~~~~C~IC~~~~~~--------------p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~if   66 (66)
T 2ecy_A           12 VEDKYKCEKCHLVLCS--------------PKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDKVF   66 (66)
T ss_dssp             CCCCEECTTTCCEESS--------------CCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTTCC
T ss_pred             CCcCCCCCCCChHhcC--------------eeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChhhcC
Confidence            3457789999999865              45589999999999999995 567899999999998875

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

Probab=99.44  E-value=5.4e-14  Score=97.65  Aligned_cols=54  Identities=26%  Similarity=0.626  Sum_probs=46.0

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhc---cCCcccccccCccccCC
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLE---EQNSCPMCRRQIQYEDL  228 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~---~~~tCP~CR~~i~~~~l  228 (230)
                      ...++..|+||++.+..              ++.++|||.||..||..|++   .+.+||+||+++..+++
T Consensus        16 ~~~~~~~C~IC~~~~~~--------------~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~   72 (73)
T 2ysl_A           16 KLQEEVICPICLDILQK--------------PVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNAI   72 (73)
T ss_dssp             CCCCCCBCTTTCSBCSS--------------EEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCCC
T ss_pred             hCccCCEeccCCcccCC--------------eEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcccC
Confidence            34557899999999865              77789999999999999997   45689999999988775

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

Probab=99.43  E-value=4.2e-14  Score=96.96  Aligned_cols=49  Identities=31%  Similarity=0.964  Sum_probs=42.5

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQY  225 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~  225 (230)
                      .+..|+||++.+..             .++.+||||.||..|+.+|++++.+||+||+++..
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            46789999998733             35788999999999999999999999999998753

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

Probab=99.42  E-value=4.4e-14  Score=97.51  Aligned_cols=51  Identities=27%  Similarity=0.924  Sum_probs=44.4

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccC
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYED  227 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~  227 (230)
                      ..++..|+||++.+             .+  +.+||+|.||..||.+|++++.+||+||+++...+
T Consensus        12 ~~~~~~C~IC~~~~-------------~~--~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (70)
T 2ecn_A           12 LTDEEECCICMDGR-------------AD--LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGAN   62 (70)
T ss_dssp             CCCCCCCSSSCCSC-------------CS--EEETTTEEECHHHHHHSSCCCSSCHHHHHCTTCCC
T ss_pred             CCCCCCCeeCCcCc-------------cC--cccCCCCcccHHHHHHHHHCcCcCCCcCCcccCCC
Confidence            34578999999986             33  67899999999999999999999999999997665

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

Probab=99.40  E-value=1.3e-13  Score=99.03  Aligned_cols=57  Identities=19%  Similarity=0.589  Sum_probs=47.3

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCc-eeEEeCCCCccchhhHHHhhccC---CcccccccCccccCC
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKT-QLITMPCHHIFHASCISRWLEEQ---NSCPMCRRQIQYEDL  228 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~-~v~~LpC~H~FH~~CI~~Wl~~~---~tCP~CR~~i~~~~l  228 (230)
                      ...++..|+||++.|..           .+ .++.++|||.||..||..|++.+   .+||+||+.+..+++
T Consensus        11 ~~~~~~~C~IC~~~~~~-----------~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~i   71 (88)
T 2ct2_A           11 ALREVLECPICMESFTE-----------EQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITSL   71 (88)
T ss_dssp             CCCSCCBCTTTCCBCCT-----------TSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCSST
T ss_pred             hccCCCCCccCCccccc-----------cCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccchhH
Confidence            34457789999999866           33 37788999999999999999876   799999999877654

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

Probab=99.40  E-value=7.5e-14  Score=109.19  Aligned_cols=49  Identities=33%  Similarity=0.899  Sum_probs=43.6

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCcccc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYE  226 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~  226 (230)
                      ++..|+||++.|.+              ++.+||||.||..||..|+..+.+||+||+++...
T Consensus        52 ~~~~C~iC~~~~~~--------------~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           52 NELQCIICSEYFIE--------------AVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             HHSBCTTTCSBCSS--------------EEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             ccCCCcccCcccCC--------------ceECCCCCCccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            35689999999866              78899999999999999999999999999998653

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

Probab=99.39  E-value=1e-13  Score=97.01  Aligned_cols=52  Identities=23%  Similarity=0.599  Sum_probs=43.8

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhccC--CcccccccCccccC
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEEQ--NSCPMCRRQIQYED  227 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~~--~tCP~CR~~i~~~~  227 (230)
                      ..++..|+||++.|.+              ++.+| |||.||..||..|++.+  .+||+||+++...+
T Consensus        12 ~~~~~~C~IC~~~~~~--------------p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2yur_A           12 IPDELLCLICKDIMTD--------------AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD   66 (74)
T ss_dssp             SCGGGSCSSSCCCCTT--------------CEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTT
T ss_pred             CCCCCCCcCCChHHhC--------------CeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCcc
Confidence            3446789999999866              77799 99999999999999865  68999999865544

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

Probab=99.38  E-value=1.6e-13  Score=96.63  Aligned_cols=53  Identities=19%  Similarity=0.464  Sum_probs=46.3

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc-CCcccccccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE-QNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~-~~tCP~CR~~i~~~~l~  229 (230)
                      .++..|+||++.|.+              ++.++|||.||..||.+|++. +.+||+||+++..++++
T Consensus         6 ~~~~~C~IC~~~~~~--------------Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~l~   59 (78)
T 1t1h_A            6 PEYFRCPISLELMKD--------------PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLT   59 (78)
T ss_dssp             SSSSSCTTTSCCCSS--------------EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCE
T ss_pred             cccCCCCCccccccC--------------CEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChhhCc
Confidence            457789999999866              778899999999999999987 78999999999877653

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

Probab=99.37  E-value=1.8e-13  Score=97.20  Aligned_cols=49  Identities=18%  Similarity=0.491  Sum_probs=43.3

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCcc
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ  224 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~  224 (230)
                      ......|+||++.+..              ++.+||||.||..||.+|++...+||+||+.+.
T Consensus        12 ~~~~~~C~IC~~~~~~--------------p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           12 EEIPFRCFICRQAFQN--------------PVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCCSBCSSSCSBCCS--------------EEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCCcCCCchhcC--------------eeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            3456789999999855              667999999999999999999999999999885

>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=99.37  E-value=6.8e-14  Score=103.61  Aligned_cols=53  Identities=38%  Similarity=0.770  Sum_probs=45.8

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEE-eCCCCccchhhHHHhhccC-CcccccccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLIT-MPCHHIFHASCISRWLEEQ-NSCPMCRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~-LpC~H~FH~~CI~~Wl~~~-~tCP~CR~~i~~~~l~  229 (230)
                      .++..|+||++.+..              ++. ++|||.||..||.+|++.+ .+||+||.++..++++
T Consensus        20 ~~~~~C~IC~~~~~~--------------p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~l~   74 (100)
T 3lrq_A           20 AEVFRCFICMEKLRD--------------ARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELV   74 (100)
T ss_dssp             HHHTBCTTTCSBCSS--------------EEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCE
T ss_pred             CCCCCCccCCccccC--------------ccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHHHhH
Confidence            346789999999865              666 8999999999999999987 6999999999887763

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

Probab=99.36  E-value=8.5e-14  Score=98.03  Aligned_cols=54  Identities=31%  Similarity=0.695  Sum_probs=45.6

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc-------CCcccccccCccccCC
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE-------QNSCPMCRRQIQYEDL  228 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~-------~~tCP~CR~~i~~~~l  228 (230)
                      ...++..|+||++.+..              ++.+||||.||..||..|++.       ..+||+||..+..+++
T Consensus         8 ~~~~~~~C~IC~~~~~~--------------p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   68 (79)
T 2egp_A            8 NVQEEVTCPICLELLTE--------------PLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEHL   68 (79)
T ss_dssp             CCCCCCEETTTTEECSS--------------CCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSGG
T ss_pred             hcccCCCCcCCCcccCC--------------eeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhhC
Confidence            34557899999999855              566899999999999999986       5689999999987655

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

Probab=99.36  E-value=1.8e-13  Score=97.64  Aligned_cols=54  Identities=28%  Similarity=0.776  Sum_probs=43.9

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeCCC-----CccchhhHHHhhccC--CcccccccCccccC
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCH-----HIFHASCISRWLEEQ--NSCPMCRRQIQYED  227 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~-----H~FH~~CI~~Wl~~~--~tCP~CR~~i~~~~  227 (230)
                      ..++..|.||++++.+           ++.+ .+||+     |.||..||++|+..+  .+||+||.++..+.
T Consensus        12 ~~~~~~C~IC~~~~~~-----------~~~l-~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~   72 (80)
T 2d8s_A           12 PSSQDICRICHCEGDD-----------ESPL-ITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMET   72 (80)
T ss_dssp             CTTSCCCSSSCCCCCS-----------SSCE-ECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCC
T ss_pred             CCCCCCCeEcCccccC-----------CCee-EeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCc
Confidence            3456789999999865           4444 58996     999999999999876  49999999987654

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

Probab=99.35  E-value=3.5e-13  Score=95.76  Aligned_cols=53  Identities=32%  Similarity=0.769  Sum_probs=45.7

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc------CCcccccccCccccCC
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE------QNSCPMCRRQIQYEDL  228 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~------~~tCP~CR~~i~~~~l  228 (230)
                      ..++..|+||++.+..              ++.+||||.||..||..|+..      ..+||+||..+..+++
T Consensus        16 ~~~~~~C~IC~~~~~~--------------p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~   74 (85)
T 2ecw_A           16 IKEEVTCPICLELLKE--------------PVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNL   74 (85)
T ss_dssp             CCTTTSCTTTCSCCSS--------------CEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTCC
T ss_pred             CccCCCCcCCChhhCc--------------ceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHhC
Confidence            3457799999999865              567999999999999999987      6789999999987765

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

Probab=99.34  E-value=4.8e-13  Score=102.62  Aligned_cols=59  Identities=22%  Similarity=0.672  Sum_probs=48.1

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDL  228 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l  228 (230)
                      .++..|+||++.|.+..       ..+..++.++|||.||..||.+|++.+.+||+||+.+..+++
T Consensus         5 ~~~~~C~IC~~~~~~~~-------~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l   63 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIV-------QNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   63 (133)
T ss_dssp             CCSCBCTTTCCBHHHHH-------HTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCE
T ss_pred             CCCCCCcccChhhhCcc-------ccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCccccc
Confidence            34678999999997610       013445889999999999999999999999999999987654

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

Probab=99.34  E-value=3.3e-13  Score=95.91  Aligned_cols=54  Identities=33%  Similarity=0.740  Sum_probs=46.1

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc------CCcccccccCccccCCC
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE------QNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~------~~tCP~CR~~i~~~~l~  229 (230)
                      ..++..|+||++.+..              ++.+||||.||..|+..|+..      ..+||+||..+..+++.
