Citrus Sinensis ID: 042112

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130--
Protein Sequence
MFGYLIRFLRCLKWACNLLLHFSFFGHRINASEQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGHGEEVLVLKFRCFNSRTERDTWWLR
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHcccccccccccccccccEEEccccccccEEEEEccccccccccHHHHHcccccccccccccccccccccccccccEEEEcccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHHHHHcHccccccccHHHHcccccccccccccccccEEEEEHHHccccccEEEccccccHcHHHHHHHHHHcccccccccccccccHcccccccEEEEEEEEEEccccccccEEcc
Coil and Loop (DISEMBL)
MFGYLIRFLRCLKWACNLLLHFSFFGHRINASEQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDtwisnnyaicpvchdsiapsrwltghgeEVLVLKFRCfnsrterdtwwlr
Flexible Loop (DISEMBL)
MFGYLIRFLRCLKWACNLLLHFSFFGHRINASEQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGHGEEVLVLKfrcfnsrterdtwwlr
Low Complexity Region (SEG)
MFGYLIRFLRCLKWACNLLLHFSFFGHRINASEQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGHGEEVLVLKFRCFNSRTERDTWWLR
Disordered region (IsUnstruct)
*FGYLIRFLRCLKWACNLLLHFSFFGHRINASEQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGHGEEVLVLKFRCFNSRTERDTWW**
Disordered Region (DISOPRED)
MFGYLIRFLRCLKWACNLLLH****************************EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDS*******************************WL*
Disordered Region (DISEMBL)
MFGYLIRFLRCLKWACNLLLHFSFFGHRINASEQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGHGEEVLVLKFRCFNSRTERDTWWLR
Disordered Region (DISPRO)
MFGYLIRFLRCLKWACNLLLHFSFFGHRINASEQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGHGEEVLVLKFRCFNSRTERD*WWL*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MFGYLIRFLRCLKWACNLLLHFSFFGHRINASEQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGHGEEVLVLKFRCFNSRTERDTWWLR
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	132	2.2.26 [Sep-21-2011]
Q0V9R0	954	E3 ubiquitin-protein liga	yes	no	0.348	0.048	0.510	7e-10
Q5R476	986	E3 ubiquitin-protein liga	yes	no	0.348	0.046	0.510	7e-10
Q99ML9	989	E3 ubiquitin-protein liga	yes	no	0.348	0.046	0.510	7e-10
Q6ZNA4	994	E3 ubiquitin-protein liga	yes	no	0.348	0.046	0.510	7e-10
Q66J97	967	E3 ubiquitin-protein liga	N/A	no	0.348	0.047	0.510	7e-10
Q6NRV8	959	E3 ubiquitin-protein liga	N/A	no	0.348	0.047	0.510	7e-10
Q90ZT7	923	E3 ubiquitin-protein liga	N/A	no	0.348	0.049	0.510	7e-10
Q90972	381	E3 ubiquitin-protein liga	no	no	0.522	0.181	0.338	6e-09
Q8L9W3	163	E3 ubiquitin-protein liga	yes	no	0.439	0.355	0.483	6e-09
Q0VD51	380	E3 ubiquitin-protein liga	no	no	0.522	0.181	0.338	6e-09

>sp|Q0V9R0|RN111_XENTR E3 ubiquitin-protein ligase arkadia OS=Xenopus tropicalis GN=rnf111 PE=2 SV=1

 Score = 62.4 bits (150), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 24/47 (51%), Positives = 32/47 (68%), Gaps = 1/47 (2%)

Query: 53  ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99
           +C +CLS +EEGE++R L C HLFH VC+D W+  N   CP+C   I
Sbjct: 901 KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKK-CPICRVDI 946

Acts in the nodal-related pathway of mesoderm patterning during embryonic development. Enhances signaling of the subset of TGF-beta factors responsible for the formation of dorso-anterior tissues of Spemann's organizer. May act as an E3 ubiquitin-protein ligase, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates.
Xenopus tropicalis (taxid: 8364)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|Q5R476|RN111_PONAB E3 ubiquitin-protein ligase Arkadia OS=Pongo abelii GN=RNF111 PE=2 SV=1

 Score = 62.4 bits (150), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 24/47 (51%), Positives = 32/47 (68%), Gaps = 1/47 (2%)

Query: 53  ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99
           +C +CLS +EEGE++R L C HLFH VC+D W+  N   CP+C   I
Sbjct: 933 KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKK-CPICRVDI 978

Acts in the NODAL pathway of mesoderm patterning during embryonic development. Acts downstream AXIN1 as an E3 ubiquitin-protein ligase which promotes the ubiquitination of inhibitory SMADs such as SMAD7, induces their proteasomal degradation and thereby enhances the transcriptional activity of TGF-beta and BMP. Activates Smad3/Smad4-dependent transcription by triggering signal-induced SnoN degradation.

Pongo abelii (taxid: 9601)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q99ML9|RN111_MOUSE E3 ubiquitin-protein ligase Arkadia OS=Mus musculus GN=Rnf111 PE=1 SV=1

 Score = 62.4 bits (150), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 24/47 (51%), Positives = 32/47 (68%), Gaps = 1/47 (2%)

Query: 53  ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99
           +C +CLS +EEGE++R L C HLFH VC+D W+  N   CP+C   I
Sbjct: 936 KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKK-CPICRVDI 981

Acts in the Nodal pathway of mesoderm patterning during embryonic development. Acts downstream AXIN1 as an E3 ubiquitin-protein ligase which promotes the ubiquitination of inhibitory SMADs such as SMAD7, induces their proteasomal degradation and thereby enhances the transcriptional activity of TGF-beta and BMP. Activates Smad3/Smad4-dependent transcription by triggering signal-induced SnoN degradation.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q6ZNA4|RN111_HUMAN E3 ubiquitin-protein ligase Arkadia OS=Homo sapiens GN=RNF111 PE=1 SV=3

 Score = 62.4 bits (150), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 24/47 (51%), Positives = 32/47 (68%), Gaps = 1/47 (2%)

Query: 53  ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99
           +C +CLS +EEGE++R L C HLFH VC+D W+  N   CP+C   I
Sbjct: 941 KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKK-CPICRVDI 986

Acts in the NODAL pathway of mesoderm patterning during embryonic development. Acts downstream AXIN1 as an E3 ubiquitin-protein ligase which promotes the ubiquitination of inhibitory SMADs such as SMAD7, induces their proteasomal degradation and thereby enhances the transcriptional activity of TGF-beta and BMP. Activates Smad3/Smad4-dependent transcription by triggering signal-induced SnoN degradation.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q66J97|R111C_XENLA E3 ubiquitin-protein ligase arkadia-C OS=Xenopus laevis GN=rnf111-c PE=2 SV=1

 Score = 62.4 bits (150), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 24/47 (51%), Positives = 32/47 (68%), Gaps = 1/47 (2%)

Query: 53  ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99
           +C +CLS +EEGE++R L C HLFH VC+D W+  N   CP+C   I
Sbjct: 914 KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKK-CPICRVDI 959

Acts in the nodal-related pathway of mesoderm patterning during embryonic development. Enhances signaling of the subset of TGF-beta factors responsible for the formation of dorso-anterior tissues of Spemann's organizer. May act as an E3 ubiquitin-protein ligase, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates.

Xenopus laevis (taxid: 8355)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q6NRV8|R111B_XENLA E3 ubiquitin-protein ligase arkadia-B OS=Xenopus laevis GN=rnf111-b PE=2 SV=1

 Score = 62.4 bits (150), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 24/47 (51%), Positives = 32/47 (68%), Gaps = 1/47 (2%)

Query: 53  ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99
           +C +CLS +EEGE++R L C HLFH VC+D W+  N   CP+C   I
Sbjct: 906 KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKK-CPICRVDI 951

Acts in the nodal-related pathway of mesoderm patterning during embryonic development. Enhances signaling of the subset of TGF-beta factors responsible for the formation of dorso-anterior tissues of Spemann's organizer. May act as an E3 ubiquitin-protein ligase, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates.

Xenopus laevis (taxid: 8355)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q90ZT7|R111A_XENLA E3 ubiquitin-protein ligase arkadia-A (Fragment) OS=Xenopus laevis GN=rnf111-a PE=2 SV=1

 Score = 62.4 bits (150), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 24/47 (51%), Positives = 32/47 (68%), Gaps = 1/47 (2%)

Query: 53  ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99
           +C +CLS +EEGE++R L C HLFH VC+D W+  N   CP+C   I
Sbjct: 870 KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKK-CPICRVDI 915

Acts in the nodal-related pathway of mesoderm patterning during embryonic development. Enhances signaling of the subset of TGF-beta factors responsible for the formation of dorso-anterior tissues of Spemann's organizer. May act as an E3 ubiquitin-protein ligase, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates.

Xenopus laevis (taxid: 8355)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q90972|RNF13_CHICK E3 ubiquitin-protein ligase RNF13 OS=Gallus gallus GN=RNF13 PE=1 SV=1

 Score = 59.7 bits (143), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 33  EQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAIC 92
           +QL  +   +F+ G   +   CA+CL   E+G+++R L C H +H  C+D W++     C
Sbjct: 221 DQLKKLPVHKFKKGDEYDV--CAICLDEYEDGDKLRILPCSHAYHCKCVDPWLTKTKKTC 278

Query: 93  PVCHDSIAPSR 103
           PVC   + PS+
Sbjct: 279 PVCKQKVVPSQ 289

E3 ubiquitin-protein ligase. May play a role in controlling cell proliferation, including that of muscle cells.

Gallus gallus (taxid: 9031)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q8L9W3|ATL23_ARATH E3 ubiquitin-protein ligase ATL23 OS=Arabidopsis thaliana GN=ATL23 PE=1 SV=2

 Score = 59.3 bits (142), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 29/60 (48%), Positives = 39/60 (65%), Gaps = 2/60 (3%)

Query: 44  ELGSRAEAVECAVCLSHIEEGEEIRELS-CHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102
           EL   A + ECAVCL  IE G+  R +  C+H FH +C DTW+S N+ +CPVC   +AP+
Sbjct: 94  ELAVIARSTECAVCLEDIESGQSTRLVPGCNHGFHQLCADTWLS-NHTVCPVCRAELAPN 152

E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8, UBC10, UBC11, UBC28 and UBC29 in vitro.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q0VD51|RNF13_BOVIN E3 ubiquitin-protein ligase RNF13 OS=Bos taurus GN=RNF13 PE=2 SV=1

 Score = 59.3 bits (142), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 33  EQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAIC 92
           +QL  +   +F+ G   +   CA+CL   E+G+++R L C H +H  C+D W++     C
Sbjct: 221 DQLKKLPVHKFKKGDEYDV--CAICLDEYEDGDKLRILPCSHAYHCKCVDPWLTKTKKTC 278

Query: 93  PVCHDSIAPSR 103
           PVC   + PS+
Sbjct: 279 PVCKQKVVPSQ 289

E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation.

Bos taurus (taxid: 9913)

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	132
359473022	172	PREDICTED: RING-H2 finger protein ATL47-	0.984	0.755	0.474	8e-22
147860139	322	hypothetical protein VITISV_039591 [Viti	0.992	0.406	0.433	8e-22
297737915	173	unnamed protein product [Vitis vinifera]	0.984	0.751	0.456	6e-21
255546935	137	conserved hypothetical protein [Ricinus	0.969	0.934	0.425	2e-20
297737919	174	unnamed protein product [Vitis vinifera]	0.984	0.747	0.420	5e-20
388507916	140	unknown [Lotus japonicus]	0.992	0.935	0.392	3e-19
297737917	104	unnamed protein product [Vitis vinifera]	0.780	0.990	0.471	4e-19
224108589	133	predicted protein [Populus trichocarpa]	0.886	0.879	0.48	7e-19
388514843	136	unknown [Medicago truncatula]	0.992	0.963	0.378	9e-19
118486923	133	unknown [Populus trichocarpa]	0.886	0.879	0.472	1e-18

>gi|359473022|ref|XP_003631232.1| PREDICTED: RING-H2 finger protein ATL47-like [Vitis vinifera] gi|297737916|emb|CBI27117.3| unnamed protein product [Vitis vinifera]

 Score =  108 bits (270), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 65/137 (47%), Positives = 79/137 (57%), Gaps = 7/137 (5%)

Query: 1   MFGYLIRFLRCLKWACNLLLHFSFF--GHRINASE---QLVNIWEDRFELGSRAEAVECA 55
           M  Y+      L WA + LLH+S F   H+IN  E   Q +NI     E GS  E VECA
Sbjct: 38  MSNYITPTASHLAWAWDFLLHYSLFPNSHKINVHENFDQGLNIGLYEPEEGSN-EVVECA 96

Query: 56  VCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGHGEEVLVL 115
           VCL  IEEGEE+REL C H+FH  CLD W+ +    CP+C    APSR +   GEEV+V+
Sbjct: 97  VCLCKIEEGEEVRELRCGHMFHRDCLDRWLGHRNGTCPLCRSCTAPSRMVNEVGEEVIVV 156

Query: 116 KFRCFNSRTERDTWWLR 132
           KF   +S   R  WWLR
Sbjct: 157 KFSS-SSPGNRSMWWLR 172

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147860139|emb|CAN82925.1| hypothetical protein VITISV_039591 [Vitis vinifera]

 Score =  108 bits (270), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 59/136 (43%), Positives = 81/136 (59%), Gaps = 5/136 (3%)

Query: 1   MFGYLIRFLRCLKWACNLLLH-FSFFGHRINA---SEQLVNIWEDRFELGSRAEAVECAV 56
           M  Y++  +   KWA + L H FSF  + +      E+ + I   + +LGS     ECAV
Sbjct: 188 MVNYIVLPITHFKWAWSFLFHRFSFASYTLGMLENGEEELRIGHYKVKLGSEESEEECAV 247

Query: 57  CLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGHGEEVLVLK 116
           CL  IEEG+EI +L C HLFH VCLD W+    + CP+C DS+AP R +   G+EVLV +
Sbjct: 248 CLCKIEEGDEISDLRCDHLFHKVCLDRWVQYKRSTCPLCRDSLAPCRAVAELGQEVLVFR 307

Query: 117 FRCFNSRTERDTWWLR 132
           F C  S  +R++WWLR
Sbjct: 308 F-CSFSSGDRNSWWLR 322

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297737915|emb|CBI27116.3| unnamed protein product [Vitis vinifera]

 Score =  105 bits (262), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 63/138 (45%), Positives = 79/138 (57%), Gaps = 8/138 (5%)

Query: 1   MFGYLIRFLRCLKWACNLLLHFSFF---GHRINAS---EQLVNIWEDRFELGSRAEAVEC 54
           M  Y+I     L WA + LLH S F    H +N     +Q + +   R ELGS  E  EC
Sbjct: 38  MSNYIIPTAAHLTWAWDFLLHHSLFLNSHHNMNVPKNGDQGLGLGLYRPELGSN-EVAEC 96

Query: 55  AVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGHGEEVLV 114
           AVCL  IEEGEEIREL C H+FH  CLD W+ +    CP+C   +AP R +   GEEV+V
Sbjct: 97  AVCLCKIEEGEEIRELRCDHMFHRDCLDRWVGHRNGTCPLCRGCLAPPRMVNEVGEEVIV 156

Query: 115 LKFRCFNSRTERDTWWLR 132
            ++  F+S T R  WWLR
Sbjct: 157 FRYCSFSSST-RSMWWLR 173

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255546935|ref|XP_002514525.1| conserved hypothetical protein [Ricinus communis] gi|223546129|gb|EEF47631.1| conserved hypothetical protein [Ricinus communis]

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 60/141 (42%), Positives = 78/141 (55%), Gaps = 13/141 (9%)

Query: 1   MFGYLIRFLRCLKWACNLLLHFSFF--------GHRINASEQLVNIWEDRFELGSRAEAV 52
           M  YL         A ++LL   FF        G +IN  +Q  +I+  +      +EA 
Sbjct: 1   MLKYLNLIATHFMRALDILLQILFFQNYQLDLPGSKINGEDQ-PSIYHHK---AGESEAT 56