T Consensus        16 ~~~~~~C~IC~~~~~~--------------p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~   75 (85)
T 2ecv_A           16 VKEEVTCPICLELLTQ--------------PLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIR   75 (85)
T ss_dssp             CCCCCCCTTTCSCCSS--------------CBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSSCC
T ss_pred             ccCCCCCCCCCcccCC--------------ceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHhcC
Confidence            4457899999999855              566899999999999999987      77999999999877653

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

Probab=99.33  E-value=3.1e-13  Score=99.57  Aligned_cols=51  Identities=25%  Similarity=0.651  Sum_probs=44.5

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEe-CCCCccchhhHHHhhccCCcccccccCccccCC
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITM-PCHHIFHASCISRWLEEQNSCPMCRRQIQYEDL  228 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l  228 (230)
                      ++..|+||++.+.+              ++.+ +|||.||..||..|+..+.+||+||..+..+++
T Consensus        21 ~~~~C~IC~~~~~~--------------p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~l   72 (99)
T 2y43_A           21 DLLRCGICFEYFNI--------------AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDL   72 (99)
T ss_dssp             HHTBCTTTCSBCSS--------------EEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGC
T ss_pred             CCCCcccCChhhCC--------------cCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCChhhC
Confidence            45789999999855              6666 899999999999999999999999999987654

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

Probab=99.29  E-value=1.7e-12  Score=88.22  Aligned_cols=55  Identities=18%  Similarity=0.517  Sum_probs=43.1

Q ss_pred             CCccccCch-hhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc-CCcccccccCccccCCC
Q 042810          165 GDNCAVCLE-ELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE-QNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       165 ~~~C~ICle-~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~-~~tCP~CR~~i~~~~l~  229 (230)
                      +..|+||++ .+...          ......++|||.||..||.+|+.+ +.+||+||+.+..+++.
T Consensus         3 ~~~C~IC~~~~~~~~----------~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~   59 (65)
T 1g25_A            3 DQGCPRCKTTKYRNP----------SLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFR   59 (65)
T ss_dssp             TTCCSTTTTHHHHCS----------SCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCCE
T ss_pred             CCcCCcCCCCccCCC----------ccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccccce
Confidence            568999999 66550          222356799999999999999764 46899999999887763

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

Probab=99.28  E-value=9.1e-13  Score=101.03  Aligned_cols=60  Identities=22%  Similarity=0.650  Sum_probs=49.0

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      ++...|+||++.+....+       .+..++.++|||.||..||.+|++.+.+||+||+++..++++
T Consensus        70 ~~~~~C~iC~~~~~~~~~-------~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~  129 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQ-------NGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYH  129 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHH-------TTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGGGEE
T ss_pred             CCCCCCCCCCCccccccc-------cCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChhcce
Confidence            346789999999976211       133457889999999999999999999999999999988763

>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=99.27  E-value=1.6e-12  Score=97.24  Aligned_cols=51  Identities=31%  Similarity=0.698  Sum_probs=44.1

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEe-CCCCccchhhHHHhhccCCcccccccCcccc
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITM-PCHHIFHASCISRWLEEQNSCPMCRRQIQYE  226 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~  226 (230)
                      ..++..|+||++.+.+              ++.+ +|||.||..||..|+..+.+||+||..+...
T Consensus        12 ~~~~~~C~IC~~~~~~--------------p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           12 LNPHLMCVLCGGYFID--------------ATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             HGGGTBCTTTSSBCSS--------------EEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             cCCcCCCccCChHHhC--------------cCEeCCCCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            3456789999999855              6666 9999999999999999999999999998754

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

Probab=99.27  E-value=1.6e-12  Score=87.79  Aligned_cols=45  Identities=31%  Similarity=0.687  Sum_probs=38.5

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhc---cCCccccc
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLE---EQNSCPMC  219 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~---~~~tCP~C  219 (230)
                      ...++..|+||++.+..              ++.++|||.||..||.+|++   .+.+||+|
T Consensus        16 ~~~~~~~C~IC~~~~~~--------------p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           16 KLQEEVICPICLDILQK--------------PVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCCBCTTTCSBCSS--------------CEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             hCccCCCCCcCCchhCC--------------eEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            34557899999999865              77789999999999999998   45689998

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

Probab=99.26  E-value=1.1e-12  Score=100.50  Aligned_cols=49  Identities=31%  Similarity=0.623  Sum_probs=42.7

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCC-cccccccCccc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN-SCPMCRRQIQY  225 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~-tCP~CR~~i~~  225 (230)
                      .++..|+||++.|..              ++.+||||.||..||..|+..+. +||+||..+..
T Consensus        50 ~~~~~C~IC~~~~~~--------------p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           50 EETFQCICCQELVFR--------------PITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHHTBCTTTSSBCSS--------------EEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             ccCCCCCcCChHHcC--------------cEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            346789999999866              77889999999999999998554 99999999976

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

Probab=99.26  E-value=2e-12  Score=93.76  Aligned_cols=49  Identities=22%  Similarity=0.614  Sum_probs=42.1

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhccC--CcccccccCc
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEEQ--NSCPMCRRQI  223 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~~--~tCP~CR~~i  223 (230)
                      ...++..|+||++.|.+              ++.+| |||.||..||..|+..+  .+||+||..+
T Consensus         9 ~~~~~~~C~IC~~~~~~--------------p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~   60 (92)
T 3ztg_A            9 PIPDELLCLICKDIMTD--------------AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQND   60 (92)
T ss_dssp             CCCTTTEETTTTEECSS--------------CEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSS
T ss_pred             cCCcCCCCCCCChhhcC--------------ceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcC
Confidence            33457899999999866              78899 99999999999999754  5899999997

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

Probab=99.24  E-value=2.9e-12  Score=89.94  Aligned_cols=51  Identities=24%  Similarity=0.565  Sum_probs=42.0

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC--CcccccccCcccc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ--NSCPMCRRQIQYE  226 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~--~tCP~CR~~i~~~  226 (230)
                      +..+.|+||++.+..           ++  +...|+|.||..||.+||+++  .+||+||+++..+
T Consensus        13 ~~i~~C~IC~~~i~~-----------g~--~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~   65 (74)
T 2ct0_A           13 DAVKICNICHSLLIQ-----------GQ--SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE   65 (74)
T ss_dssp             SSSCBCSSSCCBCSS-----------SE--ECSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSC
T ss_pred             CCCCcCcchhhHccc-----------CC--ccCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCC
Confidence            346789999999865           32  333799999999999999987  8999999998654

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

Probab=99.23  E-value=2.4e-12  Score=85.21  Aligned_cols=45  Identities=38%  Similarity=0.933  Sum_probs=37.3

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhh---ccCCccccc
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWL---EEQNSCPMC  219 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl---~~~~tCP~C  219 (230)
                      ...++..|+||++.+..              ++.++|||.||..||.+|+   +.+.+||+|
T Consensus        11 ~~~~~~~C~IC~~~~~~--------------p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           11 NLQVEASCSVCLEYLKE--------------PVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CSCCCCBCSSSCCBCSS--------------CCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccccCCCCccCCcccCc--------------cEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            34457899999999865              5668999999999999995   456789998

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

Probab=99.22  E-value=1.7e-12  Score=98.69  Aligned_cols=54  Identities=24%  Similarity=0.603  Sum_probs=45.9

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCC-cccccccCccccCC
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN-SCPMCRRQIQYEDL  228 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~-tCP~CR~~i~~~~l  228 (230)
                      ...++..|+||++.+..              ++.++|||.||..||.+|++.+. +||+||..+..+++
T Consensus        14 ~~~~~~~C~IC~~~~~~--------------p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   68 (118)
T 3hct_A           14 PLESKYECPICLMALRE--------------AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQL   68 (118)
T ss_dssp             CCCGGGBCTTTCSBCSS--------------EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGC
T ss_pred             CCCCCCCCCcCChhhcC--------------eEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHHhc
Confidence            33446789999999865              67789999999999999998765 99999999987765

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

Probab=99.22  E-value=2.6e-12  Score=96.23  Aligned_cols=51  Identities=29%  Similarity=0.754  Sum_probs=43.5

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCC---cccccccCccccCCC
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN---SCPMCRRQIQYEDLV  229 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~---tCP~CR~~i~~~~l~  229 (230)
                      ...|+||++.+..              ++.+||||.||..||..|+..+.   +||+||..+..+++.
T Consensus        21 ~~~C~IC~~~~~~--------------p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~~   74 (112)
T 1jm7_A           21 ILECPICLELIKE--------------PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQ   74 (112)
T ss_dssp             HTSCSSSCCCCSS--------------CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCB
T ss_pred             CCCCcccChhhcC--------------eEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhhcC
Confidence            5689999998855              55689999999999999998654   899999999877653

>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=99.21  E-value=1.8e-12  Score=98.07  Aligned_cols=52  Identities=31%  Similarity=0.614  Sum_probs=45.3

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc-CCcccccccCccccCCC
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE-QNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~-~~tCP~CR~~i~~~~l~  229 (230)
                      ++..|+||++.+.+              ++.++|||.||..||.+|+.. +.+||+||..+..+++.
T Consensus        22 ~~~~C~IC~~~~~~--------------p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~   74 (116)
T 1rmd_A           22 KSISCQICEHILAD--------------PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE   74 (116)
T ss_dssp             HHTBCTTTCSBCSS--------------EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCB
T ss_pred             CCCCCCCCCcHhcC--------------cEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhhcc
Confidence            36789999999865              677999999999999999987 77999999999877653

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

Probab=99.18  E-value=3.3e-12  Score=84.68  Aligned_cols=47  Identities=21%  Similarity=0.487  Sum_probs=40.1

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCcccc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYE  226 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~  226 (230)
                      .++..|+||++.+..              ++.+||||.||..||..|   ..+||+||+.+..+
T Consensus         4 ~~~~~C~IC~~~~~~--------------p~~l~CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T 1bor_A            4 FQFLRCQQCQAEAKC--------------PKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CCCSSCSSSCSSCBC--------------CSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             ccCCCceEeCCccCC--------------eEEcCCCCcccHHHHccC---CCCCCcCCcEeecC
Confidence            356789999999865              677999999999999886   67899999998654

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

Probab=99.17  E-value=1e-11  Score=89.32  Aligned_cols=53  Identities=15%  Similarity=0.125  Sum_probs=48.0

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      .++..|+||++.|.+              ++.++|||.|+..||..|+..+.+||+||..+..++|+
T Consensus        12 p~~~~CpI~~~~m~d--------------PV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~l~   64 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTD--------------PVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTESMLE   64 (85)
T ss_dssp             CTTTBCTTTCSBCSS--------------EEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCGGGCE
T ss_pred             chheECcccCchhcC--------------CeECCCCCEECHHHHHHHHhcCCCCCCCcCCCChHhcc
Confidence            457799999999877              88999999999999999999889999999999887764

>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=99.16  E-value=1.2e-11  Score=98.21  Aligned_cols=49  Identities=29%  Similarity=0.621  Sum_probs=43.2

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCC-cccccccCcccc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN-SCPMCRRQIQYE  226 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~-tCP~CR~~i~~~  226 (230)
                      ++..|+||++.|.+              ++.+||||.||..||..|+.... +||+||..+..+
T Consensus        77 ~~~~C~IC~~~~~~--------------pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVYQ--------------PVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCSS--------------EEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhhcC--------------CEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            45789999999866              77799999999999999998765 899999999876

>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=99.15  E-value=1.2e-11  Score=99.18  Aligned_cols=48  Identities=33%  Similarity=0.735  Sum_probs=41.1

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEe-CCCCccchhhHHHhhcc-CCcccccccCcccc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITM-PCHHIFHASCISRWLEE-QNSCPMCRRQIQYE  226 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~Wl~~-~~tCP~CR~~i~~~  226 (230)
                      +..|+||++.+..              ++.+ ||||.||..||..|+.. +.+||+||..+...
T Consensus        54 ~~~C~IC~~~~~~--------------p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  103 (165)
T 2ckl_B           54 ELMCPICLDMLKN--------------TMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSK  103 (165)
T ss_dssp             HHBCTTTSSBCSS--------------EEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCSG
T ss_pred             CCCCcccChHhhC--------------cCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCCc
Confidence            5589999999855              5555 89999999999999987 77899999998543

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B

Probab=99.15  E-value=1.6e-11  Score=91.01  Aligned_cols=53  Identities=17%  Similarity=0.137  Sum_probs=48.1

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      .++..|+||++.|.+              ++.+||||.|+..||..|+..+.+||+||.++..++|+
T Consensus        27 p~~~~CpI~~~~m~d--------------PV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~L~   79 (100)
T 2kre_A           27 PDEFRDPLMDTLMTD--------------PVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTESMLE   79 (100)
T ss_dssp             STTTBCTTTCSBCSS--------------EEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCTTSSE
T ss_pred             cHhhCCcCccCcccC--------------CeECCCCCEEchHHHHHHHHcCCCCCCCCCCCChhhce
Confidence            347799999999877              88999999999999999999889999999999888764

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

Probab=99.14  E-value=2.2e-11  Score=89.99  Aligned_cols=53  Identities=13%  Similarity=0.149  Sum_probs=47.9

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCC-CccchhhHHHhhccCCcccccccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCH-HIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~-H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      .++..|+||++.|.+              ++.++|| |.|+..||.+|+..+.+||+||.++..++|+
T Consensus        20 p~~~~CpI~~~~m~d--------------PV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~L~   73 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCD--------------PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIR   73 (98)
T ss_dssp             CTTTBCTTTCSBCSS--------------EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSE
T ss_pred             cHhcCCcCccccccC--------------CeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCChhhce
Confidence            347799999999877              8889999 9999999999999889999999999888764

>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=99.13  E-value=9.1e-12  Score=94.05  Aligned_cols=47  Identities=32%  Similarity=0.879  Sum_probs=41.4

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc-CCcccccccCccc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE-QNSCPMCRRQIQY  225 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~-~~tCP~CR~~i~~  225 (230)
                      +..|+||++.+..              ++.++|||.||..||..|+.. +.+||+||..+..
T Consensus        15 ~~~C~iC~~~~~~--------------p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           15 ECQCGICMEILVE--------------PVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHBCTTTCSBCSS--------------CEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCccCCcccCc--------------eeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            5689999999865              778899999999999999976 6799999998863

>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=99.11  E-value=1.4e-11  Score=83.98  Aligned_cols=47  Identities=23%  Similarity=0.538  Sum_probs=40.5

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEe--CCCCc-cchhhHHHhhccCCcccccccCcc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITM--PCHHI-FHASCISRWLEEQNSCPMCRRQIQ  224 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~L--pC~H~-FH~~CI~~Wl~~~~tCP~CR~~i~  224 (230)
                      ++..|.||++...+              ...+  ||||. |+..|+..|.+.+..||+||+++.
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            35689999998644              5666  99999 899999999998899999999885

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

Probab=99.11  E-value=2.2e-11  Score=110.05  Aligned_cols=53  Identities=30%  Similarity=0.752  Sum_probs=45.8

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhc-cCCcccccccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLE-EQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~-~~~tCP~CR~~i~~~~l~  229 (230)
                      .....|+||++.+..              ++.+||||.||..|+..|+. .+.+||+||+++...+.+
T Consensus       330 ~~~~~C~ICle~~~~--------------pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~~~i  383 (389)
T 2y1n_A          330 STFQLCKICAENDKD--------------VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPI  383 (389)
T ss_dssp             TSSSBCTTTSSSBCC--------------EEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEEEEC
T ss_pred             CCCCCCCccCcCCCC--------------eEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCceeE
Confidence            345799999998755              78899999999999999998 688999999999876544

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

Probab=99.10  E-value=2.8e-11  Score=85.74  Aligned_cols=56  Identities=25%  Similarity=0.523  Sum_probs=42.8

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeC--CCCccchhhHHHhhc-cCCcccccccCccccCCC
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP--CHHIFHASCISRWLE-EQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp--C~H~FH~~CI~~Wl~-~~~tCP~CR~~i~~~~l~  229 (230)
                      .+++..|+||++.+..            ..+..+|  |||.||..|+..|++ ....||.||+.+..+.+.
T Consensus         8 ~~~~~~CpICle~~~~------------~d~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~~   66 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEI------------DDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAV   66 (78)
T ss_dssp             CCCCCBCTTTCCBCCT------------TTTTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSSC
T ss_pred             cccCCcCCccCccCcc------------ccccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCchh
Confidence            4557899999998743            1133444  999999999999874 357899999999876653

>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=99.09  E-value=1.7e-11  Score=92.98  Aligned_cols=49  Identities=29%  Similarity=0.665  Sum_probs=42.7

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEe-CCCCccchhhHHHhhccCCcccccccCccccCC
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITM-PCHHIFHASCISRWLEEQNSCPMCRRQIQYEDL  228 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l  228 (230)
                      ++..|+||++.|..              ++.+ +|||.||..||..|+.  .+||+||..+...++
T Consensus        21 ~~~~C~IC~~~~~~--------------pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~~   70 (117)
T 1jm7_B           21 KLLRCSRCTNILRE--------------PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDL   70 (117)
T ss_dssp             HTTSCSSSCSCCSS--------------CBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSC
T ss_pred             hCCCCCCCChHhhC--------------ccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCccccc
Confidence            46789999999865              6677 8999999999999987  889999999976665

>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=99.07  E-value=3.5e-11  Score=94.51  Aligned_cols=51  Identities=22%  Similarity=0.479  Sum_probs=42.9

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCC-cccccccCccc
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN-SCPMCRRQIQY  225 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~-tCP~CR~~i~~  225 (230)
                      ..+++..|+||++.+.+              ++.++|||.||..||.+|++.+. +||+||.++..
T Consensus        27 ~l~~~~~C~IC~~~~~~--------------pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   78 (141)
T 3knv_A           27 KLEAKYLCSACRNVLRR--------------PFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIY   78 (141)
T ss_dssp             GCCGGGBCTTTCSBCSS--------------EEECTTSCEEEHHHHHHHGGGSCEECHHHHHTTCC
T ss_pred             cCCcCcCCCCCChhhcC--------------cEECCCCCccCHHHHHHHHhcCCCCCCCCCCcccc
Confidence            34456789999999866              67789999999999999998665 89999997643

>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=99.07  E-value=3.1e-11  Score=81.97  Aligned_cols=47  Identities=23%  Similarity=0.496  Sum_probs=40.1

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEe--CCCCc-cchhhHHHhhccCCcccccccCcc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITM--PCHHI-FHASCISRWLEEQNSCPMCRRQIQ  224 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~L--pC~H~-FH~~CI~~Wl~~~~tCP~CR~~i~  224 (230)
                      .+..|.||++...+              ...+  ||||. |+..|+..|.+++.+||+||+++.
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            35689999997644              4555  99998 999999999988889999999885

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=99.06  E-value=2.3e-11  Score=85.14  Aligned_cols=44  Identities=30%  Similarity=0.835  Sum_probs=38.8

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCc-cchhhHHHhhccCCcccccccCccc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHI-FHASCISRWLEEQNSCPMCRRQIQY  225 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~Wl~~~~tCP~CR~~i~~  225 (230)
                      ++..|+||++.+.+              ++.+||||. ||..|+..|    .+||+||+.+..
T Consensus        23 ~~~~C~iC~~~~~~--------------~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           23 EEKLCKICMDRNIA--------------IVFVPCGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HHTBCTTTSSSBCC--------------EEEETTCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             cCCCCCCCCCCCCC--------------EEEcCCCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            35689999998755              788999999 999999999    789999998864

>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=98.97  E-value=8.8e-11  Score=94.48  Aligned_cols=54  Identities=24%  Similarity=0.608  Sum_probs=45.6

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC-CcccccccCccccCC
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ-NSCPMCRRQIQYEDL  228 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~-~tCP~CR~~i~~~~l  228 (230)
                      ...++..|+||++.+.+              ++.++|||.||..||.+|++.+ .+||+||..+..+++
T Consensus        14 ~~~~~~~C~IC~~~~~~--------------pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   68 (170)
T 3hcs_A           14 PLESKYECPICLMALRE--------------AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQL   68 (170)
T ss_dssp             CCCGGGBCTTTCSBCSS--------------EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGC
T ss_pred             CCCCCCCCCCCChhhcC--------------cEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchhhh
Confidence            33456789999999866              6778999999999999999765 499999999987665

>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=98.95  E-value=1.5e-10  Score=84.68  Aligned_cols=53  Identities=28%  Similarity=0.640  Sum_probs=44.3

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhccC------Ccccc--cccC-ccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEEQ------NSCPM--CRRQ-IQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~~------~tCP~--CR~~-i~~~~l~  229 (230)
                      ..+..|+||++.|.+              ++.+| |||.|+..||.+|+..+      .+||+  |+.. +..++|+
T Consensus         5 ~~~~~CPI~~~~~~d--------------PV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~~~L~   67 (94)
T 2yu4_A            5 SSGFTCPITKEEMKK--------------PVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSDLI   67 (94)
T ss_dssp             SSCCBCTTTCSBCSS--------------EEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCGGGEE
T ss_pred             CcEeECcCcCchhcC--------------CEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCHhhCc
Confidence            346789999999877              88896 99999999999999764      48999  9877 7766653

>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=98.92  E-value=3.5e-10  Score=96.79  Aligned_cols=52  Identities=15%  Similarity=0.164  Sum_probs=45.7

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC-CcccccccCccccCCC
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ-NSCPMCRRQIQYEDLV  229 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~-~tCP~CR~~i~~~~l~  229 (230)
                      ....|+||++.|.+              ++.+||||.||..||..|+... .+||+||.++..++++
T Consensus       207 ~~~~c~i~~~~~~d--------------Pv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~l~  259 (281)
T 2c2l_A          207 DYLCGKISFELMRE--------------PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLI  259 (281)
T ss_dssp             STTBCTTTCSBCSS--------------EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCE
T ss_pred             cccCCcCcCCHhcC--------------CeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCchhcCc
Confidence            46789999999877              8899999999999999999864 4599999999887764

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.85  E-value=3e-10  Score=79.43  Aligned_cols=43  Identities=30%  Similarity=0.863  Sum_probs=36.6

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCc-cchhhHHHhhccCCcccccccCccc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHI-FHASCISRWLEEQNSCPMCRRQIQY  225 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~Wl~~~~tCP~CR~~i~~  225 (230)
                      +..|+||++.+.+              ++.+||||. ||..|+..    ...||+||.++..