Query: 53  ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWI-SNNYAICPVCHDSIAPSRWLTGHGEE 111
           ECAVCL+ IEEGEEIRE  C+H+FH VCLD W+ S  +  CP+C DS+ P R +T  G +
Sbjct: 57  ECAVCLTKIEEGEEIREPRCNHIFHRVCLDRWMCSYGHTSCPLCRDSLVPRRAITDLGHQ 116

Query: 112 VLVLKFRCFNSRTERDTWWLR 132
           VLV KF    +   RD WWLR
Sbjct: 117 VLVFKFSFTTADDGRDKWWLR 137

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297737919|emb|CBI27120.3| unnamed protein product [Vitis vinifera]

 Score =  102 bits (254), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 58/138 (42%), Positives = 81/138 (58%), Gaps = 8/138 (5%)

Query: 1   MFGYLIRFLRCLKWACNLLLHFSFFGHR------INASEQLVNIWEDRFELGSRAEAVEC 54
           +F Y+I     L  A + LLH+S F +       +   +  +++   + + GS+ E VEC
Sbjct: 39  LFNYIIPTAAHLSRAWDFLLHYSLFPNSHHNMSVLENGDPGLSLGLYKPKPGSK-EVVEC 97

Query: 55  AVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGHGEEVLV 114
           AVCL  IEEGEEIREL C H+FH  CLD W+ +    CP+C   +AP R +   GEEV+V
Sbjct: 98  AVCLCTIEEGEEIRELRCGHMFHRDCLDRWVGHRNGTCPLCRGCLAPPRMVNDVGEEVIV 157

Query: 115 LKFRCFNSRTERDTWWLR 132
            ++  F+SRT R  WWLR
Sbjct: 158 FRYCSFSSRT-RSMWWLR 174

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388507916|gb|AFK42024.1| unknown [Lotus japonicus]

 Score = 99.8 bits (247), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 55/140 (39%), Positives = 73/140 (52%), Gaps = 9/140 (6%)

Query: 1   MFGYLIRFLRCLKWACNLLLHFSFFG-----HRINASEQ---LVNIWEDRFELGSRAEAV 52
           +  YL      LKW  + LL++ F+        I   EQ   +   +E    +GS  E +
Sbjct: 2   LMKYLTLLYTHLKWVFDFLLYYPFYTLHGSQFPIIGEEQEQGMCQFYEPNL-IGSEEEEI 60

Query: 53  ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGHGEEV 112
           +CAVCLS IE GEEIR L C H FH  CLDTW       CP+C  S+ P R +   G +V
Sbjct: 61  DCAVCLSKIEGGEEIRVLRCDHFFHRDCLDTWFGFKNPTCPLCRGSMGPRRAINEVGAQV 120

Query: 113 LVLKFRCFNSRTERDTWWLR 132
           L+ +F    +  +RDTWWLR
Sbjct: 121 LLFEFCATRTHDDRDTWWLR 140

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297737917|emb|CBI27118.3| unnamed protein product [Vitis vinifera]

 Score = 99.4 bits (246), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 49/104 (47%), Positives = 66/104 (63%), Gaps = 1/104 (0%)

Query: 29  INASEQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN 88
           +   E+ + I   + +LGS     ECAVCL  IEEG+EI +L C HLFH VCLD W+   
Sbjct: 2   LENGEEELRIGHYKVKLGSEESEEECAVCLCKIEEGDEISDLRCDHLFHKVCLDRWVQYK 61

Query: 89  YAICPVCHDSIAPSRWLTGHGEEVLVLKFRCFNSRTERDTWWLR 132
            + CP+C DS+AP R +   G+EVLV +F C  S  +R++WWLR
Sbjct: 62  RSTCPLCRDSLAPCRAVAELGQEVLVFRF-CSFSSGDRNSWWLR 104

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224108589|ref|XP_002314901.1| predicted protein [Populus trichocarpa] gi|222863941|gb|EEF01072.1| predicted protein [Populus trichocarpa]

 Score = 98.6 bits (244), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 60/125 (48%), Positives = 74/125 (59%), Gaps = 8/125 (6%)

Query: 12  LKWACNLLLH--FSFFGHRINASEQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRE 69
           L+WA N L +  FSF  H + A   +  I E+   + + A A ECAVCLS ++EGEEIRE
Sbjct: 13  LRWAFNFLCYYPFSFQEHELFA---VTAIGEELNTVINEAPA-ECAVCLSDVQEGEEIRE 68

Query: 70  LSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT--GHGEEVLVLKFRCFNSRTERD 127
           L C H+FH  CL  W+    + CP+C  S+AP R L    H  EVL  KF  F S  ERD
Sbjct: 69  LRCGHIFHRACLYRWLDFRQSTCPLCRGSLAPRRTLILDQHRTEVLTFKFCSFTSTDERD 128

Query: 128 TWWLR 132
           TWWLR
Sbjct: 129 TWWLR 133

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388514843|gb|AFK45483.1| unknown [Medicago truncatula]

 Score = 98.2 bits (243), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 50/132 (37%), Positives = 71/132 (53%), Gaps = 1/132 (0%)

Query: 1   MFGYLIRFLRCLKWACNLLLHFSFFGHRINASEQLVNIWEDRFELGSRAEAVECAVCLSH 60
           +  YL  F   LKW  ++  ++ F+    +++  ++    D +      E VEC VCL  
Sbjct: 6   IMNYLTIFYTHLKWVLDIPTYYPFYKLH-DSNFPIIGEMYDIYNYEHTNEDVECVVCLCK 64

Query: 61  IEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGHGEEVLVLKFRCF 120
           IEEG+EI  L C H++H  CLD W+S     CP+C +S+ P R +T HG EVL   F   
Sbjct: 65  IEEGDEISVLRCDHMYHKHCLDKWLSFKNHTCPLCRESLRPERAITEHGVEVLSFDFCAI 124

Query: 121 NSRTERDTWWLR 132
            S  +RD WWLR
Sbjct: 125 RSDRDRDDWWLR 136

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118486923|gb|ABK95295.1| unknown [Populus trichocarpa]

 Score = 97.8 bits (242), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 59/125 (47%), Positives = 73/125 (58%), Gaps = 8/125 (6%)

Query: 12  LKWACNLLLH--FSFFGHRINASEQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRE 69
           L+WA N L +  FSF  H + A   +  I E+   + + A A ECAVCLS ++EGEEIRE
Sbjct: 13  LRWAFNFLCYYPFSFQEHELFA---VTAIGEELNTVINEAPA-ECAVCLSDVQEGEEIRE 68

Query: 70  LSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT--GHGEEVLVLKFRCFNSRTERD 127
           L C H+FH  CL  W+    + CP+C  S+ P R L    H  EVL  KF  F S  ERD
Sbjct: 69  LRCGHIFHRACLYRWLDFRQSTCPLCRGSLTPRRTLILDQHQTEVLTFKFCSFTSTDERD 128

Query: 128 TWWLR 132
           TWWLR
Sbjct: 129 TWWLR 133

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	132
TAIR|locus:2165735	163	AT5G42200 [Arabidopsis thalian	0.439	0.355	0.483	8.2e-12
TAIR|locus:4515102735	133	AT1G67856 [Arabidopsis thalian	0.378	0.375	0.528	2.2e-11
TAIR|locus:1006230720	113	AT1G24580 [Arabidopsis thalian	0.530	0.619	0.424	2.8e-11
TAIR|locus:2038766	147	RHA2B "RING-H2 finger protein	0.5	0.448	0.388	2.8e-11
TAIR|locus:2034210	407	AT1G80400 [Arabidopsis thalian	0.393	0.127	0.396	7.3e-11
TAIR|locus:2053791	236	AT2G42360 [Arabidopsis thalian	0.416	0.233	0.473	7.4e-11
UNIPROTKB|C9IY58	232	RNF13 "E3 ubiquitin-protein li	0.522	0.297	0.338	1.2e-10
UNIPROTKB|C9JCY0	233	RNF13 "E3 ubiquitin-protein li	0.522	0.296	0.338	1.2e-10
UNIPROTKB|B3KR12	262	RNF13 "cDNA FLJ33452 fis, clon	0.522	0.263	0.338	2.2e-10
UNIPROTKB|F1NUJ3	272	RNF13 "E3 ubiquitin-protein li	0.522	0.253	0.338	2.5e-10

TAIR|locus:2165735 AT5G42200 [Arabidopsis thaliana (taxid:3702)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 29/60 (48%), Positives = 39/60 (65%)

Query:    44 ELGSRAEAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102
             EL   A + ECAVCL  IE G+  R +  C+H FH +C DTW+SN + +CPVC   +AP+
Sbjct:    94 ELAVIARSTECAVCLEDIESGQSTRLVPGCNHGFHQLCADTWLSN-HTVCPVCRAELAPN 152

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

TAIR|locus:4515102735 AT1G67856 [Arabidopsis thaliana (taxid:3702)]

 Score = 156 (60.0 bits), Expect = 2.2e-11, P = 2.2e-11
 Identities = 28/53 (52%), Positives = 35/53 (66%)

Query:    46 GSR--AEAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVC 95
             GSR   EA++C VCL   +E EE+ EL SC H FH+ CLD W  NN+  CP+C
Sbjct:    77 GSRNEREAMDCCVCLCGFKEEEEVSELVSCKHYFHSACLDKWFGNNHTTCPLC 129

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:1006230720 AT1G24580 [Arabidopsis thaliana (taxid:3702)]

 Score = 155 (59.6 bits), Expect = 2.8e-11, P = 2.8e-11
 Identities = 31/73 (42%), Positives = 41/73 (56%)

Query:    24 FFGHRINASEQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLD 82
             F   RI+ + Q  ++ E+  E     + VEC VCL   +E EE+ EL SC H FH  CLD
Sbjct:    39 FVTRRISIT-QFKSLCEN-IEEEEEEKGVECCVCLCGFKEEEEVSELVSCKHFFHRACLD 96

Query:    83 TWISNNYAICPVC 95
              W  NN+  CP+C
Sbjct:    97 NWFGNNHTTCPLC 109

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2038766 RHA2B "RING-H2 finger protein 2B" [Arabidopsis thaliana (taxid:3702)]

 Score = 155 (59.6 bits), Expect = 2.8e-11, P = 2.8e-11
 Identities = 26/67 (38%), Positives = 39/67 (58%)

Query:    51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGHGE 110
             A +C VCLS ++ GEE+R+L C H+FH  CL+ W+ +    CP+C   + P     GHG 
Sbjct:    71 ASDCIVCLSKLKTGEEVRKLDCRHVFHKQCLEGWLQHLNFNCPLCRSPLLPHHH-QGHGS 129

Query:   111 EVLVLKF 117
             +  +  F
Sbjct:   130 DASISAF 136

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

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

GO:0080167 "response to karrikin" evidence=IEP

TAIR|locus:2034210 AT1G80400 [Arabidopsis thaliana (taxid:3702)]

 Score = 135 (52.6 bits), Expect = 7.3e-11, Sum P(2) = 7.3e-11
 Identities = 21/53 (39%), Positives = 32/53 (60%)

Query:    50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102
             E   C +CL+   + E++REL C H+FH  C+D W+  N A CP+C + +  S
Sbjct:   351 EDASCCICLTRYGDDEQVRELPCSHVFHVDCVDKWLKIN-ATCPLCKNEVGES 402

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2053791 AT2G42360 [Arabidopsis thaliana (taxid:3702)]

 Score = 151 (58.2 bits), Expect = 7.4e-11, P = 7.4e-11
 Identities = 27/57 (47%), Positives = 38/57 (66%)

Query:    46 GSRAEAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAP 101
             G  A A ECAVCLS ++E ++ REL +C H+FH  C+DTW++   + CPVC   + P
Sbjct:   100 GVAASATECAVCLSVLKEQDKARELPNCKHIFHVDCVDTWLTT-CSTCPVCRTEVEP 155

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

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

GO:0006865 "amino acid transport" evidence=RCA

GO:0010200 "response to chitin" evidence=RCA

GO:0015824 "proline transport" evidence=RCA

GO:0043090 "amino acid import" evidence=RCA

UNIPROTKB|C9IY58 RNF13 "E3 ubiquitin-protein ligase RNF13" [Homo sapiens (taxid:9606)]

 Score = 149 (57.5 bits), Expect = 1.2e-10, P = 1.2e-10
 Identities = 24/71 (33%), Positives = 40/71 (56%)

Query:    33 EQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAIC 92
             +QL  +   +F+ G   +   CA+CL   E+G+++R L C H +H  C+D W++     C
Sbjct:   102 DQLKKLPVHKFKKGDEYDV--CAICLDEYEDGDKLRILPCSHAYHCKCVDPWLTKTKKTC 159

Query:    93 PVCHDSIAPSR 103
             PVC   + PS+
Sbjct:   160 PVCKQKVVPSQ 170

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|C9JCY0 RNF13 "E3 ubiquitin-protein ligase RNF13" [Homo sapiens (taxid:9606)]

 Score = 149 (57.5 bits), Expect = 1.2e-10, P = 1.2e-10
 Identities = 24/71 (33%), Positives = 40/71 (56%)

Query:    33 EQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAIC 92
             +QL  +   +F+ G   +   CA+CL   E+G+++R L C H +H  C+D W++     C
Sbjct:   102 DQLKKLPVHKFKKGDEYDV--CAICLDEYEDGDKLRILPCSHAYHCKCVDPWLTKTKKTC 159

Query:    93 PVCHDSIAPSR 103
             PVC   + PS+
Sbjct:   160 PVCKQKVVPSQ 170

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|B3KR12 RNF13 "cDNA FLJ33452 fis, clone BRAMY2000151, highly similar to RING finger protein 13" [Homo sapiens (taxid:9606)]

 Score = 149 (57.5 bits), Expect = 2.2e-10, P = 2.2e-10
 Identities = 24/71 (33%), Positives = 40/71 (56%)

Query:    33 EQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAIC 92
             +QL  +   +F+ G   +   CA+CL   E+G+++R L C H +H  C+D W++     C
Sbjct:   102 DQLKKLPVHKFKKGDEYDV--CAICLDEYEDGDKLRILPCSHAYHCKCVDPWLTKTKKTC 159

Query:    93 PVCHDSIAPSR 103
             PVC   + PS+
Sbjct:   160 PVCKQKVVPSQ 170

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1NUJ3 RNF13 "E3 ubiquitin-protein ligase RNF13" [Gallus gallus (taxid:9031)]

 Score = 149 (57.5 bits), Expect = 2.5e-10, P = 2.5e-10
 Identities = 24/71 (33%), Positives = 40/71 (56%)

Query:    33 EQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAIC 92
             +QL  +   +F+ G   +   CA+CL   E+G+++R L C H +H  C+D W++     C
Sbjct:   179 DQLKKLPVHKFKKGDEYDV--CAICLDEYEDGDKLRILPCSHAYHCKCVDPWLTKTKKTC 236

Query:    93 PVCHDSIAPSR 103
             PVC   + PS+
Sbjct:   237 PVCKQKVVPSQ 247

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005765 "lysosomal membrane" evidence=IEA

GO:0031902 "late endosome membrane" evidence=IEA

GO:0051865 "protein autoubiquitination" 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

Your Input: eugene3.00101265 hypothetical protein (133 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	132
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	1e-10
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	1e-09
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	6e-07
smart00184	40	smart00184, RING, Ring finger	1e-05
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	4e-04
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	4e-04

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

 Score = 57.3 bits (138), Expect = 1e-10
 Identities = 21/50 (42%), Positives = 30/50 (60%)

Query: 52  VECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAP 101
           VECA+C+S+  + + +R L C H FH  C+D W+      CPVC  +I P
Sbjct: 324 VECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373

Length = 374

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

 Score = 50.1 bits (120), Expect = 1e-09
 Identities = 20/43 (46%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVC 95
          EC +CL   E GEE+  L C H+FH  CLD W+ ++   CP+C
Sbjct: 2  ECPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSN-TCPLC 43