T Consensus        25 ~~~C~IC~~~~~~--------------~~~~pCgH~~~C~~C~~~----~~~CP~Cr~~i~~   68 (75)
T 2ecg_A           25 EKLCKICMDRNIA--------------IVFVPCGHLVTCKQCAEA----VDKCPMCYTVITF   68 (75)
T ss_dssp             HHSCSSSCSSCCC--------------BCCSSSCCCCBCHHHHHH----CSBCTTTCCBCCC
T ss_pred             CCCCCcCCCCCCC--------------EEEecCCCHHHHHHHhhC----CCCCccCCceecC
Confidence            4579999998755              777999999 99999965    3789999999865

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.84  E-value=9.6e-10  Score=75.69  Aligned_cols=47  Identities=28%  Similarity=0.774  Sum_probs=39.1

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCc-cchhhHHHhhccCCcccccccCccc
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHI-FHASCISRWLEEQNSCPMCRRQIQY  225 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~Wl~~~~tCP~CR~~i~~  225 (230)
                      ...++..|.||++...+              ++.+||||. ||..|+..    ...||+||+.+..
T Consensus        11 ~~~~~~~C~IC~~~~~~--------------~v~~pCgH~~~C~~C~~~----~~~CP~CR~~i~~   58 (68)
T 2ea5_A           11 SEENSKDCVVCQNGTVN--------------WVLLPCRHTCLCDGCVKY----FQQCPMCRQFVQE   58 (68)
T ss_dssp             SCCCSSCCSSSSSSCCC--------------CEETTTTBCCSCTTHHHH----CSSCTTTCCCCCC
T ss_pred             cCCCCCCCCCcCcCCCC--------------EEEECCCChhhhHHHHhc----CCCCCCCCcchhc
Confidence            33457789999998655              888999999 99999984    4789999998854

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=98.84  E-value=1e-09  Score=89.47  Aligned_cols=53  Identities=13%  Similarity=0.143  Sum_probs=46.2

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC-CcccccccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ-NSCPMCRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~-~tCP~CR~~i~~~~l~  229 (230)
                      .....|+||++.|.+              ++.+||||.|+..||..|+... .+||+||.++..++|+
T Consensus       104 p~~f~CPI~~elm~D--------------PV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~L~  157 (179)
T 2f42_A          104 PDYLCGKISFELMRE--------------PCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLI  157 (179)
T ss_dssp             CGGGBCTTTCSBCSS--------------EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCE
T ss_pred             cHhhcccCccccCCC--------------CeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChhhCc
Confidence            346789999999877              8889999999999999999864 5799999999887764

>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=98.82  E-value=5.2e-10  Score=79.29  Aligned_cols=44  Identities=36%  Similarity=0.761  Sum_probs=37.8

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCc-cchhhHHHhhccCCcccccccCccc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHI-FHASCISRWLEEQNSCPMCRRQIQY  225 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~Wl~~~~tCP~CR~~i~~  225 (230)
                      ++..|+||++.+.+              ++.+||||. ||..|+..|    ..||+||..+..
T Consensus        17 ~~~~C~IC~~~~~~--------------~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   61 (79)
T 2yho_A           17 EAMLCMVCCEEEIN--------------STFCPCGHTVCCESCAAQL----QSCPVCRSRVEH   61 (79)
T ss_dssp             HHTBCTTTSSSBCC--------------EEEETTCBCCBCHHHHTTC----SBCTTTCCBCCE
T ss_pred             CCCEeEEeCcccCc--------------EEEECCCCHHHHHHHHHhc----CcCCCCCchhhC
Confidence            35689999998755              888999999 999999988    389999998754

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

Probab=98.77  E-value=8.8e-10  Score=97.56  Aligned_cols=57  Identities=19%  Similarity=0.574  Sum_probs=40.0

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC-----------CcccccccCccc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ-----------NSCPMCRRQIQY  225 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~-----------~tCP~CR~~i~~  225 (230)
                      +...+|+||++.+.+.....      .......+|+|.||..|+.+||++.           .+||+||++++.
T Consensus       306 e~~~ECaICys~~l~~g~lP------dk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~  373 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVP------LVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLST  373 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCC------CBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEG
T ss_pred             cCCccCcccceeecCCCCCc------cccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCc
Confidence            45778999999986511000      0111123599999999999999752           479999998854

>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=98.73  E-value=2.3e-09  Score=72.24  Aligned_cols=50  Identities=16%  Similarity=0.319  Sum_probs=45.4

Q ss_pred             CccccCchhhhhhhhhhccccccCceeEEe-CCCCccchhhHHHhhccCCcccccccCccccCCC
Q 042810          166 DNCAVCLEELIAKEEIKGQTTEKKTQLITM-PCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       166 ~~C~ICle~~~~~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      ..|+||++.+.+              ++.+ +|||+|.+.||.+|++++.+||+.+.++..++|+
T Consensus         4 ~~CpIs~~~m~d--------------PV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~Li   54 (61)
T 2bay_A            4 MLCAISGKVPRR--------------PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIV   54 (61)
T ss_dssp             CCCTTTCSCCSS--------------EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCE
T ss_pred             EEecCCCCCCCC--------------CEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhhcE
Confidence            469999999866              7788 7999999999999999888999999999999885

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=98.73  E-value=3.2e-09  Score=71.37  Aligned_cols=49  Identities=29%  Similarity=0.594  Sum_probs=37.8

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCC--C---ccchhhHHHhhcc--CCcccccccCccc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCH--H---IFHASCISRWLEE--QNSCPMCRRQIQY  225 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~--H---~FH~~CI~~Wl~~--~~tCP~CR~~i~~  225 (230)
                      +++..|.||+++.             ++.. .+||.  |   .||..|+.+|+..  +.+||+||.++..
T Consensus         4 ~~~~~CrIC~~~~-------------~~~l-~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            4 EDVPVCWICNEEL-------------GNER-FRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEEC-------------SCCC-CCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCEeEEeecCC-------------CCce-ecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            4567899999862             2233 58955  5   8999999999974  5789999998754

>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=98.64  E-value=7.9e-09  Score=92.29  Aligned_cols=45  Identities=27%  Similarity=0.833  Sum_probs=39.8

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCc-cchhhHHHhhccCCcccccccCccc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHI-FHASCISRWLEEQNSCPMCRRQIQY  225 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~Wl~~~~tCP~CR~~i~~  225 (230)
                      +++..|+||++.+..              ++.+||||. ||..|+..|    ..||+||..+..
T Consensus       293 ~~~~~C~IC~~~~~~--------------~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          293 QEERTCKVCMDKEVS--------------VVFIPCGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             HTTCBCTTTSSSBCC--------------EEEETTCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             cCCCCCCccCCcCCc--------------eEEcCCCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            457899999999766              888999999 999999999    689999998864

>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=98.60  E-value=6.3e-09  Score=75.67  Aligned_cols=51  Identities=29%  Similarity=0.680  Sum_probs=39.2

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc--------CCcccc--cccC--cccc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE--------QNSCPM--CRRQ--IQYE  226 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~--------~~tCP~--CR~~--i~~~  226 (230)
                      ..+|+||++++..           .......+|||.||..|+.++++.        .-+||.  ||..  ++.+
T Consensus         5 ~~~C~IC~~~~~~-----------~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~~   67 (94)
T 1wim_A            5 SSGCKLCLGEYPV-----------EQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQEN   67 (94)
T ss_dssp             BCCCSSSCCCCBG-----------GGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECHH
T ss_pred             CcCCcccCccccc-----------ccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCHH
Confidence            5689999999865           333444479999999999999863        237999  9998  6544

>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=98.53  E-value=2.3e-08  Score=85.61  Aligned_cols=53  Identities=25%  Similarity=0.577  Sum_probs=44.0

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEE-eCCCCccchhhHHHhhccC--Ccccc--cccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLIT-MPCHHIFHASCISRWLEEQ--NSCPM--CRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~-LpC~H~FH~~CI~~Wl~~~--~tCP~--CR~~i~~~~l~  229 (230)
                      ..+..|+||++.|.+              ++. ..|||.|++.||..|++.+  .+||+  ||+.+..++|.
T Consensus       179 ~~el~CPIcl~~f~D--------------PVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL~  236 (267)
T 3htk_C          179 KIELTCPITCKPYEA--------------PLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFV  236 (267)
T ss_dssp             BCCSBCTTTSSBCSS--------------EEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGEE
T ss_pred             ceeeECcCccCcccC--------------CeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhCC
Confidence            346799999999966              555 4899999999999999764  47999  99998877763

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

Probab=98.27  E-value=5.1e-07  Score=66.09  Aligned_cols=37  Identities=27%  Similarity=0.573  Sum_probs=31.5

Q ss_pred             CceeEEeCCCCccchhhHHHhhc-cCCcccccccCccc
Q 042810          189 KTQLITMPCHHIFHASCISRWLE-EQNSCPMCRRQIQY  225 (230)
Q Consensus       189 ~~~v~~LpC~H~FH~~CI~~Wl~-~~~tCP~CR~~i~~  225 (230)
                      ....+.+||+|+||.+|+..|.+ +.++||+||.+|..
T Consensus        12 ~iygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~r   49 (101)
T 3vk6_A           12 KVYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQR   49 (101)
T ss_dssp             SEEEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCSE
T ss_pred             EEEeeeccccccHHHHHHHHHHhccCCCCcCcCCeeee
Confidence            44578889999999999999975 46899999998854

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

Probab=98.00  E-value=3.7e-06  Score=71.28  Aligned_cols=50  Identities=24%  Similarity=0.567  Sum_probs=40.5

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCC--cccccccCcccc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN--SCPMCRRQIQYE  226 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~--tCP~CR~~i~~~  226 (230)
                      .-..|.||.+....           +  .+.-.|+|.||..|+..|++.+.  +||.|+..|+.+
T Consensus       179 ~i~~C~iC~~iv~~-----------g--~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~  230 (238)
T 3nw0_A          179 AVKICNICHSLLIQ-----------G--QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE  230 (238)
T ss_dssp             TCCBCTTTCSBCSS-----------C--EECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSC
T ss_pred             CCCcCcchhhHHhC-----------C--cccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCC
Confidence            46789999998854           2  33334999999999999998754  999999999765

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=94.75  E-value=0.023  Score=38.25  Aligned_cols=48  Identities=23%  Similarity=0.491  Sum_probs=34.2

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCC----cccccccCc
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN----SCPMCRRQI  223 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~----tCP~CR~~i  223 (230)
                      ...+..|.||.+.              ++-+..=.|...||..|+++.+....    .||.|++..
T Consensus         9 ~~~~~~C~vC~~~--------------~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C            9 LAPGARCGVCGDG--------------TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             CCTTCCCTTTSCC--------------TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCCCcCCCCCC--------------CeEEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            3456789999753              33233334999999999998886542    699998754

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=94.54  E-value=0.014  Score=41.95  Aligned_cols=35  Identities=11%  Similarity=0.321  Sum_probs=25.6

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHH-hh
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISR-WL  210 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~-Wl  210 (230)
                      +..|+||.+.+..           ......++|+|.||..|+.. |.
T Consensus         3 e~~C~~C~~~~~~-----------~av~~C~~C~~~~C~~Cl~~~h~   38 (101)
T 2jun_A            3 KVLCQFCDQDPAQ-----------DAVKTCVTCEVSYCDECLKATHP   38 (101)
T ss_dssp             CCBCTTCCSSSCC-----------BCCEEETTTTEEECHHHHHHHSC
T ss_pred             CCCCcCCCCCCCC-----------CceEECCcCChHHhHHHCHHHhc
Confidence            5689999986422           12233489999999999998 53

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=90.17  E-value=0.1  Score=34.37  Aligned_cols=49  Identities=27%  Similarity=0.582  Sum_probs=32.5

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEe-CCCCccchhhHHHhhc-----cCCcccccccC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITM-PCHHIFHASCISRWLE-----EQNSCPMCRRQ  222 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~Wl~-----~~~tCP~CR~~  222 (230)
                      .++..|+||...+.+           +...+.- .|...||..|+.--..     .+-.||.|+..
T Consensus         4 ~e~~~C~~C~~~~~~-----------~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            4 GSSGQCGACGESYAA-----------DEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SSCCCCSSSCCCCCS-----------SSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCCccCC-----------CCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            346779999887643           2223333 4999999999864321     23479999764

>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=89.38  E-value=0.14  Score=33.58  Aligned_cols=48  Identities=25%  Similarity=0.474  Sum_probs=32.4

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC----CcccccccCc
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ----NSCPMCRRQI  223 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~----~tCP~CR~~i  223 (230)
                      +..+..|.||.+.              ++-+..=.|...||..|+.+-+...    =.||.|+...
T Consensus         6 d~~~~~C~vC~~~--------------g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            6 DHHMEFCRVCKDG--------------GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             CSSCSSCTTTCCC--------------SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             cCCCCcCCCCCCC--------------CCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            3457789999862              3223333499999999998655432    2599998754

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=88.88  E-value=0.25  Score=32.40  Aligned_cols=47  Identities=26%  Similarity=0.675  Sum_probs=32.0

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC----CcccccccC
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ----NSCPMCRRQ  222 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~----~tCP~CR~~  222 (230)
                      ...+..|.||...              ++-+..-.|...||..|+..-+...    =.||.|++.
T Consensus         8 ~~~~~~C~vC~~~--------------g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A            8 TDHQDYCEVCQQG--------------GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             SCCCSSCTTTSCC--------------SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCCCccCCCC--------------CcEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            3457789999863              3223333499999999999855432    269999763

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A

Probab=88.09  E-value=0.25  Score=49.16  Aligned_cols=52  Identities=15%  Similarity=0.163  Sum_probs=45.6

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCC-CccchhhHHHhhccCCcccccccCccccCCC
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCH-HIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~-H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      +.-.|+|=++-+.+              ++.+|-| +.|-+..|.+|+..+.+||+=|.++..++++
T Consensus       890 ~~F~cPIs~~lM~D--------------PVilpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~li  942 (968)
T 3m62_A          890 DEFLDPLMYTIMKD--------------PVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVT  942 (968)
T ss_dssp             GGGBCTTTCSBCSS--------------EEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCE
T ss_pred             HHhCCcchhhHHhC--------------CeEcCCCCEEECHHHHHHHHhcCCCCCCCCCCCCccccc
Confidence            35679999999877              8899987 6899999999999999999999999887764

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=87.84  E-value=0.093  Score=34.28  Aligned_cols=46  Identities=28%  Similarity=0.685  Sum_probs=31.5

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC----CcccccccCc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ----NSCPMCRRQI  223 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~----~tCP~CR~~i  223 (230)
                      .+..|.||...              ++-+..=.|...||..|+.+=+...    =.||.|+...
T Consensus         4 ~~~~C~vC~~~--------------g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   53 (60)
T 2puy_A            4 HEDFCSVCRKS--------------GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQM   53 (60)
T ss_dssp             CCSSCTTTCCC--------------SSCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHH
T ss_pred             CCCCCcCCCCC--------------CcEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccChh
Confidence            46789999873              3223333499999999998655432    2599997654

>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=87.46  E-value=0.29  Score=34.39  Aligned_cols=34  Identities=32%  Similarity=0.657  Sum_probs=23.5

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeC---CCCccchhhHHHh
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP---CHHIFHASCISRW  209 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp---C~H~FH~~CI~~W  209 (230)
                      ....|+.|.||---- .              -..+|   |+-+||..|+.+.
T Consensus        11 ~~~~D~~C~VC~~~t-~--------------~~l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           11 PVVNDEMCDVCEVWT-A--------------ESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCCSCCCTTTCCCC-S--------------SCCSSCSSSSSCCCHHHHHHH
T ss_pred             CCCCCcccCcccccc-c--------------cceeccccccccccHhhcccc
Confidence            344688999996321 1              11233   8999999999996

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=87.15  E-value=0.53  Score=33.37  Aligned_cols=51  Identities=25%  Similarity=0.542  Sum_probs=34.8

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhccC----CcccccccCcccc
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEEQ----NSCPMCRRQIQYE  226 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~~----~tCP~CR~~i~~~  226 (230)
                      ....+..|.+|...              ++ +..-. |.-.||..|+.+=+...    =.||.|+..-..+
T Consensus        21 ~d~n~~~C~vC~~~--------------g~-LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~~~k   76 (88)
T 1fp0_A           21 LDDSATICRVCQKP--------------GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLK   76 (88)
T ss_dssp             SSSSSSCCSSSCSS--------------SC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCSSC
T ss_pred             cCCCCCcCcCcCCC--------------CC-EEECCCCCCceecccCCCCCCCCcCCCcCCccccCCCccc
Confidence            34557899999873              32 33334 88999999997765432    2699998654433

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=87.12  E-value=0.15  Score=32.79  Aligned_cols=46  Identities=26%  Similarity=0.632  Sum_probs=31.1

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC----Cccccccc
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ----NSCPMCRR  221 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~----~tCP~CR~  221 (230)
                      ...+..|.||...              ++-+..-.|...||..|+.+-+...    =.||.|+.
T Consensus         6 ~~~~~~C~vC~~~--------------g~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            6 SGHEDFCSVCRKS--------------GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             CSSCCSCSSSCCS--------------SCCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCCccCCCC--------------CeEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            3457789999873              3223333499999999998755432    25998864

>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=85.94  E-value=0.23  Score=32.85  Aligned_cols=54  Identities=17%  Similarity=0.460  Sum_probs=35.1

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhcc-------CCcccccccCcccc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEE-------QNSCPMCRRQIQYE  226 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~-------~~tCP~CR~~i~~~  226 (230)
                      .++..|.||.......          ...+..-. |.-.||..|+.+=+..       .=.||.|+.....+
T Consensus         4 ~~~~~C~vC~~~~~~~----------~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~~~k   65 (66)
T 2yt5_A            4 GSSGVCTICQEEYSEA----------PNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFATTTK   65 (66)
T ss_dssp             CCCCCBSSSCCCCCBT----------TBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTTSCC
T ss_pred             CCCCCCCCCCCCCCCC----------CCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCccccC
Confidence            3577899998753220          23344444 9999999999874422       22699998765443

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=84.42  E-value=0.34  Score=32.18  Aligned_cols=45  Identities=38%  Similarity=0.719  Sum_probs=31.4

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEe-CCCCccchhhHHHhhccC----CcccccccC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITM-PCHHIFHASCISRWLEEQ----NSCPMCRRQ  222 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~Wl~~~----~tCP~CR~~  222 (230)
                      ..+..|.||.+.              ++ +..- .|.-.||..|+.+-+...    =.||.|+..
T Consensus         6 ~~~~~C~vC~~~--------------g~-ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~   55 (66)
T 1xwh_A            6 KNEDECAVCRDG--------------GE-LICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQA   55 (66)
T ss_dssp             SCCCSBSSSSCC--------------SS-CEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHT
T ss_pred             CCCCCCccCCCC--------------CC-EEEcCCCChhhcccccCCCcCcCCCCCeECccccCc
Confidence            457889999863              32 3333 499999999998655432    259999764

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=84.03  E-value=0.49  Score=33.40  Aligned_cols=56  Identities=16%  Similarity=0.357  Sum_probs=34.7

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhc--cCCcccccccCccccCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLE--EQNSCPMCRRQIQYEDL  228 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~--~~~tCP~CR~~i~~~~l  228 (230)
                      +++..|.||...-..          ....+..-. |.-.||..|+..-..  ..=.||.|+.....++|
T Consensus        23 ~~~~~C~vC~~~~s~----------~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~~~~~~   81 (88)
T 2l43_A           23 DEDAVCSICMDGESQ----------NSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRARPAL   81 (88)
T ss_dssp             CCCCCCSSCCSSSSC----------SEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHTTSCC-
T ss_pred             CCCCcCCcCCCCCCC----------CCCCEEECCCCCchhhcccCCCCccCCCceECccccCccchhhh
Confidence            457899999874211          022343334 989999999975321  12259999876655543

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=83.45  E-value=0.7  Score=35.65  Aligned_cols=46  Identities=33%  Similarity=0.637  Sum_probs=32.9

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhcc-----------CCcccccccC
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEE-----------QNSCPMCRRQ  222 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~-----------~~tCP~CR~~  222 (230)
                      +..++.|.+|.+.              ++ +..-. |-..||..||.+=+..           .=.||+|+..
T Consensus        60 Dg~~d~C~vC~~G--------------G~-LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~~  117 (142)
T 2lbm_A           60 DGMDEQCRWCAEG--------------GN-LICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPE  117 (142)
T ss_dssp             TSCBCSCSSSCCC--------------SS-EEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCCC
T ss_pred             CCCCCeecccCCC--------------Cc-EEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccCc
Confidence            4457889999984              33 44444 9999999999976531           2269999753

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=83.32  E-value=0.2  Score=34.06  Aligned_cols=51  Identities=22%  Similarity=0.433  Sum_probs=33.3

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhcc----CCcccccccCcccc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEE----QNSCPMCRRQIQYE  226 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~----~~tCP~CR~~i~~~  226 (230)
                      +...|.||.... .           +...+.-. |.-.||..|+..-...    .-.||.|+..+...
T Consensus        17 ~~~~C~~C~~~~-~-----------~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~k~   72 (75)
T 2k16_A           17 QIWICPGCNKPD-D-----------GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKKD   72 (75)
T ss_dssp             EEECBTTTTBCC-S-----------SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHCSC
T ss_pred             CCcCCCCCCCCC-C-----------CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchhhc
Confidence            345699997653 1           32333334 9999999999765432    23699998876543

>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine trimethylation, protein, histone-binding protein, transcription-structural complex; HET: M3L; 0.93A {Homo sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A

Probab=82.47  E-value=0.92  Score=34.41  Aligned_cols=45  Identities=33%  Similarity=0.623  Sum_probs=30.8

Q ss_pred             ccCCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhh------cc-----CCccccccc
Q 042810          162 VKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWL------EE-----QNSCPMCRR  221 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl------~~-----~~tCP~CR~  221 (230)
                      +..++.|.||.+.               -++..=. |-..||..||.+-+      +.     .=.|++|+.