Length = 46

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

 Score = 43.2 bits (102), Expect = 6e-07
 Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99
          EC +CL   E  E +  L C H+F   C+D W+ +    CP+C   I
Sbjct: 1  ECPICLE--EFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 39.4 bits (92), Expect = 1e-05
 Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 2/42 (4%)

Query: 54 CAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVC 95
          C +CL    +  +   L C H F   C+  W+ +    CP+C
Sbjct: 1  CPICLEEYLK--DPVILPCGHTFCRSCIRKWLESGNNTCPIC 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 = 35.5 bits (82), Expect = 4e-04
 Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 2/42 (4%)

Query: 54 CAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVC 95
          C +CL   ++   +  L C HLF + C+ +W+ +    CP+C
Sbjct: 1  CPICLEEPKD--PVTILPCGHLFCSKCILSWLESGNVTCPLC 40

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

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

 Score = 38.5 bits (89), Expect = 4e-04
 Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 5/52 (9%)

Query: 53   ECAVCLSHIEEGEEI----RELSCHHLFHAVCLDTWI-SNNYAICPVCHDSI 99
            ECA+C S ++  +      R  +C + FH  CL  W  S+  + CP+C   I
Sbjct: 1471 ECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522

Length = 1525

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	132
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.77
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.62
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.48
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.4
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.35
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.34
PHA02929	238	N1R/p28-like protein; Provisional	99.33
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.28
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.27
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.22
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.21
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.16
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	99.15
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.13
PHA02926	242	zinc finger-like protein; Provisional	99.12
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.11
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.1
PF14634	44	zf-RING_5: zinc-RING finger domain	99.08
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.01
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	99.0
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	99.0
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.98
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.91
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.9
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.9
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.79
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.71
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.69
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.65
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.59
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.56
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.56
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.51
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.41
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.38
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.36
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.32
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.31
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.27
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.25
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.2
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.19
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.15
KOG0297	391	consensus TNF receptor-associated factor [Signal t	98.09
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.07
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.04
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.97
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.91
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.83
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.8
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.79
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.61
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.56
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.5
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.49
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.39
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.37
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	97.34
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.33
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.26
PHA02825	162	LAP/PHD finger-like protein; Provisional	97.2
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	97.1
PHA02862	156	5L protein; Provisional	97.0
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	96.99
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.83
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	96.82
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.77
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	96.75
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	96.73
KOG3039	303	consensus Uncharacterized conserved protein [Funct	96.73
COG5152	259	Uncharacterized conserved protein, contains RING a	96.69
COG5236	493	Uncharacterized conserved protein, contains RING Z	96.67
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.67
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	96.64
KOG4445	368	consensus Uncharacterized conserved protein, conta	96.47
PF04641	260	Rtf2: Rtf2 RING-finger	96.45
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	96.41
COG5222	427	Uncharacterized conserved protein, contains RING Z	96.38
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	96.34
KOG4739	233	consensus Uncharacterized protein involved in syna	96.28
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	96.16
KOG2660	331	consensus Locus-specific chromosome binding protei	96.15
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.15
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.11
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.09
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	95.98
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	95.97
PHA03096	284	p28-like protein; Provisional	95.94
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	95.84
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	95.37
KOG1940	276	consensus Zn-finger protein [General function pred	95.3
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	94.99
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	94.91
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	94.75
KOG3002	299	consensus Zn finger protein [General function pred	94.59
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	94.19
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	94.12
KOG1001	674	consensus Helicase-like transcription factor HLTF/	94.09
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	93.81
KOG3053	293	consensus Uncharacterized conserved protein [Funct	93.06
COG5109	396	Uncharacterized conserved protein, contains RING Z	92.8
KOG1609	323	consensus Protein involved in mRNA turnover and st	92.45
KOG3899	381	consensus Uncharacterized conserved protein [Funct	92.41
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	92.29
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	91.72
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	91.14
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	90.47
KOG4367	699	consensus Predicted Zn-finger protein [Function un	90.28
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	89.87
KOG3113	293	consensus Uncharacterized conserved protein [Funct	89.51
PF14569	80	zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.	86.02
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	85.55
KOG0298	1394	consensus DEAD box-containing helicase-like transc	85.37
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	84.65
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	83.51
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	81.98
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	81.69
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	81.31
KOG0269	839	consensus WD40 repeat-containing protein [Function	81.2
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	81.11
KOG1829	580	consensus Uncharacterized conserved protein, conta	80.29
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	80.23
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	80.23

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

Probab=99.77  E-value=8.8e-19  Score=134.12  Aligned_cols=72  Identities=29%  Similarity=0.659  Sum_probs=56.8

Q ss_pred             ccccceecccccCCCCcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCC
Q 042112           34 QLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT  106 (132)
Q Consensus        34 ~~~~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~  106 (132)
                      .+++...|......... ..|+||+|+|++|++++.|||+|.||..||++|+.+....||+|+.++.......
T Consensus       213 ~~~p~~~f~~~~~~~~~-~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~~~~  284 (348)
T KOG4628|consen  213 KKLPVRTFTKGDDEDAT-DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDSGSE  284 (348)
T ss_pred             hhCCcEEeccccccCCC-ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCCCCCC
Confidence            35566666655554333 6999999999999999999999999999999999765456999999886554433

>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=99.62  E-value=1.6e-16  Score=88.37  Aligned_cols=44  Identities=41%  Similarity=1.132  Sum_probs=38.8

Q ss_pred             cccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCC
Q 042112           52 VECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCH   96 (132)
Q Consensus        52 ~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr   96 (132)
                      ++|+||++++..++.+..++|+|.||.+|+.+|++. +.+||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~-~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKR-NNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHH-SSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHh-CCcCCccC
Confidence            479999999998888888999999999999999986 47999997

...

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

Probab=99.48  E-value=2.5e-14  Score=107.15  Aligned_cols=52  Identities=40%  Similarity=1.007  Sum_probs=47.1

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAP  101 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  101 (132)
                      .+-+|+|||+++..+++.+.+||+|.||..|+++|+......||+||+++++
T Consensus       322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            4679999999999999999999999999999999996445689999999986

>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=99.40  E-value=3e-13  Score=82.95  Aligned_cols=45  Identities=31%  Similarity=0.827  Sum_probs=34.4

Q ss_pred             ccccccccccccCC----------CceEEeCCCCcccHHhHHHHHhcCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEG----------EEIRELSCHHLFHAVCLDTWISNNYAICPVCH   96 (132)
Q Consensus        51 ~~~C~IC~~~~~~~----------~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr   96 (132)
                      ++.|+||++++.+.          -.+...+|||.||..||.+|++. +.+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ-NNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT-SSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc-CCcCCCCC
Confidence            45699999999332          12343499999999999999975 46999997

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=99.35  E-value=1.3e-12  Score=100.40  Aligned_cols=51  Identities=24%  Similarity=0.817  Sum_probs=42.5

Q ss_pred             Ccccccccccccc-cCC---------CceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHI-EEG---------EEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~-~~~---------~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      .++..|.||++++ ..+         ..++.|||||.+|.+|++.|+. ++++||.||.++.
T Consensus       285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~E-RqQTCPICr~p~i  345 (491)
T COG5243         285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLE-RQQTCPICRRPVI  345 (491)
T ss_pred             CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHH-hccCCCcccCccc
Confidence            5688999999994 333         2467899999999999999997 4689999999953

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

Probab=99.34  E-value=1.8e-12  Score=96.52  Aligned_cols=52  Identities=29%  Similarity=0.766  Sum_probs=44.4

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      +....|.+|++..++   +..+||||+||..||..|...+ ..||+||.++.+.+.
T Consensus       237 ~a~~kC~LCLe~~~~---pSaTpCGHiFCWsCI~~w~~ek-~eCPlCR~~~~pskv  288 (293)
T KOG0317|consen  237 EATRKCSLCLENRSN---PSATPCGHIFCWSCILEWCSEK-AECPLCREKFQPSKV  288 (293)
T ss_pred             CCCCceEEEecCCCC---CCcCcCcchHHHHHHHHHHccc-cCCCcccccCCCcce
Confidence            456899999998777   6668999999999999999764 679999999877654

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.33  E-value=1e-12  Score=96.83  Aligned_cols=51  Identities=29%  Similarity=0.753  Sum_probs=41.0

Q ss_pred             CcccccccccccccCCCc-----eEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEE-----IRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~-----~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      ..+.+|+||++.+.+++.     ...++|+|.||..||.+|++. +.+||+||.++.
T Consensus       172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-~~tCPlCR~~~~  227 (238)
T PHA02929        172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-KNTCPVCRTPFI  227 (238)
T ss_pred             CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc-CCCCCCCCCEee
Confidence            346799999999876431     233489999999999999975 579999999775

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.28  E-value=3.6e-12  Score=90.75  Aligned_cols=56  Identities=23%  Similarity=0.652  Sum_probs=43.8

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhc---------------CCCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN---------------NYAICPVCHDSIAPSRWLTG  107 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~---------------~~~~CP~Cr~~~~~~~~~~~  107 (132)
                      .++.+|+||++.+++   +..++|||.||..||..|+..               +...||+||.++......+-
T Consensus        16 ~~~~~CpICld~~~d---PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPi   86 (193)
T PLN03208         16 GGDFDCNICLDQVRD---PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPI   86 (193)
T ss_pred             CCccCCccCCCcCCC---cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEe
Confidence            356799999998876   566799999999999999842               12479999999976544433

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

Probab=99.27  E-value=3.6e-12  Score=79.46  Aligned_cols=52  Identities=25%  Similarity=0.677  Sum_probs=39.3

Q ss_pred             cccccccccccccC--------CCc-eEEe-CCCCcccHHhHHHHHhc--CCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEE--------GEE-IREL-SCHHLFHAVCLDTWISN--NYAICPVCHDSIAP  101 (132)
Q Consensus        50 ~~~~C~IC~~~~~~--------~~~-~~~l-~C~H~fh~~Ci~~wl~~--~~~~CP~Cr~~~~~  101 (132)
                      +++.|.||...|..        ++. +..+ .|+|.||..||.+|+..  .+..||+||+++..
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~   83 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF   83 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence            36789999988852        222 2333 89999999999999953  34689999998754

>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=99.22  E-value=1.1e-11  Score=70.60  Aligned_cols=47  Identities=30%  Similarity=0.796  Sum_probs=38.3

Q ss_pred             cccccccccccccCCCceEEeCCCCc-ccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHL-FHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      ++..|.||++...+   +..+||||. ||..|+..|++. ...||+||+++.
T Consensus         1 ~~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~~~~-~~~CP~Cr~~i~   48 (50)
T PF13920_consen    1 EDEECPICFENPRD---VVLLPCGHLCFCEECAERLLKR-KKKCPICRQPIE   48 (50)
T ss_dssp             -HSB-TTTSSSBSS---EEEETTCEEEEEHHHHHHHHHT-TSBBTTTTBB-S
T ss_pred             CcCCCccCCccCCc---eEEeCCCChHHHHHHhHHhccc-CCCCCcCChhhc
Confidence            35689999998665   777899999 999999999984 589999999874

...

>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=99.21  E-value=1.7e-11  Score=67.17  Aligned_cols=45  Identities=36%  Similarity=1.004  Sum_probs=36.1

Q ss_pred             ccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCC
Q 042112           53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI   99 (132)
Q Consensus        53 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~   99 (132)
                      +|+||++.+..  .....+|+|.||..|+..|++.++..||+||..+
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            59999999832  3444479999999999999976457899999764

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

Probab=99.16  E-value=2.1e-11  Score=88.46  Aligned_cols=53  Identities=26%  Similarity=0.640  Sum_probs=42.5

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC--CCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN--YAICPVCHDSIAPSRW  104 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~--~~~CP~Cr~~~~~~~~  104 (132)
                      ....+|.||++.-++   +.++.|||.||..||.+|++..  ...||+|+..+..++.
T Consensus        45 ~~~FdCNICLd~akd---PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~v   99 (230)
T KOG0823|consen   45 GGFFDCNICLDLAKD---PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTV   99 (230)
T ss_pred             CCceeeeeeccccCC---CEEeecccceehHHHHHHHhhcCCCeeCCccccccccceE
Confidence            456799999998666   6777899999999999999432  3468999998875543

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

Probab=99.15  E-value=2.2e-11  Score=90.11  Aligned_cols=64  Identities=28%  Similarity=0.660  Sum_probs=52.0

Q ss_pred             CcccccccccccccCCC-------ceEEeCCCCcccHHhHHHHH-hcCCCCCCCCCCCCCCCCCCCCCCCcE
Q 042112           49 AEAVECAVCLSHIEEGE-------EIRELSCHHLFHAVCLDTWI-SNNYAICPVCHDSIAPSRWLTGHGEEV  112 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~-------~~~~l~C~H~fh~~Ci~~wl-~~~~~~CP~Cr~~~~~~~~~~~~~~~~  112 (132)
                      .++..|+||-..+....       +.-.|.|+|+||..||+.|. .++..+||.|+..++.+++-.++.+..
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~rmfsnpWekp  293 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKRMFSNPWEKP  293 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhhhccCccccc
Confidence            46789999999885544       56678999999999999998 445679999999999888877765543

>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=99.13  E-value=4.8e-11  Score=64.47  Aligned_cols=39  Identities=28%  Similarity=0.924  Sum_probs=32.1

Q ss_pred             cccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCC
Q 042112           54 CAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVC   95 (132)
Q Consensus        54 C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~C   95 (132)
                      |+||++.+.+  .+..++|||.||..|+.+|++. +..||+|
T Consensus         1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~-~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEK-NPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHC-TSB-TTT
T ss_pred             CCCCCCcccC--cCEECCCCCchhHHHHHHHHHC-cCCCcCC
Confidence            8999998877  2356799999999999999986 5899998

>PHA02926 zinc finger-like protein; Provisional

Probab=99.12  E-value=4.7e-11  Score=86.35  Aligned_cols=52  Identities=25%  Similarity=0.745  Sum_probs=38.9

Q ss_pred             CcccccccccccccCC----C-ceEEe-CCCCcccHHhHHHHHhcC-----CCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEG----E-EIREL-SCHHLFHAVCLDTWISNN-----YAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~----~-~~~~l-~C~H~fh~~Ci~~wl~~~-----~~~CP~Cr~~~~  100 (132)
                      ..+.+|+||++..-+.    + ....| +|+|.||..||..|.+.+     ..+||+||..+.
T Consensus       168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            4568999999986432    1 12344 999999999999999643     245999999764

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

Probab=99.11  E-value=9.3e-11  Score=64.37  Aligned_cols=39  Identities=31%  Similarity=0.772  Sum_probs=29.8

Q ss_pred             cccccccccCCCceEEeCCCCcccHHhHHHHHhcCC---CCCCCC
Q 042112           54 CAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNY---AICPVC   95 (132)
Q Consensus        54 C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~---~~CP~C   95 (132)
                      |+||++.+.+   +..|+|||.|+..||..|.+..+   ..||.|
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            8999999998   78799999999999999995433   369987

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

Probab=99.10  E-value=6.3e-11  Score=82.89  Aligned_cols=54  Identities=24%  Similarity=0.669  Sum_probs=43.4

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      ++-..|+|||+.+.+... .-+.|||+||..||+..++. ...||+|++.+..+..
T Consensus       129 ~~~~~CPiCl~~~sek~~-vsTkCGHvFC~~Cik~alk~-~~~CP~C~kkIt~k~~  182 (187)
T KOG0320|consen  129 EGTYKCPICLDSVSEKVP-VSTKCGHVFCSQCIKDALKN-TNKCPTCRKKITHKQF  182 (187)
T ss_pred             ccccCCCceecchhhccc-cccccchhHHHHHHHHHHHh-CCCCCCcccccchhhh
Confidence            456799999999887432 33689999999999999975 4789999998865543

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.08  E-value=1.3e-10  Score=64.37  Aligned_cols=44  Identities=30%  Similarity=0.762  Sum_probs=37.4