T Consensus        54 Dg~~~~C~vC~dG---------------G~LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~  110 (129)
T 3ql9_A           54 DGMDEQCRWCAEG---------------GNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHP  110 (129)
T ss_dssp             TSCBSSCTTTCCC---------------SEEEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCC
T ss_pred             CCCCCcCeecCCC---------------CeeEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCC
Confidence            4456789999973               2333334 89999999999742      11     126999965

>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein, signal transduction, transcription, metal BI WNT proteins; 1.90A {Homo sapiens}

Probab=81.88  E-value=0.35  Score=35.29  Aligned_cols=49  Identities=18%  Similarity=0.472  Sum_probs=30.9

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEe-CCCCccchhhHHHhh----------ccCCcccccccCc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITM-PCHHIFHASCISRWL----------EEQNSCPMCRRQI  223 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~Wl----------~~~~tCP~CR~~i  223 (230)
                      ...|+||...+.++          +..+..= .|.-.||..|+.-=-          ..+-.||.|+..-
T Consensus         3 ~~~C~iC~~p~~~~----------~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~   62 (105)
T 2xb1_A            3 VYPCGACRSEVNDD----------QDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTK   62 (105)
T ss_dssp             CCBCTTTCSBCCTT----------SCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTT
T ss_pred             cCCCCCCCCccCCC----------CCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcC
Confidence            45799999887541          2333332 489999999984210          0233699997643

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=81.61  E-value=0.24  Score=34.61  Aligned_cols=60  Identities=13%  Similarity=0.308  Sum_probs=41.1

Q ss_pred             cccCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhh--------ccCCcccccccCccccCCCC
Q 042810          161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWL--------EEQNSCPMCRRQIQYEDLVG  230 (230)
Q Consensus       161 ~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl--------~~~~tCP~CR~~i~~~~l~~  230 (230)
                      .+.+...|.+|...|...          ..+-..-.||++||..|.....        +..+.|-.|-..+...+++|
T Consensus        17 pd~~~~~C~~C~~~Fs~~----------~RrHHCR~CG~v~C~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~~~~~~   84 (84)
T 1z2q_A           17 EDEDAPACNGCGCVFTTT----------VRRHHCRNCGYVLCGDCSRHRAAIPMRGITEPERVCDACYLALRSSNMAG   84 (84)
T ss_dssp             CTTTCCBCTTTCCBCCTT----------SCCEECTTTCCEECTGGGCCEEEETTTTEEEEEECCHHHHHHHHTSCCCC
T ss_pred             cCCCCCCCcCcCCccccc----------hhcccccCCCcEEChHHhCCeEeccCCCCCCCCEECHHHHHHHhhcccCC
Confidence            344567899999998661          2223333599999999987653        22356888877777776654

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=80.20  E-value=0.69  Score=33.72  Aligned_cols=38  Identities=26%  Similarity=0.517  Sum_probs=26.1

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLE  211 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~  211 (230)
                      .+++.|.||.+.-+.           .+-+.--.|...||..|+..++.
T Consensus         5 ~~~~~C~~C~~~g~~-----------~~ll~C~~C~~~~H~~Cl~~~~~   42 (111)
T 2ysm_A            5 SSGANCAVCDSPGDL-----------LDQFFCTTCGQHYHGMCLDIAVT   42 (111)
T ss_dssp             CCCSCBTTTCCCCCT-----------TTSEECSSSCCEECTTTTTCCCC
T ss_pred             CCCCCCcCCCCCCCC-----------cCCeECCCCCCCcChHHhCCccc
Confidence            457889999875211           11233345999999999988764

---

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	230
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	6e-15
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	2e-13
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	1e-12
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	9e-10
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	3e-08
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	6e-08
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	7e-08
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	3e-07
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	4e-07
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	1e-06
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	7e-06
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	3e-04
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	5e-04

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.5 bits (159), Expect = 6e-15
 Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 4/65 (6%)

Query: 166 DNCAVCLEELIAK----EEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRR 221
           DNCA+C   ++      +  +   T ++  +    C+H FH  CISRWL+ +  CP+  R
Sbjct: 22  DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 81

Query: 222 QIQYE 226
           + +++
Sbjct: 82  EWEFQ 86

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 60.7 bits (147), Expect = 2e-13
 Identities = 22/59 (37%), Positives = 28/59 (47%), Gaps = 10/59 (16%)

Query: 165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQI 223
           G  CAVCL EL   EE +              C H FHA C+  WL   ++CP+CR  +
Sbjct: 5   GVECAVCLAELEDGEEAR----------FLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 59.2 bits (143), Expect = 1e-12
 Identities = 15/64 (23%), Positives = 29/64 (45%), Gaps = 13/64 (20%)

Query: 161 LVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCR 220
           +    + C +CLE+                  + +PC H F   CI+RW+ +  +CP+C+
Sbjct: 1   MATVAERCPICLEDPSNYS-------------MALPCLHAFCYVCITRWIRQNPTCPLCK 47

Query: 221 RQIQ 224
             ++
Sbjct: 48  VPVE 51

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.5 bits (123), Expect = 9e-10
 Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 15/63 (23%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ-NSCPMCRRQIQYE 226
           C +C E                  +   PC H+   SC++ W E +   CP CR +I+  
Sbjct: 26  CKICAEND--------------KDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT 71

Query: 227 DLV 229
           + +
Sbjct: 72  EPI 74

>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 = 47.1 bits (111), Expect = 3e-08
 Identities = 11/64 (17%), Positives = 18/64 (28%), Gaps = 10/64 (15%)

Query: 166 DNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE-QNSCPMCRRQIQ 224
             C  C         +K         L+   C H    SC+         +CP C   ++
Sbjct: 4   QGCPRCKTTKYRNPSLK---------LMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLR 54

Query: 225 YEDL 228
             + 
Sbjct: 55  KSNF 58

>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 = 47.3 bits (111), Expect = 6e-08
 Identities = 15/67 (22%), Positives = 22/67 (32%), Gaps = 9/67 (13%)

Query: 166 DNCAVCLEELIAKEEIKGQTTEKKTQ----LITMPCHHIFHASCISRWLEEQN-----SC 216
           ++C +C+E+L         T  K            C H FH  C+       N      C
Sbjct: 26  EDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQC 85

Query: 217 PMCRRQI 223
           P C+   
Sbjct: 86  PSCKTIY 92

>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 = 45.6 bits (108), Expect = 7e-08
 Identities = 10/56 (17%), Positives = 15/56 (26%), Gaps = 17/56 (30%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQI 223
           C  C  E                    +PC H   + C+         CP+C+   
Sbjct: 9   CQQCQAEA--------------KCPKLLPCLHTLCSGCLEAS---GMQCPICQAPW 47

>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 = 43.9 bits (103), Expect = 3e-07
 Identities = 12/60 (20%), Positives = 20/60 (33%), Gaps = 11/60 (18%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN-SCPMCRRQIQYE 226
           C +C+E L   +                 C +     C  R   ++N  CP CR+    +
Sbjct: 3   CPLCMEPLEIDDIN----------FFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED 52

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.5 bits (105), Expect = 4e-07
 Identities = 20/79 (25%), Positives = 28/79 (35%), Gaps = 15/79 (18%)

Query: 152 RVLDLDFNKLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLE 211
           ++L +DF        +C +C   L                 +   C H+F   CI R L+
Sbjct: 10  KLLAVDFPAHFVKSISCQICEHIL--------------ADPVETSCKHLFCRICILRCLK 55

Query: 212 EQNS-CPMCRRQIQYEDLV 229
              S CP CR      DL 
Sbjct: 56  VMGSYCPSCRYPCFPTDLE 74

>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 = 43.5 bits (102), Expect = 1e-06
 Identities = 15/66 (22%), Positives = 26/66 (39%), Gaps = 17/66 (25%)

Query: 167 NCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN---SCPMCRRQI 223
            C +CLE +               + ++  C HIF   C+ + L ++     CP+C+  I
Sbjct: 23  ECPICLELI--------------KEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDI 68

Query: 224 QYEDLV 229
               L 
Sbjct: 69  TKRSLQ 74

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

 Score = 40.2 bits (93), Expect = 7e-06
 Identities = 14/59 (23%), Positives = 19/59 (32%), Gaps = 11/59 (18%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ--NSCPMCRRQIQ 224
           C +C EEL           E+             H SC+S WL      +C +C     
Sbjct: 9   CWICNEEL---------GNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN 58

>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 = 36.7 bits (84), Expect = 3e-04
 Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 15/62 (24%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYED 227
           C+ C   L             +  +    C HIF ++C+S  +     CP+C      +D
Sbjct: 25  CSRCTNIL-------------REPVCLGGCEHIFCSNCVSDCIGTG--CPVCYTPAWIQD 69

Query: 228 LV 229
           L 
Sbjct: 70  LK 71

>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 = 35.1 bits (80), Expect = 5e-04
 Identities = 8/62 (12%), Positives = 25/62 (40%), Gaps = 13/62 (20%)

Query: 168 CAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYED 227
           CA+  +               +  +++     IF  S + +++++  + P+    +  E+
Sbjct: 3   CAISGKVP-------------RRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEE 49

Query: 228 LV 229
           +V
Sbjct: 50  IV 51

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	230
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.71
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.58
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.57
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.54
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.52
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.52
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.45
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.44
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.39
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.36
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.31
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.21
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.19
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.18
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.16
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.96
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.48
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	93.14
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	91.58
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	91.42
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	91.18
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	89.52
d2epqa1	32	PATZ1 {Human (Homo sapiens) [TaxId: 9606]}	89.23
d1srka_	35	Zinc finger protein ZFPM1 (FOG-1) {Mouse (Mus musc	88.01
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	86.44
d2adra1	29	ADR1 {Synthetic, based on Saccharomyces cerevisiae	85.63
d2dlqa4	27	GLI-Krueppel family member HKR3 {Mouse (Mus muscul	85.33
d1a1ia2	28	ZIF268 {Mouse (Mus musculus) [TaxId: 10090]}	83.58
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	82.1
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	81.6
d1sp1a_	29	Transcription factor sp1 {Human (Homo sapiens) [Ta	80.81

>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=99.71  E-value=1.4e-18  Score=114.08  Aligned_cols=51  Identities=41%  Similarity=0.957  Sum_probs=45.4

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhccCCcccccccCcc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEEQNSCPMCRRQIQ  224 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~~~tCP~CR~~i~  224 (230)
                      +++.+|+||+++|..           ++.+.++| |+|.||.+||.+|++++++||+||+++.
T Consensus         3 ed~~~C~ICl~~~~~-----------~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           3 DDGVECAVCLAELED-----------GEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCT-----------TSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCCeEECccccC-----------CCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            346679999999987           77788886 9999999999999999999999999873

>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=99.58  E-value=2.9e-16  Score=107.13  Aligned_cols=48  Identities=31%  Similarity=0.997  Sum_probs=42.0

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCcc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQ  224 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~  224 (230)
                      ..++|+||++.+.+             .++.+||||.||..||.+|++++++||+||+++.
T Consensus         4 ~~d~C~IC~~~~~~-------------~~~~~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~   51 (68)
T d1chca_           4 VAERCPICLEDPSN-------------YSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCCSSCCSCCCS-------------CEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCCccCCcCccC-------------CcEEeCCCCcCcHHHHHHHHHhCCcCCCCCcchH
Confidence            35679999999833             3667899999999999999999999999999875

>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=99.57  E-value=4.9e-16  Score=111.20  Aligned_cols=66  Identities=29%  Similarity=0.615  Sum_probs=49.1

Q ss_pred             ccCCCccccCchhhhhhhhhh----ccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccC
Q 042810          162 VKAGDNCAVCLEELIAKEEIK----GQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYED  227 (230)
Q Consensus       162 ~~~~~~C~ICle~~~~~~~~~----~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~  227 (230)
                      +..++.|+||++.+.+.....    .........+..++|||.||.+||.+||+.+++||+||+++..++
T Consensus        18 d~~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~   87 (88)
T d3dplr1          18 DIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQK   87 (88)
T ss_dssp             SSCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCCEEE
T ss_pred             cCCCCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCCcCCCCCCcccccc
Confidence            345677999999887633211    111222345778899999999999999999999999999987664

>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=99.54  E-value=2.7e-15  Score=101.35  Aligned_cols=56  Identities=18%  Similarity=0.511  Sum_probs=44.0

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc-CCcccccccCccccCC
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE-QNSCPMCRRQIQYEDL  228 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~-~~tCP~CR~~i~~~~l  228 (230)
                      ++..|+||++++...         +......++|||.||..||.+|+.+ +++||+||+++...++
T Consensus         2 dd~~CpIC~~~~~~~---------~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~~   58 (65)
T d1g25a_           2 DDQGCPRCKTTKYRN---------PSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNF   58 (65)
T ss_dssp             CTTCCSTTTTHHHHC---------SSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCC
T ss_pred             CCCCCCcCCceeecC---------CceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCcccccc
Confidence            367899999987651         1233456689999999999999965 5689999999977653

>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=99.52  E-value=2.6e-15  Score=105.30  Aligned_cols=52  Identities=31%  Similarity=0.765  Sum_probs=44.1

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhc-cCCcccccccCccccCCC
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLE-EQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~-~~~tCP~CR~~i~~~~l~  229 (230)
                      ....|+||++.+..              ++.+||||.||..||..|+. ++++||+||..|...+.+
T Consensus        22 ~~~~C~IC~~~~~~--------------~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~i   74 (79)
T d1fbva4          22 TFQLCKICAENDKD--------------VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPI   74 (79)
T ss_dssp             CTTBCTTTSSSBCC--------------EECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCCS
T ss_pred             CCCCCccCCCcCCC--------------eEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCcee
Confidence            34679999998755              78899999999999999997 457899999999876643

>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=99.52  E-value=1.1e-15  Score=98.88  Aligned_cols=50  Identities=22%  Similarity=0.575  Sum_probs=40.6

Q ss_pred             ccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc-CCcccccccCcccc
Q 042810          167 NCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE-QNSCPMCRRQIQYE  226 (230)
Q Consensus       167 ~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~-~~tCP~CR~~i~~~  226 (230)
                      +|+||+++|...          +..+..++|||.||..|+++|++. +.+||+||+++..+
T Consensus         2 eCpICl~~~~~~----------~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~d   52 (52)
T d1ur6b_           2 ECPLCMEPLEID----------DINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED   52 (52)
T ss_dssp             EETTTTEECCGG----------GTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSCC
T ss_pred             CCcCCChhhhCC----------CceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCCC
Confidence            699999999762          233455689999999999999986 45799999998754

>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=99.45  E-value=6.2e-15  Score=96.64  Aligned_cols=49  Identities=18%  Similarity=0.401  Sum_probs=44.9

Q ss_pred             ccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhccCCcccccccCccccCCC
Q 042810          167 NCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       167 ~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      .|+||++.+.+              ++.++ |||+||..||.+|++++++||+||+++..+||+
T Consensus         2 ~C~Ic~~~~~~--------------Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dLi   51 (56)
T d2baya1           2 LCAISGKVPRR--------------PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIV   51 (56)
T ss_dssp             CCTTTCSCCSS--------------EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCE
T ss_pred             CCccCCchHHh--------------cCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhce
Confidence            59999999866              77776 999999999999999999999999999999986

>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=99.44  E-value=2e-14  Score=107.10  Aligned_cols=63  Identities=19%  Similarity=0.437  Sum_probs=44.2

Q ss_pred             CCCccccCchhhhhhhhhhc---c-ccccCceeEEeCCCCccchhhHHHhhccC-----CcccccccCcccc
Q 042810          164 AGDNCAVCLEELIAKEEIKG---Q-TTEKKTQLITMPCHHIFHASCISRWLEEQ-----NSCPMCRRQIQYE  226 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~---~-~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~-----~tCP~CR~~i~~~  226 (230)
                      .++.|+||++.+........   . .......+.+++|+|+||..||..|++.+     .+||+||+.+..+
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             ccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            36789999999865321111   0 11123446677899999999999999754     3899999977554

>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=99.39  E-value=3e-14  Score=101.26  Aligned_cols=52  Identities=31%  Similarity=0.614  Sum_probs=45.2

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc-CCcccccccCccccCCC
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE-QNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~-~~tCP~CR~~i~~~~l~  229 (230)
                      ....|+||++.+.+              ++.++|||.||..||.+|++. +++||+||.++...++.
T Consensus        22 ~~l~C~IC~~~~~~--------------pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l~   74 (86)
T d1rmda2          22 KSISCQICEHILAD--------------PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE   74 (86)
T ss_dssp             HHTBCTTTCSBCSS--------------EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCB
T ss_pred             cCcCCccCCcchhc--------------ceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChhhcc
Confidence            34689999999866              888999999999999999974 46899999999888764

>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=99.36  E-value=4e-14  Score=92.69  Aligned_cols=47  Identities=21%  Similarity=0.509  Sum_probs=40.4

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCCcccccccCccccC
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQNSCPMCRRQIQYED  227 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~  227 (230)
                      +...|+||++.+.+              ++.+||||.||..||.+|   +.+||+||++++...
T Consensus         5 ~~l~C~IC~~~~~~--------------p~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T d1bora_           5 QFLRCQQCQAEAKC--------------PKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CCSSCSSSCSSCBC--------------CSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             CCCCCcccCcccCC--------------CEEecCCCHHhHHHHHcC---CCcCcCCCCcccCCC
Confidence            35689999999865              677999999999999987   678999999997654

>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=99.31  E-value=2.2e-13  Score=99.77  Aligned_cols=50  Identities=30%  Similarity=0.779  Sum_probs=42.8

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCC---cccccccCccccCC
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN---SCPMCRRQIQYEDL  228 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~---tCP~CR~~i~~~~l  228 (230)
                      ...|+||++.|.+              ++.+||||.||..||..|+++++   +||+||.++..+++
T Consensus        21 ~l~CpIC~~~~~~--------------pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l   73 (103)
T d1jm7a_          21 ILECPICLELIKE--------------PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL   73 (103)
T ss_dssp             HTSCSSSCCCCSS--------------CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTC
T ss_pred             CcCCCccCchhCC--------------eEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhC
Confidence            4579999998865              66789999999999999997653   79999999987765

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.21  E-value=2.7e-12  Score=92.81  Aligned_cols=49  Identities=29%  Similarity=0.614  Sum_probs=40.7

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEE-eCCCCccchhhHHHhhccCCcccccccCccccCCC
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLIT-MPCHHIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~-LpC~H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      ...|+||++.|..              ++. .+|||.||..||.+|+.  ++||.||.++..+++.
T Consensus        22 ~l~C~IC~~~~~~--------------pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~l~   71 (97)
T d1jm7b_          22 LLRCSRCTNILRE--------------PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLK   71 (97)
T ss_dssp             TTSCSSSCSCCSS--------------CBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCC
T ss_pred             cCCCccCCchhhc--------------CceeCCCCCchhHHHHHHHHh--ccccccCCcCchhhCc
Confidence            5689999999855              444 47999999999999984  4699999998877763

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.19  E-value=3.9e-12  Score=88.78  Aligned_cols=53  Identities=15%  Similarity=0.160  Sum_probs=45.9

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhcc-CCcccccccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEE-QNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~-~~tCP~CR~~i~~~~l~  229 (230)
                      .++..|+||++.|.+              ++.++|||.|+..||.+|+.+ +.+||.||.++..++++
T Consensus         5 P~~l~CpIc~~l~~d--------------Pv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~l~   58 (80)
T d2c2la2           5 PDYLCGKISFELMRE--------------PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLI   58 (80)
T ss_dssp             CSTTBCTTTCSBCSS--------------EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCE
T ss_pred             CccccCcCcCchhhh--------------hcccCCcCeecHHHHHHHHhcCCccCCCccccccccccc
Confidence            356789999999876              778999999999999999975 56899999999887764

>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=99.18  E-value=2.4e-12  Score=85.11  Aligned_cols=49  Identities=27%  Similarity=0.444  Sum_probs=37.6

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeC-----CCCccchhhHHHhhcc--CCcccccccCccc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-----CHHIFHASCISRWLEE--QNSCPMCRRQIQY  225 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-----C~H~FH~~CI~~Wl~~--~~tCP~CR~~i~~  225 (230)
                      ++...|.||++++..              ....|     |+|.||..||.+|+..  +.+||+||+++..
T Consensus         4 ed~~~C~IC~~~~~~--------------~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           4 EDVPVCWICNEELGN--------------ERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEECSC--------------CCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCCccCCccCCC--------------ceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            457789999998643              12233     4599999999999954  5689999998764

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.16  E-value=6e-12  Score=87.34  Aligned_cols=53  Identities=19%  Similarity=0.450  Sum_probs=46.2

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC-CcccccccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ-NSCPMCRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~-~tCP~CR~~i~~~~l~  229 (230)
                      .++..|+||++.|.+              ++.++|||.|+..||.+|++.+ .+||.||.++..++++
T Consensus         6 P~~l~CpIc~~~m~d--------------PV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~l~   59 (78)
T d1t1ha_           6 PEYFRCPISLELMKD--------------PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLT   59 (78)
T ss_dssp             SSSSSCTTTSCCCSS--------------EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCE
T ss_pred             CccCCCcCcCchhhC--------------ceEccCCCcchHHHHHHHHHHCCCCCCcccccCCccccc
Confidence            357789999999977              7789999999999999999864 6799999999887763

>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=98.96  E-value=1.5e-10  Score=83.79  Aligned_cols=53  Identities=13%  Similarity=0.149  Sum_probs=47.3

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCC-CccchhhHHHhhccCCcccccccCccccCCC
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCH-HIFHASCISRWLEEQNSCPMCRRQIQYEDLV  229 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~-H~FH~~CI~~Wl~~~~tCP~CR~~i~~~~l~  229 (230)
                      -++..|+||.+.|.+              ++++||+ |.|++.||..|++++.+||+||.++..++|+
T Consensus        20 P~~f~CPI~~~lm~d--------------PV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L~   73 (98)
T d1wgma_          20 CDEFLDPIMSTLMCD--------------PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIR   73 (98)
T ss_dssp             CTTTBCTTTCSBCSS--------------EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSE
T ss_pred             cHHhCCcCchhHHHH--------------HHhcccccchhhHHHHHHHHHhcCCcccccccccchhhc
Confidence            347899999999977              8899965 5899999999999999999999999988874

>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=98.48  E-value=1.5e-08  Score=71.91  Aligned_cols=46  Identities=26%  Similarity=0.604  Sum_probs=35.7

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC--------Ccccccc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ--------NSCPMCR  220 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~--------~tCP~CR  220 (230)
                      ....|+||++++..           .+.+..++|+|.||..|+..|++.+        -+||.|+
T Consensus         4 ~~~~C~IC~~~~~~-----------~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           4 GSSGCKLCLGEYPV-----------EQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             SBCCCSSSCCCCBG-----------GGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCCcCccCCCcccC-----------CceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            35689999999865           4445556799999999999999632        2699864

>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=93.14  E-value=0.024  Score=36.75  Aligned_cols=47  Identities=23%  Similarity=0.552  Sum_probs=31.4

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccCC----cccccccCcc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQN----SCPMCRRQIQ  224 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~~----tCP~CR~~i~  224 (230)
                      ....|.||.+.              ++-+.-=.|...||..|+.+.+....    .||.|+..-.