Q ss_pred             ccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCC
Q 042112           53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHD   97 (132)
Q Consensus        53 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~   97 (132)
                      .|++|++++.+......++|||.||..|+.... .....||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-GKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-CCCCCCcCCCC
Confidence            499999999666667878999999999999988 34578999985

>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=99.01  E-value=3.3e-10  Score=61.61  Aligned_cols=40  Identities=35%  Similarity=0.966  Sum_probs=33.4

Q ss_pred             cccccccccCCCceEEeCCCCcccHHhHHHHHh-cCCCCCCCC
Q 042112           54 CAVCLSHIEEGEEIRELSCHHLFHAVCLDTWIS-NNYAICPVC   95 (132)
Q Consensus        54 C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~-~~~~~CP~C   95 (132)
                      |+||++.+.+.  ...++|+|.||..|+.+|++ .+...||+|
T Consensus         1 C~iC~~~~~~~--~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDP--VILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSE--EEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCC--CEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            89999988773  23679999999999999997 445679998

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

>smart00184 RING Ring finger

Probab=99.00  E-value=4.6e-10  Score=59.31  Aligned_cols=39  Identities=31%  Similarity=1.011  Sum_probs=32.4

Q ss_pred             cccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCC
Q 042112           54 CAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVC   95 (132)
Q Consensus        54 C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~C   95 (132)
                      |+||++...   ....++|+|.||..|++.|++..+..||+|
T Consensus         1 C~iC~~~~~---~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELK---DPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCC---CcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            789998833   367789999999999999997445779987

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)

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

Probab=99.00  E-value=8.2e-10  Score=87.68  Aligned_cols=53  Identities=32%  Similarity=0.857  Sum_probs=41.1

Q ss_pred             CcccccccccccccCCC--------------ceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGE--------------EIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAP  101 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~--------------~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  101 (132)
                      +...+|+|||.++.--.              ....+||+|+||..|+.+|....+-.||+||.++++
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            34568999999873211              124459999999999999997445689999999975

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

Probab=98.98  E-value=2.3e-10  Score=93.56  Aligned_cols=51  Identities=29%  Similarity=0.858  Sum_probs=43.6

Q ss_pred             CcccccccccccccCCCc--eEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEE--IRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~--~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      ..+..|+||++.+..+.+  ++.++|+|.||..|+..|++. +++||+||..+.
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er-~qtCP~CR~~~~  341 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER-QQTCPTCRTVLY  341 (543)
T ss_pred             hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHH-hCcCCcchhhhh
Confidence            347899999999988655  677899999999999999985 589999999554

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

Probab=98.91  E-value=1.1e-09  Score=67.03  Aligned_cols=51  Identities=29%  Similarity=0.772  Sum_probs=37.5

Q ss_pred             cccccccccc-----------cCCCceEEe--CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCC
Q 042112           52 VECAVCLSHI-----------EEGEEIREL--SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR  103 (132)
Q Consensus        52 ~~C~IC~~~~-----------~~~~~~~~l--~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  103 (132)
                      +.|+||...+           ..+++....  .|+|.||..||.+|+.. +..||++|+++...+
T Consensus        21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T-k~~CPld~q~w~~~~   84 (88)
T COG5194          21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT-KGVCPLDRQTWVLAD   84 (88)
T ss_pred             chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh-CCCCCCCCceeEEec
Confidence            4566666554           344554433  79999999999999976 479999999876544

>smart00504 Ubox Modified RING finger domain

Probab=98.90  E-value=1.9e-09  Score=63.66  Aligned_cols=51  Identities=12%  Similarity=0.333  Sum_probs=42.2

Q ss_pred             cccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCC
Q 042112           52 VECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT  106 (132)
Q Consensus        52 ~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~  106 (132)
                      ..|+||.+.+.+   +..++|||+|++.||.+|++. +..||+|+.++..+....
T Consensus         2 ~~Cpi~~~~~~~---Pv~~~~G~v~~~~~i~~~~~~-~~~cP~~~~~~~~~~l~~   52 (63)
T smart00504        2 FLCPISLEVMKD---PVILPSGQTYERRAIEKWLLS-HGTDPVTGQPLTHEDLIP   52 (63)
T ss_pred             cCCcCCCCcCCC---CEECCCCCEEeHHHHHHHHHH-CCCCCCCcCCCChhhcee
Confidence            469999999887   455799999999999999975 578999999886554433

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

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

Probab=98.90  E-value=2.5e-10  Score=69.23  Aligned_cols=51  Identities=25%  Similarity=0.749  Sum_probs=37.8

Q ss_pred             cccccccccccccC--------CCceE-Ee-CCCCcccHHhHHHHH--hcCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEE--------GEEIR-EL-SCHHLFHAVCLDTWI--SNNYAICPVCHDSIA  100 (132)
Q Consensus        50 ~~~~C~IC~~~~~~--------~~~~~-~l-~C~H~fh~~Ci~~wl--~~~~~~CP~Cr~~~~  100 (132)
                      .+++|.||.-+|..        ++... ++ .|.|.||..||.+|+  .+++..||+||+.+.
T Consensus        19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            45589999888743        23333 23 799999999999999  334567999999764

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.79  E-value=5.1e-09  Score=82.37  Aligned_cols=50  Identities=26%  Similarity=0.634  Sum_probs=42.2

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS  102 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  102 (132)
                      +....|+||++.+..   +..++|+|.||..||..|+.. ...||+||.++...
T Consensus        24 e~~l~C~IC~d~~~~---PvitpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~~~   73 (397)
T TIGR00599        24 DTSLRCHICKDFFDV---PVLTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQES   73 (397)
T ss_pred             ccccCCCcCchhhhC---ccCCCCCCchhHHHHHHHHhC-CCCCCCCCCccccc
Confidence            456799999999876   456799999999999999975 46899999988654

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

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

Probab=98.71  E-value=7.6e-09  Score=76.54  Aligned_cols=53  Identities=30%  Similarity=0.743  Sum_probs=42.8

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHH-HHhcCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDT-WISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~-wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      ..+..|+||++....   +..++|||+||..||-. |-.++...||+||+...+++.
T Consensus       213 ~~d~kC~lC~e~~~~---ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v  266 (271)
T COG5574         213 LADYKCFLCLEEPEV---PSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV  266 (271)
T ss_pred             ccccceeeeecccCC---cccccccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence            457899999998776   66689999999999999 876544459999998766543

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

Probab=98.69  E-value=1.4e-08  Score=55.90  Aligned_cols=39  Identities=28%  Similarity=0.642  Sum_probs=22.3

Q ss_pred             cccccccccCCC-ceEEeCCCCcccHHhHHHHHhcC---CCCCC
Q 042112           54 CAVCLSHIEEGE-EIRELSCHHLFHAVCLDTWISNN---YAICP   93 (132)
Q Consensus        54 C~IC~~~~~~~~-~~~~l~C~H~fh~~Ci~~wl~~~---~~~CP   93 (132)
                      |+||.+ +...+ .+..|+|||.|+.+|+.++++.+   ...||
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 75544 46778999999999999999643   34576

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.65  E-value=3e-08  Score=75.47  Aligned_cols=56  Identities=16%  Similarity=0.491  Sum_probs=41.1

Q ss_pred             cccccccccccccCCCceEEe--CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIREL--SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWL  105 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l--~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~  105 (132)
                      ++..||+|...--.+...+.+  +|||.||..|++..+..+...||.|+.++......
T Consensus         2 d~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr   59 (309)
T TIGR00570         2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFR   59 (309)
T ss_pred             CCCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhcc
Confidence            356899999964333333223  79999999999997755557899999988766543

All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

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

Probab=98.59  E-value=3.2e-08  Score=63.47  Aligned_cols=52  Identities=29%  Similarity=0.724  Sum_probs=38.0

Q ss_pred             cccccccccccc-------c-----CCCceEEe--CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHI-------E-----EGEEIREL--SCHHLFHAVCLDTWISNNYAICPVCHDSIAPS  102 (132)
Q Consensus        50 ~~~~C~IC~~~~-------~-----~~~~~~~l--~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  102 (132)
                      .-+.|+||...+       +     ..++....  .|+|.||..||.+|++++ ..||+|.++....
T Consensus        45 ~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr-~vCPLdn~eW~~q  110 (114)
T KOG2930|consen   45 VVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTR-NVCPLDNKEWVFQ  110 (114)
T ss_pred             eechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhc-CcCCCcCcceeEe
Confidence            456899998765       1     11223333  799999999999999865 7899998876543

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

Probab=98.56  E-value=3e-08  Score=79.18  Aligned_cols=55  Identities=22%  Similarity=0.570  Sum_probs=42.4

Q ss_pred             ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC----CCCCCCCCCCCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN----YAICPVCHDSIAPSRWLTGH  108 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~----~~~CP~Cr~~~~~~~~~~~~  108 (132)
                      +..||||+++...   +..+.|||+||..||-+++...    ...||+||..+..++..+-.
T Consensus       186 ~~~CPICL~~~~~---p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~  244 (513)
T KOG2164|consen  186 DMQCPICLEPPSV---PVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVF  244 (513)
T ss_pred             CCcCCcccCCCCc---ccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeeee
Confidence            7789999998665   4446799999999999887432    35799999998876554443

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

Probab=98.56  E-value=9.1e-08  Score=54.13  Aligned_cols=43  Identities=23%  Similarity=0.714  Sum_probs=32.0

Q ss_pred             ccccccccccCCCceEEeCCC-----CcccHHhHHHHHhcC-CCCCCCCC
Q 042112           53 ECAVCLSHIEEGEEIRELSCH-----HLFHAVCLDTWISNN-YAICPVCH   96 (132)
Q Consensus        53 ~C~IC~~~~~~~~~~~~l~C~-----H~fh~~Ci~~wl~~~-~~~CP~Cr   96 (132)
                      .|.||++.. .++.....||.     |.+|..|+.+|+..+ +.+||+|+
T Consensus         1 ~CrIC~~~~-~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEG-DEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCCC-CCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            489999833 33445557885     899999999999443 45799995

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

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

Probab=98.51  E-value=7.9e-08  Score=58.76  Aligned_cols=54  Identities=13%  Similarity=0.342  Sum_probs=41.4

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT  106 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~  106 (132)
                      +...|+|+.+-|.+   +..+++||.|.+.+|..|+..++..||+++.++.......
T Consensus         3 ~~f~CpIt~~lM~d---PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~p   56 (73)
T PF04564_consen    3 DEFLCPITGELMRD---PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIP   56 (73)
T ss_dssp             GGGB-TTTSSB-SS---EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE
T ss_pred             cccCCcCcCcHhhC---ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceE
Confidence            45689999999998   7778999999999999999765689999999887655443

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 ....

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

Probab=98.41  E-value=1.1e-07  Score=74.98  Aligned_cols=49  Identities=33%  Similarity=0.774  Sum_probs=39.3

Q ss_pred             CcccccccccccccCCCce-EEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEI-RELSCHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~-~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      .+-++||||+|.+...... ....|.|.||..|+..|.   ..+||+||.-..
T Consensus       173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~---~~scpvcR~~q~  222 (493)
T KOG0804|consen  173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW---DSSCPVCRYCQS  222 (493)
T ss_pred             ccCCCcchhHhhcCccccceeeeecccccchHHHhhcc---cCcChhhhhhcC
Confidence            3678999999998775433 334899999999999995   468999997655

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

Probab=98.38  E-value=4.5e-08  Score=59.43  Aligned_cols=50  Identities=34%  Similarity=0.802  Sum_probs=22.9

Q ss_pred             cccccccccccc-CCCceEEe----CCCCcccHHhHHHHHhc--CC--------CCCCCCCCCCC
Q 042112           51 AVECAVCLSHIE-EGEEIREL----SCHHLFHAVCLDTWISN--NY--------AICPVCHDSIA  100 (132)
Q Consensus        51 ~~~C~IC~~~~~-~~~~~~~l----~C~H~fh~~Ci~~wl~~--~~--------~~CP~Cr~~~~  100 (132)
                      +.+|.||++... .++.+...    .|+..||..|+.+|+..  +.        ..||.|++++.
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~   66 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS   66 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence            457999999865 33333322    68999999999999932  11        15999998774

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

Probab=98.36  E-value=1.4e-07  Score=72.27  Aligned_cols=51  Identities=22%  Similarity=0.628  Sum_probs=43.2

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      .-..|.||.+-|..   +..+||+|.||..||...+.. +..||.|+.++.+...
T Consensus        22 ~lLRC~IC~eyf~i---p~itpCsHtfCSlCIR~~L~~-~p~CP~C~~~~~Es~L   72 (442)
T KOG0287|consen   22 DLLRCGICFEYFNI---PMITPCSHTFCSLCIRKFLSY-KPQCPTCCVTVTESDL   72 (442)
T ss_pred             HHHHHhHHHHHhcC---ceeccccchHHHHHHHHHhcc-CCCCCceecccchhhh
Confidence            45689999999887   666799999999999999985 5899999988876544

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

Probab=98.32  E-value=2.6e-07  Score=69.55  Aligned_cols=51  Identities=27%  Similarity=0.690  Sum_probs=42.2

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      .-..|.||.+-+..   +..++|||.||..||...+.. +..||+||.+..+...
T Consensus        24 s~lrC~IC~~~i~i---p~~TtCgHtFCslCIR~hL~~-qp~CP~Cr~~~~esrl   74 (391)
T COG5432          24 SMLRCRICDCRISI---PCETTCGHTFCSLCIRRHLGT-QPFCPVCREDPCESRL   74 (391)
T ss_pred             hHHHhhhhhheeec---ceecccccchhHHHHHHHhcC-CCCCccccccHHhhhc
Confidence            45679999998887   566799999999999999974 6899999988765443

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

Probab=98.31  E-value=1.7e-07  Score=79.62  Aligned_cols=52  Identities=31%  Similarity=0.772  Sum_probs=38.4

Q ss_pred             CcccccccccccccCCCc----eEEeCCCCcccHHhHHHHHhc-CCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEE----IRELSCHHLFHAVCLDTWISN-NYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~----~~~l~C~H~fh~~Ci~~wl~~-~~~~CP~Cr~~~~  100 (132)
                      .+-++|+||+..+..-+.    -+.-.|.|.||..|+.+|++. ++++||+||.+++
T Consensus      1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            456789999987752111    122369999999999999943 4568999998875

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

Probab=98.27  E-value=3.6e-07  Score=67.74  Aligned_cols=44  Identities=34%  Similarity=0.713  Sum_probs=38.6

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCH   96 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr   96 (132)
                      .+...|+||++.+...   ..++|+|.||..|+..+.. ....||.||
T Consensus        11 ~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr   54 (386)
T KOG2177|consen   11 QEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE-GPLSCPVCR   54 (386)
T ss_pred             cccccChhhHHHhhcC---ccccccchHhHHHHHHhcC-CCcCCcccC
Confidence            4567899999999985   6679999999999999887 457899999

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

Probab=98.25  E-value=4.6e-07  Score=68.35  Aligned_cols=50  Identities=26%  Similarity=0.557  Sum_probs=41.5

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS  102 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  102 (132)
                      -..+|+||+.....   +..|+|+|.||..||+.-.+....+||+||.+++..
T Consensus         6 ~~~eC~IC~nt~n~---Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    6 KKKECLICYNTGNC---PVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDST   55 (324)
T ss_pred             cCCcceeeeccCCc---CccccccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence            45689999987665   455899999999999987766667899999999754

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

Probab=98.20  E-value=1.5e-06  Score=66.87  Aligned_cols=49  Identities=29%  Similarity=0.676  Sum_probs=39.0

Q ss_pred             CcccccccccccccCCCceEEeCCCCc-ccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHL-FHAVCLDTWISNNYAICPVCHDSIAP  101 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~~  101 (132)
                      +.+.+|.||+.+.++   +.+|||.|. .|..|.+...- .+.+||+||+++..
T Consensus       288 ~~gkeCVIClse~rd---t~vLPCRHLCLCs~Ca~~Lr~-q~n~CPICRqpi~~  337 (349)
T KOG4265|consen  288 ESGKECVICLSESRD---TVVLPCRHLCLCSGCAKSLRY-QTNNCPICRQPIEE  337 (349)
T ss_pred             cCCCeeEEEecCCcc---eEEecchhhehhHhHHHHHHH-hhcCCCccccchHh
Confidence            457899999998777   788999986 67788887652 24689999999853