T Consensus         6 ~c~~C~~C~~~--------------~~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   56 (70)
T d1fp0a1           6 SATICRVCQKP--------------GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   56 (70)
T ss_dssp             SSSCCSSSCSS--------------SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             CCCCCCCCCCc--------------CEEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCc
Confidence            45567777642              33233324999999999998875432    5999976443

>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=91.58  E-value=0.031  Score=33.74  Aligned_cols=26  Identities=35%  Similarity=0.818  Sum_probs=20.7

Q ss_pred             CCCCccchhhHHHhhccCC----ccccccc
Q 042810          196 PCHHIFHASCISRWLEEQN----SCPMCRR  221 (230)
Q Consensus       196 pC~H~FH~~CI~~Wl~~~~----tCP~CR~  221 (230)
                      .|...||..|+++-+....    .||.||.
T Consensus        20 ~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_          20 ECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             TTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            3999999999998765432    5999975

>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=91.42  E-value=0.025  Score=35.91  Aligned_cols=49  Identities=29%  Similarity=0.602  Sum_probs=32.6

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEe-CCCCccchhhHHHhh---c--cCCcccccccCc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITM-PCHHIFHASCISRWL---E--EQNSCPMCRRQI  223 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~Wl---~--~~~tCP~CR~~i  223 (230)
                      ....|.+|.....+           +...+.= .|+..||..|+..=.   .  .+-.||.|+..-
T Consensus         5 ~~~~C~~C~~~~~~-----------~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~~   59 (64)
T d1we9a_           5 SSGQCGACGESYAA-----------DEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKS   59 (64)
T ss_dssp             SCCCCSSSCCCCCS-----------SSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTTT
T ss_pred             CCCcCcCcCCCCCC-----------CCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCcC
Confidence            35689999886544           4444433 499999999995321   1  233799997643

>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=91.18  E-value=0.039  Score=34.69  Aligned_cols=47  Identities=26%  Similarity=0.504  Sum_probs=32.2

Q ss_pred             cCCCccccCchhhhhhhhhhccccccCceeEEeCCCCccchhhHHHhhccC----CcccccccCc
Q 042810          163 KAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMPCHHIFHASCISRWLEEQ----NSCPMCRRQI  223 (230)
Q Consensus       163 ~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~Wl~~~----~tCP~CR~~i  223 (230)
                      ..++.|.+|.+.              ++-+.-=.|.-.||..|+...+...    =.||.|+..-
T Consensus         7 ~~~~~C~~C~~~--------------g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           7 HHMEFCRVCKDG--------------GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC--------------SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCcCCCcCCCCC--------------CeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            446679999752              3333333499999999998766532    2699997654

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.52  E-value=0.042  Score=36.81  Aligned_cols=35  Identities=34%  Similarity=0.777  Sum_probs=25.3

Q ss_pred             hcccCCCccccCchhhhhhhhhhccccccCceeEEeC---CCCccchhhHHHh
Q 042810          160 KLVKAGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP---CHHIFHASCISRW  209 (230)
Q Consensus       160 ~~~~~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp---C~H~FH~~CI~~W  209 (230)
                      +....|..|.|| +.+..            +  .++|   |+-+||..|+++.
T Consensus        10 e~v~~D~mC~vC-~v~t~------------~--~l~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          10 EPVVNDEMCDVC-EVWTA------------E--SLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCCCSCCCTTT-CCCCS------------S--CCSSCSSSSSCCCHHHHHHH
T ss_pred             cCCCcCcccccc-Ccccc------------c--ceecceeecchhhHHHHHHh
Confidence            345568899999 55533            1  1235   8999999999987

>d2epqa1 g.37.1.1 (A:380-411) PATZ1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: PATZ1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.23  E-value=0.047  Score=29.14  Aligned_cols=13  Identities=31%  Similarity=0.744  Sum_probs=10.5

Q ss_pred             CCcccccccccee
Q 042810           18 NPLMCPVGNIGIV   30 (230)
Q Consensus        18 ~~~~~~~~~~~~~   30 (230)
                      .||.||||+--|-
T Consensus         2 kp~~cpic~qrfk   14 (32)
T d2epqa1           2 KPYSCPVCGLRFK   14 (32)
T ss_dssp             CSSEETTTTEECS
T ss_pred             CCcccchHHHHhh
Confidence            6999999986553

>d1srka_ g.37.1.1 (A:) Zinc finger protein ZFPM1 (FOG-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Zinc finger protein ZFPM1 (FOG-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.01  E-value=0.094  Score=29.33  Aligned_cols=24  Identities=25%  Similarity=0.602  Sum_probs=18.4

Q ss_pred             eccCCCCccccccccceeeeeecc
Q 042810           13 GSCSNNPLMCPVGNIGIVLKQRCQ   36 (230)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~~~   36 (230)
                      |+....||.|++|.+.|...-..+
T Consensus         1 g~TGekPy~C~~C~k~F~~~~~L~   24 (35)
T d1srka_           1 GSSGKRPFVCRICLSAFTTKANCA   24 (35)
T ss_dssp             CCSCCSCEECSSSCCEESSHHHHH
T ss_pred             CCCCCccccCCCCCCcccChHHHH
Confidence            455678999999999997654443

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=86.44  E-value=0.064  Score=35.35  Aligned_cols=45  Identities=29%  Similarity=0.569  Sum_probs=27.8

Q ss_pred             CccccCchhhhhhhhhhccccccCceeEEeC---CCCccchhhHHH----hhc-----cCCcccccccCc
Q 042810          166 DNCAVCLEELIAKEEIKGQTTEKKTQLITMP---CHHIFHASCISR----WLE-----EQNSCPMCRRQI  223 (230)
Q Consensus       166 ~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp---C~H~FH~~CI~~----Wl~-----~~~tCP~CR~~i  223 (230)
                      ..| ||......           +. .+...   |...||..|+.-    +-.     .+-.||.|+..-
T Consensus        17 ~~C-~C~~~~~~-----------~~-~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~   73 (78)
T d1wewa_          17 VRC-VCGNSLET-----------DS-MIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS   73 (78)
T ss_dssp             CCC-SSCCCCCC-----------SC-EEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCC
T ss_pred             cEe-ECCCccCC-----------Cc-EEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcC
Confidence            456 99876533           33 34553   999999999831    100     124699997643

>d2adra1 g.37.1.1 (A:102-130) ADR1 {Synthetic, based on Saccharomyces cerevisiae sequence}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: ADR1
species: Synthetic, based on Saccharomyces cerevisiae sequence

Probab=85.63  E-value=0.12  Score=27.56  Aligned_cols=14  Identities=14%  Similarity=0.339  Sum_probs=12.0

Q ss_pred             CCccccccccceee
Q 042810           18 NPLMCPVGNIGIVL   31 (230)
Q Consensus        18 ~~~~~~~~~~~~~~   31 (230)
                      .||+|++|.+.|--
T Consensus         1 kp~~C~~C~k~F~~   14 (29)
T d2adra1           1 RSFVCEVCTRAFAR   14 (29)
T ss_dssp             CCBCCTTTCCCBSC
T ss_pred             CcCCCCCCCCCCCC
Confidence            49999999999854

>d2dlqa4 g.37.1.1 (A:8-34) GLI-Krueppel family member HKR3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: GLI-Krueppel family member HKR3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=85.33  E-value=0.031  Score=28.64  Aligned_cols=20  Identities=25%  Similarity=0.306  Sum_probs=15.0

Q ss_pred             cccccccceeeeeecccccc
Q 042810           21 MCPVGNIGIVLKQRCQKVNR   40 (230)
Q Consensus        21 ~~~~~~~~~~~~~~~~~~~~   40 (230)
                      .||.||+.|.-+-+....||
T Consensus         2 qcp~c~k~f~skyylkvhnr   21 (27)
T d2dlqa4           2 ECPTCHKKFLSKYYLKVHNR   21 (27)
T ss_dssp             CCTTTCCCCSSHHHHHHHHH
T ss_pred             cCcchHHHHHHhHhhhhccc
Confidence            59999999987766555444

>d1a1ia2 g.37.1.1 (A:132-159) ZIF268 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: ZIF268
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.58  E-value=0.17  Score=26.72  Aligned_cols=14  Identities=14%  Similarity=0.351  Sum_probs=12.3

Q ss_pred             CCccccccccceee
Q 042810           18 NPLMCPVGNIGIVL   31 (230)
Q Consensus        18 ~~~~~~~~~~~~~~   31 (230)
                      .||.|++|.+.|--
T Consensus         2 KPy~C~~C~k~F~~   15 (28)
T d1a1ia2           2 KPFQCRICMRNFSR   15 (28)
T ss_dssp             CCEECTTTCCEESC
T ss_pred             cCccCCCCcCEecc
Confidence            59999999999964

>d1z60a1 g.49.1.2 (A:328-386) TFIIH p44 subunit cysteine-rich domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: TFIIH p44 subunit cysteine-rich domain
domain: TFIIH p44 subunit cysteine-rich domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.10  E-value=0.17  Score=31.50  Aligned_cols=44  Identities=25%  Similarity=0.549  Sum_probs=31.4

Q ss_pred             CCCccccCchhhhhhhhhhccccccCceeEEeC-CCCccchhhHHHhhccCCccccc
Q 042810          164 AGDNCAVCLEELIAKEEIKGQTTEKKTQLITMP-CHHIFHASCISRWLEEQNSCPMC  219 (230)
Q Consensus       164 ~~~~C~ICle~~~~~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~Wl~~~~tCP~C  219 (230)
                      ....|--|...+.+            .....-| |++.|+.+|=----+.-.+||.|
T Consensus        14 ~~~~C~gC~~~l~~------------~~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKD------------QHVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTT------------SEEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCCccCCCCcCCC------------CceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            45679999887754            2234445 99999999955444556789988

>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=81.60  E-value=0.12  Score=34.57  Aligned_cols=49  Identities=31%  Similarity=0.719  Sum_probs=30.8

Q ss_pred             CCccccCchhhhhhhhhhccccccCceeEEe-CCCCccchhhHHHhhcc--------CCcccccccCc
Q 042810          165 GDNCAVCLEELIAKEEIKGQTTEKKTQLITM-PCHHIFHASCISRWLEE--------QNSCPMCRRQI  223 (230)
Q Consensus       165 ~~~C~ICle~~~~~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~Wl~~--------~~tCP~CR~~i  223 (230)
                      ...|.||.......          ...++.= -|...||..|+.+.+..        .-.||.|....
T Consensus        16 ~~~C~iC~~~~~~~----------~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~   73 (88)
T d1weva_          16 GLACVVCRQMTVAS----------GNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQM   73 (88)
T ss_dssp             CCSCSSSCCCCCCT----------TCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHH
T ss_pred             cCCccCCCCccCCC----------CCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchH
Confidence            56799997643220          2223333 39999999998865421        22599997543

>d1sp1a_ g.37.1.1 (A:) Transcription factor sp1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Transcription factor sp1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.81  E-value=0.23  Score=26.44  Aligned_cols=15  Identities=13%  Similarity=0.295  Sum_probs=12.6

Q ss_pred             CCccccccccceeee
Q 042810           18 NPLMCPVGNIGIVLK   32 (230)
Q Consensus        18 ~~~~~~~~~~~~~~~   32 (230)
                      .||+|++|.+.|.-.
T Consensus         1 Kpy~C~~C~k~F~~~   15 (29)
T d1sp1a_           1 KKFACPECPKRFMRS   15 (29)
T ss_dssp             CCSCCTTTTCCCSCS
T ss_pred             CCEECCcCCCeecch
Confidence            489999999999643