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

Probab=98.19  E-value=2.5e-07  Score=71.10  Aligned_cols=56  Identities=25%  Similarity=0.506  Sum_probs=45.4

Q ss_pred             CcccccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTG  107 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~  107 (132)
                      ..+..|+||++.++.   .+.. .|.|.||.+||..-++.++..||.||+.+.......+
T Consensus        41 ~~~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr~   97 (381)
T KOG0311|consen   41 DIQVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLRI   97 (381)
T ss_pred             hhhhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCCC
Confidence            356789999999887   3333 7999999999999997777899999999876665443

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

Probab=98.15  E-value=6.4e-07  Score=74.52  Aligned_cols=52  Identities=21%  Similarity=0.547  Sum_probs=42.9

Q ss_pred             ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWL  105 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~  105 (132)
                      -..|++|-..+.+   .....|+|+||..|+..-+..+++.||.|-..|.+.+..
T Consensus       643 ~LkCs~Cn~R~Kd---~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~  694 (698)
T KOG0978|consen  643 LLKCSVCNTRWKD---AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVH  694 (698)
T ss_pred             ceeCCCccCchhh---HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccccc
Confidence            4589999976655   555689999999999999977789999999988766543

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

Probab=98.09  E-value=1.6e-06  Score=68.64  Aligned_cols=80  Identities=28%  Similarity=0.473  Sum_probs=59.3

Q ss_pred             CCCcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCCCC---CCcEEEeeeecCCCc
Q 042112           47 SRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGH---GEEVLVLKFRCFNSR  123 (132)
Q Consensus        47 ~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~---~~~~~~~~~~~~~~~  123 (132)
                      ..+++..|++|+..+.++-..  +.|||.||..|+..|+.. +..||.|+..+..++.....   ..+++.+...+.+..
T Consensus        17 ~~~~~l~C~~C~~vl~~p~~~--~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~~~~~~~~~~~~~~~~~l~i~c~~~~   93 (391)
T KOG0297|consen   17 PLDENLLCPICMSVLRDPVQT--TTCGHRFCAGCLLESLSN-HQKCPVCRQELTQAEELPVPRALRRELLKLPIRCIFAS   93 (391)
T ss_pred             CCcccccCccccccccCCCCC--CCCCCcccccccchhhcc-CcCCcccccccchhhccCchHHHHHHHHhcccccccCC
Confidence            346778999999998874321  589999999999999986 68999999988766655432   344444555666666


Q ss_pred             ccccccc
Q 042112          124 TERDTWW  130 (132)
Q Consensus       124 ~~~~~~~  130 (132)
                      . ||.|-
T Consensus        94 ~-GC~~~   99 (391)
T KOG0297|consen   94 R-GCRAD   99 (391)
T ss_pred             C-Ccccc
Confidence            6 77774

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

Probab=98.07  E-value=1.9e-06  Score=67.13  Aligned_cols=51  Identities=27%  Similarity=0.805  Sum_probs=36.1

Q ss_pred             ccccccccccccCC-CceEEe-CCCCcccHHhHHHHHhcCC--CCCCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEG-EEIREL-SCHHLFHAVCLDTWISNNY--AICPVCHDSIAPS  102 (132)
Q Consensus        51 ~~~C~IC~~~~~~~-~~~~~l-~C~H~fh~~Ci~~wl~~~~--~~CP~Cr~~~~~~  102 (132)
                      ...|.|| .++.+. ..+.-. .|||+||..|+.+|+..-.  +.||.||-.++..
T Consensus         4 ~A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r   58 (465)
T KOG0827|consen    4 MAECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQER   58 (465)
T ss_pred             cceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccce
Confidence            4579999 444443 334334 5999999999999995433  4799999555443

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

Probab=98.04  E-value=2.3e-06  Score=66.41  Aligned_cols=52  Identities=25%  Similarity=0.605  Sum_probs=38.9

Q ss_pred             CcccccccccccccCCC-----ceEEeCCCCcccHHhHHHHHhcCC------CCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGE-----EIRELSCHHLFHAVCLDTWISNNY------AICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~-----~~~~l~C~H~fh~~Ci~~wl~~~~------~~CP~Cr~~~~  100 (132)
                      ..+.+|.||++...+..     --+..+|.|.||..||..|-+.++      +.||.||....
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~  221 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS  221 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence            35789999999876543     112237999999999999984333      68999997653

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

Probab=97.97  E-value=1.3e-06  Score=51.61  Aligned_cols=50  Identities=26%  Similarity=0.672  Sum_probs=24.5

Q ss_pred             ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWL  105 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~  105 (132)
                      --.|++|.+-++++  +....|+|.||..||..-+.   ..||+|+.+--.++..
T Consensus         7 lLrCs~C~~~l~~p--v~l~~CeH~fCs~Ci~~~~~---~~CPvC~~Paw~qD~~   56 (65)
T PF14835_consen    7 LLRCSICFDILKEP--VCLGGCEHIFCSSCIRDCIG---SECPVCHTPAWIQDIQ   56 (65)
T ss_dssp             TTS-SSS-S--SS---B---SSS--B-TTTGGGGTT---TB-SSS--B-S-SS--
T ss_pred             hcCCcHHHHHhcCC--ceeccCccHHHHHHhHHhcC---CCCCCcCChHHHHHHH
Confidence            34799999988762  33348999999999988553   4599999876555443

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

Probab=97.91  E-value=1.9e-06  Score=49.22  Aligned_cols=46  Identities=24%  Similarity=0.561  Sum_probs=33.2

Q ss_pred             ccccccccccccCCCceEEeCCCCc-ccHHhHHHHHhcCCCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEGEEIRELSCHHL-FHAVCLDTWISNNYAICPVCHDSI   99 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~   99 (132)
                      +++|.||++...+   .....|||. .|..|-.+-++..+..||.||.++
T Consensus         7 ~dECTICye~pvd---sVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi   53 (62)
T KOG4172|consen    7 SDECTICYEHPVD---SVLYTCGHMCMCYACGLRLKKALHGCCPICRAPI   53 (62)
T ss_pred             ccceeeeccCcch---HHHHHcchHHhHHHHHHHHHHccCCcCcchhhHH
Confidence            4789999987544   333479986 456776665554568999999976

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

Probab=97.83  E-value=1.6e-05  Score=62.35  Aligned_cols=49  Identities=29%  Similarity=0.820  Sum_probs=38.0

Q ss_pred             cccccccccccccCCCceEE--eCCCCcccHHhHHHHHh-cCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRE--LSCHHLFHAVCLDTWIS-NNYAICPVCHDS   98 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~--l~C~H~fh~~Ci~~wl~-~~~~~CP~Cr~~   98 (132)
                      ...+|+||++.+.-....+.  +.|+|.|..+||..|+. .....||.|...
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~k   54 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGK   54 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCCh
Confidence            45689999999876554333  58999999999999993 223579999754

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

Probab=97.80  E-value=5.4e-06  Score=67.01  Aligned_cols=79  Identities=29%  Similarity=0.586  Sum_probs=56.0

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHH----hcCCCCCCCCCCCCCCCCCCCCC-CCcEEEeeeecCCCc
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWI----SNNYAICPVCHDSIAPSRWLTGH-GEEVLVLKFRCFNSR  123 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl----~~~~~~CP~Cr~~~~~~~~~~~~-~~~~~~~~~~~~~~~  123 (132)
                      .+..+|.+|.++-++   .....|.|.||+.|+..+.    ...+-+||+|-..+.-....+.. ......++-+|+=++
T Consensus       534 k~~~~C~lc~d~aed---~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~alek~~l~~Fk~sSIlnR  610 (791)
T KOG1002|consen  534 KGEVECGLCHDPAED---YIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPALEKTDLKGFKASSILNR  610 (791)
T ss_pred             cCceeecccCChhhh---hHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccchhhhhcchhhhhhHHHhhh
Confidence            467799999998666   6667899999999998876    33346899998877544332222 133444556777777


Q ss_pred             ccccccc
Q 042112          124 TERDTWW  130 (132)
Q Consensus       124 ~~~~~~~  130 (132)
                      .+-++|.
T Consensus       611 inm~~~q  617 (791)
T KOG1002|consen  611 INMDDWQ  617 (791)
T ss_pred             cchhhhc
Confidence            7788885

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

Probab=97.79  E-value=5.8e-06  Score=69.35  Aligned_cols=57  Identities=23%  Similarity=0.471  Sum_probs=40.9

Q ss_pred             ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGH  108 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~  108 (132)
                      ...|++|+..+.+.......+|+|.||..|+..|-+. ..+||+||..+..-......
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~-aqTCPiDR~EF~~v~V~eS~  179 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRC-AQTCPVDRGEFGEVKVLEST  179 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhh-cccCchhhhhhheeeeeccc
Confidence            3456677666655444344589999999999999975 47999999988644443333

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

Probab=97.61  E-value=5.9e-05  Score=55.13  Aligned_cols=56  Identities=32%  Similarity=0.674  Sum_probs=44.7

Q ss_pred             CCCCcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC-------CCCCCCCCCCCCCC
Q 042112           46 GSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN-------YAICPVCHDSIAPS  102 (132)
Q Consensus        46 ~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~-------~~~CP~Cr~~~~~~  102 (132)
                      ..++....|..|-..+..++.++ |.|-|.||.+|+..|..+-       .-.||-|-.++.+.
T Consensus        45 ~DsDY~pNC~LC~t~La~gdt~R-LvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp  107 (299)
T KOG3970|consen   45 QDSDYNPNCRLCNTPLASGDTTR-LVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP  107 (299)
T ss_pred             hhcCCCCCCceeCCccccCccee-ehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence            34456778999999999988766 7799999999999997421       13799999888654

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

Probab=97.56  E-value=3e-05  Score=60.94  Aligned_cols=48  Identities=25%  Similarity=0.686  Sum_probs=37.6

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC-CCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN-YAICPVCHDSIA  100 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~-~~~CP~Cr~~~~  100 (132)
                      .-.-|.||-+.=.   .++.-||||..|..|+..|-... ...||.||.++.
T Consensus       368 TFeLCKICaendK---dvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK  416 (563)
T KOG1785|consen  368 TFELCKICAENDK---DVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIK  416 (563)
T ss_pred             hHHHHHHhhccCC---CcccccccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence            3457999987533   36767999999999999998322 468999998775

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

Probab=97.50  E-value=7.3e-05  Score=41.85  Aligned_cols=45  Identities=20%  Similarity=0.589  Sum_probs=22.5

Q ss_pred             cccccccccCCCceEEe--CCCCcccHHhHHHHHhcCCCCCCCCCCCC
Q 042112           54 CAVCLSHIEEGEEIREL--SCHHLFHAVCLDTWISNNYAICPVCHDSI   99 (132)
Q Consensus        54 C~IC~~~~~~~~~~~~l--~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~   99 (132)
                      |++|.+++...+. ...  +|++..+..|...-++..+..||-||++.
T Consensus         1 cp~C~e~~d~~d~-~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDK-DFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCT-T--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCC-ccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            7899999844433 223  67899999998887754457899999875

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

Probab=97.49  E-value=3.5e-05  Score=60.34  Aligned_cols=48  Identities=31%  Similarity=0.755  Sum_probs=37.6

Q ss_pred             cccccccccccccCC-CceEEeCCCCcccHHhHHHHHhc-CCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEG-EEIRELSCHHLFHAVCLDTWISN-NYAICPVCHD   97 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~-~~~~~l~C~H~fh~~Ci~~wl~~-~~~~CP~Cr~   97 (132)
                      -+..|..|-+.+... +....|||.|+||..|+...+.+ ...+||.||+
T Consensus       364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            356799999987543 34566799999999999999943 3468999984

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

Probab=97.39  E-value=0.00014  Score=64.92  Aligned_cols=67  Identities=19%  Similarity=0.499  Sum_probs=48.3

Q ss_pred             cccceecccccCCCCcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC---------CCCCCCCCCCCCC
Q 042112           35 LVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN---------YAICPVCHDSIAP  101 (132)
Q Consensus        35 ~~~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~---------~~~CP~Cr~~~~~  101 (132)
                      -+|-+.-.......+.++.|.||..+--.....++|.|+|.||..|...-+..+         -.+||.|+.++..
T Consensus      3470 CLPCl~Cdks~tkQD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3470 CLPCLHCDKSATKQDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred             cccccccChhhhhcccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence            345444433333435788999999887666778889999999999997755321         1379999988753

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

Probab=97.37  E-value=0.00011  Score=58.28  Aligned_cols=49  Identities=29%  Similarity=0.627  Sum_probs=41.4

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAP  101 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  101 (132)
                      ..+.+|.||+..+.+   +..+||||.||..||.+-+.. ...||.||.++..
T Consensus        82 ~sef~c~vc~~~l~~---pv~tpcghs~c~~Cl~r~ld~-~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   82 RSEFECCVCSRALYP---PVVTPCGHSFCLECLDRSLDQ-ETECPLCRDELVE  130 (398)
T ss_pred             cchhhhhhhHhhcCC---CccccccccccHHHHHHHhcc-CCCCccccccccc
Confidence            467899999988777   566799999999999997763 5789999999875

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

Probab=97.34  E-value=0.00012  Score=40.90  Aligned_cols=41  Identities=34%  Similarity=0.839  Sum_probs=26.9

Q ss_pred             cccccccccCCCceEEeCCC-----CcccHHhHHHHHh-cCCCCCCCC
Q 042112           54 CAVCLSHIEEGEEIRELSCH-----HLFHAVCLDTWIS-NNYAICPVC   95 (132)
Q Consensus        54 C~IC~~~~~~~~~~~~l~C~-----H~fh~~Ci~~wl~-~~~~~CP~C   95 (132)
                      |-||++.-.+++ .-..||+     ...|..|+.+|+. .++.+|++|
T Consensus         1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            779998866655 2335665     3789999999994 334679887

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

Probab=97.33  E-value=0.00016  Score=42.01  Aligned_cols=44  Identities=25%  Similarity=0.597  Sum_probs=28.2

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHh-cCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWIS-NNYAICPV   94 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~-~~~~~CP~   94 (132)
                      .....|||.+..++++  ++-..|+|.|-+..|.++++ .+...||+
T Consensus         9 ~~~~~CPiT~~~~~~P--V~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen    9 TISLKCPITLQPFEDP--VKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             B--SB-TTTSSB-SSE--EEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             EeccCCCCcCChhhCC--cCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            3467899999998872  44458999999999999993 23457998

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

Probab=97.26  E-value=0.0011  Score=49.86  Aligned_cols=50  Identities=22%  Similarity=0.430  Sum_probs=37.6

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhc-CCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN-NYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~-~~~~CP~Cr~~~~  100 (132)
                      ..+.+|++|-+.-..+  ....+|+|+||..|+..-... ....||.|-.+..
T Consensus       237 t~~~~C~~Cg~~PtiP--~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  237 TSDTECPVCGEPPTIP--HVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cCCceeeccCCCCCCC--eeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            4678999999875542  333489999999999886632 1368999988775

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=97.20  E-value=0.00036  Score=48.45  Aligned_cols=50  Identities=20%  Similarity=0.570  Sum_probs=36.3

Q ss_pred             CcccccccccccccCCCceEEeCCC--C---cccHHhHHHHHhc-CCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCH--H---LFHAVCLDTWISN-NYAICPVCHDSIAPS  102 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~--H---~fh~~Ci~~wl~~-~~~~CP~Cr~~~~~~  102 (132)
                      ..+..|-||.++-.+  .  ..||.  .   ..|.+|+..|+.. +...||.|+.++...
T Consensus         6 ~~~~~CRIC~~~~~~--~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          6 LMDKCCWICKDEYDV--V--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCCCeeEecCCCCCC--c--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            567899999987432  1  13555  3   6699999999943 456799999987544

>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=97.10  E-value=0.00023  Score=48.14  Aligned_cols=36  Identities=25%  Similarity=0.663  Sum_probs=30.2

Q ss_pred             ccccccccccccCCCceEEeCCC------CcccHHhHHHHHh
Q 042112           51 AVECAVCLSHIEEGEEIRELSCH------HLFHAVCLDTWIS   86 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~~~~~l~C~------H~fh~~Ci~~wl~   86 (132)
                      .-+|.||++.+.+++.+..++|+      |.||.+|+.+|-.
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence            56899999999885666667776      9999999999953

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

>PHA02862 5L protein; Provisional

Probab=97.00  E-value=0.00059  Score=46.65  Aligned_cols=48  Identities=21%  Similarity=0.537  Sum_probs=34.8

Q ss_pred             ccccccccccccCCCceEEeCCC-----CcccHHhHHHHHhc-CCCCCCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEGEEIRELSCH-----HLFHAVCLDTWISN-NYAICPVCHDSIAPS  102 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~~~~~l~C~-----H~fh~~Ci~~wl~~-~~~~CP~Cr~~~~~~  102 (132)
                      ++.|-||.++-.++    .-||.     ...|.+|+.+|+.. ++..||.|+.++..+
T Consensus         2 ~diCWIC~~~~~e~----~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik   55 (156)
T PHA02862          2 SDICWICNDVCDER----NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK   55 (156)
T ss_pred             CCEEEEecCcCCCC----cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence            46799999974332    23554     67899999999943 345799999887533

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

Probab=96.99  E-value=0.00051  Score=52.19  Aligned_cols=48  Identities=25%  Similarity=0.653  Sum_probs=40.7

Q ss_pred             cccccccccccCCC---ceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCC
Q 042112           52 VECAVCLSHIEEGE---EIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI   99 (132)
Q Consensus        52 ~~C~IC~~~~~~~~---~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~   99 (132)
                      ..|-||-++|...+   .++.|.|||.++..|+..-+......||.||.+.
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            57999999998764   3677899999999999998876556799999985

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

Probab=96.83  E-value=0.00046  Score=44.48  Aligned_cols=33  Identities=24%  Similarity=0.656  Sum_probs=26.5

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHH
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLD   82 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~   82 (132)
                      .++..|++|...+.. ......||||+||..|++
T Consensus        76 ~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   76 TESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence            456789999999877 344556999999999975

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 [].

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

Probab=96.82  E-value=0.0004  Score=48.42  Aligned_cols=41  Identities=24%  Similarity=0.554  Sum_probs=31.8

Q ss_pred             cceecccccCCCCcccccccccccccCCCceEEeCCCCcccH
Q 042112           37 NIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHA   78 (132)
Q Consensus        37 ~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~   78 (132)
                      |.+.|++.... ++..+|.||+|++..++.+..|||-.+||+
T Consensus       164 PrlsYNdDVL~-ddkGECvICLEdL~~GdtIARLPCLCIYHK  204 (205)
T KOG0801|consen  164 PRLSYNDDVLK-DDKGECVICLEDLEAGDTIARLPCLCIYHK  204 (205)
T ss_pred             cccccccchhc-ccCCcEEEEhhhccCCCceeccceEEEeec
Confidence            33444444333 567789999999999999999999999986

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.77  E-value=0.00099  Score=51.58  Aligned_cols=54  Identities=17%  Similarity=0.385  Sum_probs=39.8

Q ss_pred             CcccccccccccccCCCceEE-eCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRE-LSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS  102 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~-l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  102 (132)
                      ++++.|+.|++++...++-.. -+||-..|..|...--+.-+..||-||.....+
T Consensus        12 deed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~de   66 (480)
T COG5175          12 DEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDE   66 (480)
T ss_pred             cccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhcccc
Confidence            445569999999876655332 379998899887766554467899999877654

>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=96.75  E-value=0.00075  Score=36.94  Aligned_cols=42  Identities=21%  Similarity=0.700  Sum_probs=23.3

Q ss_pred             cccccccccCCCceEEeCCCCcccHHhHHHHHhcCCC-CCCCC
Q 042112           54 CAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYA-ICPVC   95 (132)
Q Consensus        54 C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~-~CP~C   95 (132)
                      |.+|.+....|+......|+-.+|..|+..+++.+.. .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            6778877776654443368889999999999965433 59987

; PDB: 3NW0_A 2CT0_A.

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

Probab=96.73  E-value=0.0009  Score=56.96  Aligned_cols=49  Identities=29%  Similarity=0.758  Sum_probs=36.6

Q ss_pred             CcccccccccccccCCCce-EEeCCCCcccHHhHHHHHhcCC------CCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEI-RELSCHHLFHAVCLDTWISNNY------AICPVCHD   97 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~-~~l~C~H~fh~~Ci~~wl~~~~------~~CP~Cr~   97 (132)
                      ....+|.||.+.+.....+ .--.|-|+||..||..|.....      =.||.|+.
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs  244 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS  244 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence            4678999999998765432 2225889999999999984321      15999984

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.73  E-value=0.0019  Score=48.00  Aligned_cols=53  Identities=15%  Similarity=0.288  Sum_probs=45.7

Q ss_pred             cccccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR  103 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  103 (132)
                      ..+.|++|.+.+.+...+..| ||||+|+..|+.+.... -..||+|-.++...+
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~-D~v~pv~d~plkdrd  273 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK-DMVDPVTDKPLKDRD  273 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc-cccccCCCCcCcccc
Confidence            567899999999998888878 99999999999999874 478999988876554

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

Probab=96.69  E-value=0.00061  Score=49.05  Aligned_cols=45  Identities=22%  Similarity=0.454  Sum_probs=36.9

Q ss_pred             ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI   99 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~   99 (132)
                      ...|.||.++|+.   +..+.|||.||..|...-++. ...|-+|-+..
T Consensus       196 PF~C~iCKkdy~s---pvvt~CGH~FC~~Cai~~y~k-g~~C~~Cgk~t  240 (259)
T COG5152         196 PFLCGICKKDYES---PVVTECGHSFCSLCAIRKYQK-GDECGVCGKAT  240 (259)
T ss_pred             ceeehhchhhccc---hhhhhcchhHHHHHHHHHhcc-CCcceecchhh
Confidence            3489999999988   566789999999999887764 47899997654

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

Probab=96.67  E-value=0.0015  Score=50.78  Aligned_cols=57  Identities=16%  Similarity=0.340  Sum_probs=41.0

Q ss_pred             cccccCCCCcccccccccccccCCCceEEeCCCCcccHHhHHHHH-hcCCCCCCCCCCCCC
Q 042112           41 DRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWI-SNNYAICPVCHDSIA  100 (132)
Q Consensus        41 ~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl-~~~~~~CP~Cr~~~~  100 (132)
                      .......+++...|.||-+.+.-   ...+||+|..|--|..+-- -..+..||.||++..
T Consensus        51 tsSaddtDEen~~C~ICA~~~TY---s~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e  108 (493)
T COG5236          51 TSSADDTDEENMNCQICAGSTTY---SARYPCGHQICHACAVRLRALYMQKGCPLCRTETE  108 (493)
T ss_pred             cccccccccccceeEEecCCceE---EEeccCCchHHHHHHHHHHHHHhccCCCccccccc
Confidence            33344454677899999987765   5667999999999986543 123468999998754

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

Probab=96.67  E-value=0.001  Score=51.69  Aligned_cols=45  Identities=27%  Similarity=0.558  Sum_probs=34.4

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      ...+.|.||+++..+   ...+||||.-|  |......  ..+||+||..+.
T Consensus       303 ~~p~lcVVcl~e~~~---~~fvpcGh~cc--ct~cs~~--l~~CPvCR~rI~  347 (355)
T KOG1571|consen  303 PQPDLCVVCLDEPKS---AVFVPCGHVCC--CTLCSKH--LPQCPVCRQRIR  347 (355)
T ss_pred             CCCCceEEecCCccc---eeeecCCcEEE--chHHHhh--CCCCchhHHHHH
Confidence            456789999998766   77789999955  7666544  357999998763

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=96.64  E-value=0.0012  Score=37.91  Aligned_cols=46  Identities=26%  Similarity=0.527  Sum_probs=32.2

Q ss_pred             cccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCC
Q 042112           52 VECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR  103 (132)
Q Consensus        52 ~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  103 (132)
                      ..|..|...   +.+-..+||+|..+..|..-+   +-+-||.|-+++...+
T Consensus         8 ~~~~~~~~~---~~~~~~~pCgH~I~~~~f~~~---rYngCPfC~~~~~~~~   53 (55)
T PF14447_consen    8 QPCVFCGFV---GTKGTVLPCGHLICDNCFPGE---RYNGCPFCGTPFEFDD   53 (55)
T ss_pred             eeEEEcccc---ccccccccccceeeccccChh---hccCCCCCCCcccCCC
Confidence            345555543   223455799999999998764   3467999999886554

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

Probab=96.47  E-value=0.0019  Score=49.17  Aligned_cols=53  Identities=26%  Similarity=0.712  Sum_probs=42.2

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhc-----------------C-----CCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN-----------------N-----YAICPVCHDSIAP  101 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~-----------------~-----~~~CP~Cr~~~~~  101 (132)
                      -....|.||+-.|..++....++|.|.||..|+.++++.                 +     ...||+||..+..
T Consensus       113 ~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~  187 (368)
T KOG4445|consen  113 HPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI  187 (368)
T ss_pred             CCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence            456689999999999888888999999999999776511                 0     1269999988753

>PF04641 Rtf2: Rtf2 RING-finger

Probab=96.45  E-value=0.0049  Score=46.31  Aligned_cols=54  Identities=19%  Similarity=0.347  Sum_probs=43.3

Q ss_pred             CcccccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      .....|||...+|........+ +|||+|...++..--  ....||+|-.++...+.
T Consensus       111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~~~Di  165 (260)
T PF04641_consen  111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFTEEDI  165 (260)
T ss_pred             CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc--ccccccccCCccccCCE
Confidence            5678999999999665555556 999999999999973  24679999999876554

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

Probab=96.41  E-value=0.0031  Score=47.77  Aligned_cols=52  Identities=21%  Similarity=0.504  Sum_probs=37.8

Q ss_pred             ccccccccccCCCceEEe--CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112           53 ECAVCLSHIEEGEEIREL--SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        53 ~C~IC~~~~~~~~~~~~l--~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      .|++|..+.--+..+..+  +|+|..|.+|++.-+..+...||.|-..+-....
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nf   55 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNNF   55 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhccc
Confidence            589998754332222222  9999999999999997777899999776644433

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

Probab=96.38  E-value=0.0017  Score=49.53  Aligned_cols=54  Identities=19%  Similarity=0.506  Sum_probs=39.5

Q ss_pred             ccccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCC-CCCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVC-HDSIAPSRWLTG  107 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~C-r~~~~~~~~~~~  107 (132)
                      ...|+.|..-+.+.   ..+ -|+|.||..||...|......||.| |+++.......+
T Consensus       274 ~LkCplc~~Llrnp---~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdvlld~l~pD  329 (427)
T COG5222         274 SLKCPLCHCLLRNP---MKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLDGLTPD  329 (427)
T ss_pred             cccCcchhhhhhCc---ccCccccchHHHHHHhhhhhhccccCCCcccccchhhccCcc
Confidence            36899999887773   334 5899999999999886556899999 445544444333

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

Probab=96.34  E-value=0.0034  Score=49.34  Aligned_cols=50  Identities=20%  Similarity=0.333  Sum_probs=41.6

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCC--CCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNY--AICPVCHDSI   99 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~--~~CP~Cr~~~   99 (132)
                      .--.|||=.+.-.+...+..|.|||+..++-+.+..+++.  ..||.|=...
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~  384 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ  384 (394)
T ss_pred             ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence            4568999999888878888899999999999999887655  5799995433

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

Probab=96.28  E-value=0.0024  Score=47.16  Aligned_cols=51  Identities=24%  Similarity=0.552  Sum_probs=35.9

Q ss_pred             ccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCCC
Q 042112           53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTG  107 (132)
Q Consensus        53 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~  107 (132)
                      .|..|..--. ++....+.|.|+||..|...-.   ...||.|++++-...+..+
T Consensus         5 hCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~---~~~C~lCkk~ir~i~l~~s   55 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLTACRHVFCEPCLKASS---PDVCPLCKKSIRIIQLNRS   55 (233)
T ss_pred             EeccccccCC-CCceeeeechhhhhhhhcccCC---ccccccccceeeeeecccc
Confidence            4777765444 5566777999999999987632   2489999998755444443

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

Probab=96.16  E-value=0.019  Score=44.34  Aligned_cols=47  Identities=23%  Similarity=0.465  Sum_probs=36.1

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDS   98 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~   98 (132)
                      .+...|++|+....++.  ....-|-+||..|+-.+.. +...||+=-.+
T Consensus       298 ~~~~~CpvClk~r~Npt--vl~vSGyVfCY~Ci~~Yv~-~~~~CPVT~~p  344 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQNPT--VLEVSGYVFCYPCIFSYVV-NYGHCPVTGYP  344 (357)
T ss_pred             CccccChhHHhccCCCc--eEEecceEEeHHHHHHHHH-hcCCCCccCCc
Confidence            46779999999877632  2225799999999999998 46899985444

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

Probab=96.15  E-value=0.0016  Score=50.01  Aligned_cols=51  Identities=20%  Similarity=0.555  Sum_probs=40.4

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR  103 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  103 (132)
                      ...+|.+|-.-+.++.  ....|-|.||+.||...+.. +..||+|...+....
T Consensus        14 ~~itC~LC~GYliDAT--TI~eCLHTFCkSCivk~l~~-~~~CP~C~i~ih~t~   64 (331)
T KOG2660|consen   14 PHITCRLCGGYLIDAT--TITECLHTFCKSCIVKYLEE-SKYCPTCDIVIHKTH   64 (331)
T ss_pred             cceehhhccceeecch--hHHHHHHHHHHHHHHHHHHH-hccCCccceeccCcc
Confidence            5678999988777643  33479999999999999986 579999988775444

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

Probab=96.15  E-value=0.0034  Score=48.96  Aligned_cols=48  Identities=19%  Similarity=0.405  Sum_probs=38.8

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      .++..|+||...--.   ....||+|.-|..||.+-+.+ .+.|=.|++.+.
T Consensus       420 sEd~lCpICyA~pi~---Avf~PC~H~SC~~CI~qHlmN-~k~CFfCktTv~  467 (489)
T KOG4692|consen  420 SEDNLCPICYAGPIN---AVFAPCSHRSCYGCITQHLMN-CKRCFFCKTTVI  467 (489)
T ss_pred             cccccCcceecccch---hhccCCCCchHHHHHHHHHhc-CCeeeEecceee
Confidence            478899999875333   444699999999999999984 578999988765

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

Probab=96.11  E-value=0.0032  Score=47.83  Aligned_cols=47  Identities=21%  Similarity=0.376  Sum_probs=38.2

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      -...|-||...|..   +.+..|+|.||..|...=++. ...|++|-+...
T Consensus       240 ~Pf~c~icr~~f~~---pVvt~c~h~fc~~ca~~~~qk-~~~c~vC~~~t~  286 (313)
T KOG1813|consen  240 LPFKCFICRKYFYR---PVVTKCGHYFCEVCALKPYQK-GEKCYVCSQQTH  286 (313)
T ss_pred             CCcccccccccccc---chhhcCCceeehhhhcccccc-CCcceecccccc
Confidence            35579999999988   566789999999999887764 478999977653

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

Probab=96.09  E-value=0.0054  Score=48.54  Aligned_cols=36  Identities=22%  Similarity=0.661  Sum_probs=29.5

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHH
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWI   85 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl   85 (132)
                      .-..|.||+++..-......+||+|+||+.|...++
T Consensus       183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~  218 (445)
T KOG1814|consen  183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYF  218 (445)
T ss_pred             hcccceeeehhhcCcceeeecccchHHHHHHHHHHH
Confidence            356899999986544556667999999999999998

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

Probab=95.98  E-value=0.0068  Score=43.04  Aligned_cols=34  Identities=35%  Similarity=0.914  Sum_probs=26.6

Q ss_pred             eCCCCcccHHhHHHHHhc----CC------CCCCCCCCCCCCCC
Q 042112           70 LSCHHLFHAVCLDTWISN----NY------AICPVCHDSIAPSR  103 (132)
Q Consensus        70 l~C~H~fh~~Ci~~wl~~----~~------~~CP~Cr~~~~~~~  103 (132)
                      ..||.-||.-|+..|++.    ++      ..||.|-.++..+-
T Consensus       188 ~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKm  231 (234)
T KOG3268|consen  188 IQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKM  231 (234)
T ss_pred             cccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeec
Confidence            479999999999999832    22      27999999886543

>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=95.97  E-value=0.0035  Score=46.43  Aligned_cols=50  Identities=32%  Similarity=0.594  Sum_probs=38.1

Q ss_pred             cccccccccccccCCCceEEe--C-CCCcccHHhHHHHHhcCCCCCC--CCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIREL--S-CHHLFHAVCLDTWISNNYAICP--VCHDSI   99 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l--~-C~H~fh~~Ci~~wl~~~~~~CP--~Cr~~~   99 (132)
                      .+..||+|..+--.+-.+..+  | |-|..|.+|+++-+..+...||  -|-+-+
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL   63 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL   63 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence            466899999875443334444  5 9999999999999977788999  785433

>PHA03096 p28-like protein; Provisional

Probab=95.94  E-value=0.0042  Score=47.32  Aligned_cols=46  Identities=22%  Similarity=0.516  Sum_probs=31.5

Q ss_pred             cccccccccccCCC----ceEEe-CCCCcccHHhHHHHHhcCC--CCCCCCCC
Q 042112           52 VECAVCLSHIEEGE----EIREL-SCHHLFHAVCLDTWISNNY--AICPVCHD   97 (132)
Q Consensus        52 ~~C~IC~~~~~~~~----~~~~l-~C~H~fh~~Ci~~wl~~~~--~~CP~Cr~   97 (132)
                      ..|.||++......    .-..| .|.|.||..|+..|...+.  ..||.||.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            68999999775432    12334 8999999999999984332  34555443

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

Probab=95.84  E-value=0.011  Score=46.40  Aligned_cols=30  Identities=20%  Similarity=0.790  Sum_probs=23.2

Q ss_pred             CCCcccHHhHHHHHhcCC------------CCCCCCCCCCCC
Q 042112           72 CHHLFHAVCLDTWISNNY------------AICPVCHDSIAP  101 (132)
Q Consensus        72 C~H~fh~~Ci~~wl~~~~------------~~CP~Cr~~~~~  101 (132)
                      |....|.+|+.+|+..++            ..||+||+.+..
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi  352 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI  352 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence            557789999999994433            269999998764

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

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

Probab=95.37  E-value=0.0034  Score=47.67  Aligned_cols=41  Identities=27%  Similarity=0.662  Sum_probs=30.5

Q ss_pred             ccccccccccccCCCceEEeCCCCcc-cHHhHHHHHhcCCCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEGEEIRELSCHHLF-HAVCLDTWISNNYAICPVCHDSI   99 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~~~~~l~C~H~f-h~~Ci~~wl~~~~~~CP~Cr~~~   99 (132)
                      +.-|+||++...+   ...|+|||.. |..|-+.     -..||+||+.+
T Consensus       300 ~~LC~ICmDaP~D---CvfLeCGHmVtCt~CGkr-----m~eCPICRqyi  341 (350)
T KOG4275|consen  300 RRLCAICMDAPRD---CVFLECGHMVTCTKCGKR-----MNECPICRQYI  341 (350)
T ss_pred             HHHHHHHhcCCcc---eEEeecCcEEeehhhccc-----cccCchHHHHH
Confidence            6789999998766   7889999963 3455333     24799999755

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

Probab=95.30  E-value=0.011  Score=44.82  Aligned_cols=47  Identities=26%  Similarity=0.671  Sum_probs=37.9

Q ss_pred             cccccccccccccCCCc-eEEeCCCCcccHHhHHHHHhcCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEE-IRELSCHHLFHAVCLDTWISNNYAICPVCHD   97 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~-~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~   97 (132)
                      ....||||.+.+..... +..++|||.-|..|+......+ .+||+|.+
T Consensus       157 ~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~  204 (276)
T KOG1940|consen  157 SEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK  204 (276)
T ss_pred             ccCCCchhHHHhccccccCCccCcccchHHHHHHHHhccC-CCCCcccc
Confidence            34459999997766543 5667999999999999988755 89999987

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

Probab=94.99  E-value=0.014  Score=50.02  Aligned_cols=43  Identities=23%  Similarity=0.685  Sum_probs=32.9

Q ss_pred             ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI   99 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~   99 (132)
                      ...|..|-..+..+  ..-..|+|.||.+|+..    +...||.|+.+.
T Consensus       840 ~skCs~C~~~LdlP--~VhF~CgHsyHqhC~e~----~~~~CP~C~~e~  882 (933)
T KOG2114|consen  840 VSKCSACEGTLDLP--FVHFLCGHSYHQHCLED----KEDKCPKCLPEL  882 (933)
T ss_pred             eeeecccCCccccc--eeeeecccHHHHHhhcc----CcccCCccchhh
Confidence            46899998887763  23347999999999982    457899998743

>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=94.91  E-value=0.0081  Score=33.39  Aligned_cols=43  Identities=23%  Similarity=0.627  Sum_probs=24.0

Q ss_pred             ccccccccccCCCceEEeCCC-CcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112           53 ECAVCLSHIEEGEEIRELSCH-HLFHAVCLDTWISNNYAICPVCHDSIAP  101 (132)
Q Consensus        53 ~C~IC~~~~~~~~~~~~l~C~-H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  101 (132)
                      .|.-|+-....     .+.|+ |..|..|+...+.. ...||+|..+++.
T Consensus         4 nCKsCWf~~k~-----Li~C~dHYLCl~CLt~ml~~-s~~C~iC~~~LPt   47 (50)
T PF03854_consen    4 NCKSCWFANKG-----LIKCSDHYLCLNCLTLMLSR-SDRCPICGKPLPT   47 (50)
T ss_dssp             ---SS-S--SS-----EEE-SS-EEEHHHHHHT-SS-SSEETTTTEE---
T ss_pred             cChhhhhcCCC-----eeeecchhHHHHHHHHHhcc-ccCCCcccCcCcc
Confidence            47777754322     23586 99999999999874 4789999998874

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.

>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=94.75  E-value=0.041  Score=38.33  Aligned_cols=36  Identities=31%  Similarity=0.697  Sum_probs=22.6

Q ss_pred             cccccccccccccCCC---------ceEEeCCC-CcccHHhHHHHH
Q 042112           50 EAVECAVCLSHIEEGE---------EIRELSCH-HLFHAVCLDTWI   85 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~---------~~~~l~C~-H~fh~~Ci~~wl   85 (132)
                      ++..|+|||+--.++-         ..+-.-|+ -.-|..|++++.
T Consensus         1 ed~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfk   46 (162)
T PF07800_consen    1 EDVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFK   46 (162)
T ss_pred             CCccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHH
Confidence            4578999999765521         11212244 345789999875

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=94.59  E-value=0.0097  Score=45.66  Aligned_cols=43  Identities=26%  Similarity=0.673  Sum_probs=33.5

Q ss_pred             cccccccccccccCCCceEEeCC--CCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSC--HHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C--~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      +-.+||||.+.+..+   + ..|  ||..|..|-.+    ....||.||.++.
T Consensus        47 ~lleCPvC~~~l~~P---i-~QC~nGHlaCssC~~~----~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   47 DLLDCPVCFNPLSPP---I-FQCDNGHLACSSCRTK----VSNKCPTCRLPIG   91 (299)
T ss_pred             hhccCchhhccCccc---c-eecCCCcEehhhhhhh----hcccCCccccccc
Confidence            456899999998862   2 456  59999988764    3468999999987

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

Probab=94.19  E-value=0.045  Score=47.03  Aligned_cols=69  Identities=14%  Similarity=0.412  Sum_probs=48.6

Q ss_pred             CCCcccccccccccccCCCceEEeCCC-----CcccHHhHHHHHhc-CCCCCCCCCCCCCCCCCCCCCCCcEEEee
Q 042112           47 SRAEAVECAVCLSHIEEGEEIRELSCH-----HLFHAVCLDTWISN-NYAICPVCHDSIAPSRWLTGHGEEVLVLK  116 (132)
Q Consensus        47 ~~~~~~~C~IC~~~~~~~~~~~~l~C~-----H~fh~~Ci~~wl~~-~~~~CP~Cr~~~~~~~~~~~~~~~~~~~~  116 (132)
                      ..+++..|.||..+-.++++.- -||.     ...|.+|+.+|+.- +...|-.|..++..++.-...-.++..+.
T Consensus         8 mN~d~~~CRICr~e~~~d~pLf-hPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~IY~e~mP~~IPfs   82 (1175)
T COG5183           8 MNEDKRSCRICRTEDIRDDPLF-HPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDIYKEDMPQIIPFS   82 (1175)
T ss_pred             CCccchhceeecCCCCCCCcCc-ccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeeecccCCCccccee
Confidence            3356789999998766655422 3665     57899999999942 33579999999887776666555555443

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

Probab=94.12  E-value=0.026  Score=48.55  Aligned_cols=35  Identities=23%  Similarity=0.399  Sum_probs=27.6

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHH
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTW   84 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w   84 (132)
                      ++++.|.+|..++... .-...||||.||.+|+.+-
T Consensus       815 ep~d~C~~C~~~ll~~-pF~vf~CgH~FH~~Cl~~~  849 (911)
T KOG2034|consen  815 EPQDSCDHCGRPLLIK-PFYVFPCGHCFHRDCLIRH  849 (911)
T ss_pred             cCccchHHhcchhhcC-cceeeeccchHHHHHHHHH
Confidence            5678999999887653 3444599999999999664

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

Probab=94.09  E-value=0.012  Score=49.87  Aligned_cols=49  Identities=24%  Similarity=0.545  Sum_probs=37.6

Q ss_pred             cccccccccccCCCceEEeCCCCcccHHhHHHHHhcCC-CCCCCCCCCCCCCCC
Q 042112           52 VECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNY-AICPVCHDSIAPSRW  104 (132)
Q Consensus        52 ~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~-~~CP~Cr~~~~~~~~  104 (132)
                      ..|.+|++    .+.+...+|+|.||..|+..-++..+ ..||.||..+.....
T Consensus       455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l  504 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKL  504 (674)
T ss_pred             cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHH
Confidence            78999998    23366679999999999999885433 359999987765443

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

Probab=93.81  E-value=0.0028  Score=49.83  Aligned_cols=51  Identities=18%  Similarity=0.594  Sum_probs=42.2

Q ss_pred             ccccccccccccCC-CceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEG-EEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS  102 (132)
Q Consensus        51 ~~~C~IC~~~~~~~-~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  102 (132)
                      ...|+||.+.+... ++...+-|||.+|..|+.+|+.. ...||.|+..++..
T Consensus       196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~-~~kl~~~~rel~~~  247 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLAT-KRKLPSCRRELPKN  247 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHH-HHHhHHHHhhhhhh
Confidence            45799999988776 55666789999999999999965 47899999988643

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.06  E-value=0.049  Score=40.82  Aligned_cols=52  Identities=23%  Similarity=0.579  Sum_probs=35.5

Q ss_pred             CcccccccccccccCCCce-EEeCCC-----CcccHHhHHHHHhcCCC-------CCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEI-RELSCH-----HLFHAVCLDTWISNNYA-------ICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~-~~l~C~-----H~fh~~Ci~~wl~~~~~-------~CP~Cr~~~~  100 (132)
                      +.+..|-||+..=+++... =+-||.     |=.|..|+..|..+++.       .||.|+++..
T Consensus        18 e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi   82 (293)
T KOG3053|consen   18 ELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI   82 (293)
T ss_pred             ccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence            5677899999864443221 112664     78899999999943322       5999998764

>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=92.80  E-value=0.35  Score=37.45  Aligned_cols=48  Identities=21%  Similarity=0.351  Sum_probs=37.3

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCC--CCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNY--AICPVCH   96 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~--~~CP~Cr   96 (132)
                      -.--.||+-.+.-.+...+..|.|||+.-+.-++..-+++.  ..||.|-
T Consensus       334 Hs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP  383 (396)
T COG5109         334 HSLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP  383 (396)
T ss_pred             cceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence            34568999888777766677789999999999998775442  4699994

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

Probab=92.45  E-value=0.085  Score=40.05  Aligned_cols=50  Identities=24%  Similarity=0.600  Sum_probs=35.8

Q ss_pred             ccccccccccccCCCc-eEEeCCC-----CcccHHhHHHHHhc-CCCCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEGEE-IRELSCH-----HLFHAVCLDTWISN-NYAICPVCHDSIA  100 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~~-~~~l~C~-----H~fh~~Ci~~wl~~-~~~~CP~Cr~~~~  100 (132)
                      +..|-||..+...... ....||.     +..|..|+..|+.. +...|.+|.....
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~  134 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI  134 (323)
T ss_pred             CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence            4689999997654322 2334665     77899999999953 3467999987654

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.41  E-value=0.071  Score=40.75  Aligned_cols=30  Identities=27%  Similarity=0.659  Sum_probs=23.3

Q ss_pred             CCCcccHHhHHHHHhcCC------------CCCCCCCCCCCC
Q 042112           72 CHHLFHAVCLDTWISNNY------------AICPVCHDSIAP  101 (132)
Q Consensus        72 C~H~fh~~Ci~~wl~~~~------------~~CP~Cr~~~~~  101 (132)
                      |....|.+|+.+|+..++            .+||+||+.+.-
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci  366 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCI  366 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEE
Confidence            567889999999984432            379999998764

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

Probab=92.29  E-value=0.065  Score=42.57  Aligned_cols=37  Identities=27%  Similarity=0.593  Sum_probs=27.1

Q ss_pred             cccccccccccccCC-CceEEeCCCCcccHHhHHHHHh
Q 042112           50 EAVECAVCLSHIEEG-EEIRELSCHHLFHAVCLDTWIS   86 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~-~~~~~l~C~H~fh~~Ci~~wl~   86 (132)
                      ...+|.||..+...+ +......|+|.||.+|..+.++
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~ie  182 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIE  182 (384)
T ss_pred             ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhh
Confidence            467899999444333 3333458999999999998885

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

Probab=91.72  E-value=0.091  Score=40.47  Aligned_cols=43  Identities=30%  Similarity=0.617  Sum_probs=28.1

Q ss_pred             ccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        53 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      -|.-|-..+..  --+..||.|+||.+|...=   .-+.||.|-..+.
T Consensus        92 fCd~Cd~PI~I--YGRmIPCkHvFCl~CAr~~---~dK~Cp~C~d~Vq  134 (389)
T KOG2932|consen   92 FCDRCDFPIAI--YGRMIPCKHVFCLECARSD---SDKICPLCDDRVQ  134 (389)
T ss_pred             eecccCCccee--eecccccchhhhhhhhhcC---ccccCcCcccHHH
Confidence            46666554433  1244599999999997641   2357999976553

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

Probab=91.14  E-value=0.24  Score=33.58  Aligned_cols=54  Identities=28%  Similarity=0.660  Sum_probs=35.5

Q ss_pred             cccccccccccccCCCceEE-eCCCCcccHHhHHH-HH-hcCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRE-LSCHHLFHAVCLDT-WI-SNNYAICPVCHDSIAPSR  103 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~-l~C~H~fh~~Ci~~-wl-~~~~~~CP~Cr~~~~~~~  103 (132)
                      .-.+|.||.|.-.+..-..- --||-..|.-|-.. |- ..-+..||+|++++..+.
T Consensus        79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~  135 (140)
T PF05290_consen   79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS  135 (140)
T ss_pred             CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence            45789999987655321110 13898888887765 54 222478999999885443

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

Probab=90.47  E-value=0.2  Score=43.00  Aligned_cols=39  Identities=26%  Similarity=0.696  Sum_probs=26.2

Q ss_pred             cccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCC
Q 042112           54 CAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPV   94 (132)
Q Consensus        54 C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~   94 (132)
                      |+||........ .....|+|+.|.+|...|+..+ ..||.
T Consensus      1031 C~~C~l~V~gss-~~Cg~C~Hv~H~sc~~eWf~~g-d~Cps 1069 (1081)
T KOG0309|consen 1031 CAICHLAVRGSS-NFCGTCGHVGHTSCMMEWFRTG-DVCPS 1069 (1081)
T ss_pred             eeeEeeEeeccc-hhhccccccccHHHHHHHHhcC-CcCCC
Confidence            555544433221 2234799999999999999864 68874

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

Probab=90.28  E-value=0.17  Score=40.84  Aligned_cols=35  Identities=29%  Similarity=0.538  Sum_probs=30.3

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHh
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWIS   86 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~   86 (132)
                      +++..|+||..-|++   ++.|||+|..|..|...-+.
T Consensus         2 eeelkc~vc~~f~~e---piil~c~h~lc~~ca~~~~~   36 (699)
T KOG4367|consen    2 EEELKCPVCGSFYRE---PIILPCSHNLCQACARNILV   36 (699)
T ss_pred             cccccCceehhhccC---ceEeecccHHHHHHHHhhcc
Confidence            467789999998887   78899999999999987664

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=89.87  E-value=0.51  Score=27.01  Aligned_cols=44  Identities=25%  Similarity=0.625  Sum_probs=30.9

Q ss_pred             cccccccccccccCCCceEE-eCCCCcccHHhHHHHHhcCCCCCCC--CCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRE-LSCHHLFHAVCLDTWISNNYAICPV--CHDS   98 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~-l~C~H~fh~~Ci~~wl~~~~~~CP~--Cr~~   98 (132)
                      ....|++|-+++.+++...+ -.|+--+|+.|...     ...|-.  |..+
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~-----~g~C~~~~c~~~   50 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK-----AGGCINYSCGTG   50 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh-----CCceEeccCCCC
Confidence            45679999999986555443 38999999999543     245654  5443

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.51  E-value=0.42  Score=35.90  Aligned_cols=53  Identities=17%  Similarity=0.332  Sum_probs=40.0

Q ss_pred             cccccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWL  105 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~  105 (132)
                      ....|+|=.-+|.....-..+ +|||+|-..-+.+-   +..+|++|...+...+..
T Consensus       110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei---kas~C~~C~a~y~~~dvI  163 (293)
T KOG3113|consen  110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI---KASVCHVCGAAYQEDDVI  163 (293)
T ss_pred             ceeecccccceecceEEEEEEeccceeccHHHHHHh---hhccccccCCcccccCeE
Confidence            456899988777765544445 99999999888774   347899999998776643

>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A

Probab=86.02  E-value=0.81  Score=28.14  Aligned_cols=51  Identities=16%  Similarity=0.396  Sum_probs=22.7

Q ss_pred             cccccccccccccCCCc--eEE--eCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEE--IRE--LSCHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~--~~~--l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      ....|.||-++......  +-.  ..|+--.|+.|..-=.+.+++.||.|+++..
T Consensus         8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk   62 (80)
T PF14569_consen    8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK   62 (80)
T ss_dssp             SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred             CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence            45689999998744322  222  2677778899988766667789999998875

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

Probab=85.55  E-value=0.19  Score=42.55  Aligned_cols=49  Identities=31%  Similarity=0.807  Sum_probs=37.7

Q ss_pred             ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC--CCCCCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN--YAICPVCHDSIAPS  102 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~--~~~CP~Cr~~~~~~  102 (132)
                      ..+|+||.+.+..+   ..+.|.|.|+..|+..-+...  ...||+|+..+...
T Consensus        21 ~lEc~ic~~~~~~p---~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~   71 (684)
T KOG4362|consen   21 ILECPICLEHVKEP---SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKR   71 (684)
T ss_pred             hccCCceeEEeecc---chhhhhHHHHhhhhhceeeccCccccchhhhhhhhhh
Confidence            56799999998874   456899999999998766322  35799999776533

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

Probab=85.37  E-value=0.24  Score=44.64  Aligned_cols=47  Identities=21%  Similarity=0.574  Sum_probs=36.7

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI   99 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~   99 (132)
                      +...|.||++.+..-.  ....|+|.+|..|...|+.. +..||.|+...
T Consensus      1152 ~~~~c~ic~dil~~~~--~I~~cgh~~c~~c~~~~l~~-~s~~~~~ksi~ 1198 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQG--GIAGCGHEPCCRCDELWLYA-SSRCPICKSIK 1198 (1394)
T ss_pred             cccchHHHHHHHHhcC--CeeeechhHhhhHHHHHHHH-hccCcchhhhh
Confidence            4458999999987421  22469999999999999975 57899998543

>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3

Probab=84.65  E-value=1.3  Score=22.40  Aligned_cols=38  Identities=26%  Similarity=0.595  Sum_probs=24.2

Q ss_pred             ccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        53 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      .|..|.+.+..++... ..=+..||..|         ..|..|..++.
T Consensus         1 ~C~~C~~~i~~~~~~~-~~~~~~~H~~C---------f~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVL-RALGKVWHPEC---------FKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEE-EeCCccccccC---------CCCcccCCcCc
Confidence            3778888877652322 23467888766         56777776653

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

>smart00249 PHD PHD zinc finger

Probab=83.51  E-value=0.39  Score=25.38  Aligned_cols=31  Identities=29%  Similarity=0.656  Sum_probs=19.6

Q ss_pred             ccccccccccCCCceEEeCCCCcccHHhHHH
Q 042112           53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDT   83 (132)
Q Consensus        53 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~   83 (132)
                      .|.+|......+..+.--.|...||..|+..
T Consensus         1 ~C~~C~~~~~~~~~i~C~~C~~~~H~~C~~~   31 (47)
T smart00249        1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGP   31 (47)
T ss_pred             CcccCCCcCCCCCEEECCCCCchhhhhhCCC
Confidence            3778877653322222237889999999754

The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the

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

Probab=81.98  E-value=0.57  Score=39.61  Aligned_cols=43  Identities=26%  Similarity=0.537  Sum_probs=31.3

Q ss_pred             ccccccccccccCCC-ceEEeCCCCcccHHhHHHHHhcCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEGE-EIRELSCHHLFHAVCLDTWISNNYAICPVCHD   97 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~-~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~   97 (132)
                      -..|.||+..|-... .++-+.|||..|..|+..-.   +.+|| |..
T Consensus        11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly---n~scp-~~~   54 (861)
T KOG3161|consen   11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY---NASCP-TKR   54 (861)
T ss_pred             HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHh---hccCC-CCc
Confidence            346999987775433 24557899999999999864   36899 543

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

Probab=81.69  E-value=1.2  Score=37.01  Aligned_cols=52  Identities=29%  Similarity=0.802  Sum_probs=39.0

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGH  108 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~  108 (132)
                      +....|.+|++..    ..+..+|.   |..|+.+|+.. +..||.|+..+......+..
T Consensus       477 ~~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~-~~~~pl~~~~~~~~~~~~~~  528 (543)
T KOG0802|consen  477 EPNDVCAICYQEM----SARITPCS---HALCLRKWLYV-QEVCPLCHTYMKEDDFLSKN  528 (543)
T ss_pred             cccCcchHHHHHH----Hhcccccc---chhHHHhhhhh-ccccCCCchhhhcccccCcc
Confidence            4577899999987    24545677   89999999974 47899999887665554443

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=81.31  E-value=0.92  Score=32.86  Aligned_cols=40  Identities=28%  Similarity=0.755  Sum_probs=26.3

Q ss_pred             cccccccccc-----ccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCC
Q 042112           51 AVECAVCLSH-----IEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCH   96 (132)
Q Consensus        51 ~~~C~IC~~~-----~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr   96 (132)
                      +..|.+|-++     |+.+...+--.|+-+||..|..+      ..||-|.
T Consensus       152 GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~------~~CpkC~  196 (202)
T PF13901_consen  152 GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK------KSCPKCA  196 (202)
T ss_pred             CCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC------CCCCCcH
Confidence            5678888642     22222234347999999999762      4699994

>KOG0269 consensus WD40 repeat-containing protein [Function unknown]

Probab=81.20  E-value=1.8  Score=37.23  Aligned_cols=42  Identities=24%  Similarity=0.443  Sum_probs=29.7

Q ss_pred             ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCC
Q 042112           51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPV   94 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~   94 (132)
                      ...|.+|...+..-. .-.--|+|.-|.+|+.+|+.. +..||.
T Consensus       779 ~~~CtVC~~vi~G~~-~~c~~C~H~gH~sh~~sw~~~-~s~ca~  820 (839)
T KOG0269|consen  779 SAKCTVCDLVIRGVD-VWCQVCGHGGHDSHLKSWFFK-ASPCAK  820 (839)
T ss_pred             hcCceeecceeeeeE-eecccccccccHHHHHHHHhc-CCCCcc
Confidence            457888877655411 111259999999999999974 567876

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

Probab=81.11  E-value=0.79  Score=33.42  Aligned_cols=39  Identities=28%  Similarity=0.786  Sum_probs=25.8

Q ss_pred             cccccccccCCCceEEeCCCCc-ccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           54 CAVCLSHIEEGEEIRELSCHHL-FHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        54 C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      |..|.+.-   ..+..+||.|. +|..|-..     -..||+|+.+..
T Consensus       161 Cr~C~~~~---~~VlllPCrHl~lC~~C~~~-----~~~CPiC~~~~~  200 (207)
T KOG1100|consen  161 CRKCGERE---ATVLLLPCRHLCLCGICDES-----LRICPICRSPKT  200 (207)
T ss_pred             ceecCcCC---ceEEeecccceEeccccccc-----CccCCCCcChhh
Confidence            88887652   22566699865 55577443     246999987653

>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]

Probab=80.29  E-value=0.58  Score=39.08  Aligned_cols=24  Identities=38%  Similarity=0.892  Sum_probs=18.9

Q ss_pred             EEeCCCCcccHHhHHHHHhcCCCCCCCC
Q 042112           68 RELSCHHLFHAVCLDTWISNNYAICPVC   95 (132)
Q Consensus        68 ~~l~C~H~fh~~Ci~~wl~~~~~~CP~C   95 (132)
                      +...|+++||..|...    ++..||.|
T Consensus       533 rC~~C~avfH~~C~~r----~s~~CPrC  556 (580)
T KOG1829|consen  533 RCSTCLAVFHKKCLRR----KSPCCPRC  556 (580)
T ss_pred             eHHHHHHHHHHHHHhc----cCCCCCch
Confidence            4458999999999765    44559999

>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]

Probab=80.23  E-value=0.97  Score=33.09  Aligned_cols=45  Identities=33%  Similarity=0.792  Sum_probs=34.0

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHD   97 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~   97 (132)
                      .-..|.+|..-.-.+  .+.=.|+-.+|..|+...++. ...||.|-.
T Consensus       180 nlk~Cn~Ch~LvIqg--~rCg~c~i~~h~~c~qty~q~-~~~cphc~d  224 (235)
T KOG4718|consen  180 NLKNCNLCHCLVIQG--IRCGSCNIQYHRGCIQTYLQR-RDICPHCGD  224 (235)
T ss_pred             HHHHHhHhHHHhhee--eccCcccchhhhHHHHHHhcc-cCcCCchhc
Confidence            345899999865443  333368889999999999985 478999944

>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=80.23  E-value=1.9  Score=24.07  Aligned_cols=44  Identities=23%  Similarity=0.612  Sum_probs=18.9

Q ss_pred             cccccccccccCCCceEEeCCCCcccHHhHHHHH----hcCCCCCCCCCCC
Q 042112           52 VECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWI----SNNYAICPVCHDS   98 (132)
Q Consensus        52 ~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl----~~~~~~CP~Cr~~   98 (132)
                      ..|+|....+..  .++...|.|.-+.+ +..|+    +.+.-.||+|.++
T Consensus         3 L~CPls~~~i~~--P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRI--PVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SS--EEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEEEe--CccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            368888877765  35555899985422 23444    2223469999764

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	132
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		6e-09
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		7e-07
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		5e-06
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		1e-05
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		1e-04

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99
          +C +CLS +EEGE++R L C HLFH VC+D W+  N   CP+C   I
Sbjct: 16 KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKK-CPICRVDI 61

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 36/51 (70%), Gaps = 2/51 (3%)
Query: 50 EAVECAVCLSHIEEGEEIRELS-CHHLFHAVCLDTWISNNYAICPVCHDSI 99
          + VECAVCL+ +E+GEE R L  C H FHA C+D W+  +++ CP+C  ++
Sbjct: 4  DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWL-GSHSTCPLCRLTV 53

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 48  RAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102
           ++E   C VC+   E  + +R L C+H FHA C+D W+  N   CP+C     PS
Sbjct: 20  QSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANR-TCPICRADSGPS 73

>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 = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 49  AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT 106
              +EC VC      GE +R+L C+HLFH  C+  W+   +  CPVC  S+      T
Sbjct: 13  GSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWL-EQHDSCPVCRKSLTGQNTAT 69

>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 = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 46  GSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102
           G+  + + C +C S   +G+   EL CHH FH  C+  W+  +   CPVC     P 
Sbjct: 35  GAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKS-GTCPVCRCMFPPP 90

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	132
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	3e-16
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	8e-15
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	2e-14
2ect_A	78	Ring finger protein 126; metal binding protein, st	2e-14
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	6e-14
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	7e-14
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	4e-11
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	3e-09
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	3e-07
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	4e-07
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	4e-07
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	6e-07
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	1e-06
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	1e-06
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	8e-06
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	1e-05
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	3e-05
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	5e-05
3nw0_A	238	Non-structural maintenance of chromosomes element	1e-04
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	6e-04
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	7e-04

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

 Score = 67.4 bits (165), Expect = 3e-16
 Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 49  AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102
           +E   C VC+   E  + +R L C+H FHA C+D W+  N   CP+C     PS
Sbjct: 21  SEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKAN-RTCPICRADSGPS 73

>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens} Length = 69

 Score = 63.5 bits (155), Expect = 8e-15
 Identities = 24/53 (45%), Positives = 32/53 (60%), Gaps = 1/53 (1%)

Query: 50  EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102
              +C +CLS +EEGE++R L C HLFH VC+D W+  N   CP+C   I   
Sbjct: 13  TEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITN-KKCPICRVDIEAQ 64

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

 Score = 63.1 bits (154), Expect = 2e-14
 Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 44 ELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVC 95
          + G+  + + C +C S   +G+   EL CHH FH  C+  W+  +   CPVC
Sbjct: 33 DHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKS-GTCPVC 83

>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 = 62.4 bits (152), Expect = 2e-14
 Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 7/67 (10%)

Query: 49  AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVC------HDSIAPS 102
              +EC VC      GE +R+L C+HLFH  C+  W+  +   CPVC       ++    
Sbjct: 13  GSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQH-DSCPVCRKSLTGQNTATNP 71

Query: 103 RWLTGHG 109
             LTG G
Sbjct: 72  PGLTGVG 78

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

 Score = 60.7 bits (148), Expect = 6e-14
 Identities = 24/47 (51%), Positives = 34/47 (72%), Gaps = 2/47 (4%)

Query: 50 EAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVC 95
          + VECAVCL+ +E+GEE R L  C H FHA C+D W+ ++ + CP+C
Sbjct: 4  DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSH-STCPLC 49

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

 Score = 61.3 bits (149), Expect = 7e-14
 Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 53  ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102
            CAVCL   +  +E+    C H FH  CL  W+     +CP+C+  +   
Sbjct: 17  LCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVR-KVCPLCNMPVLQL 65

>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 = 53.4 bits (129), Expect = 4e-11
 Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 2/49 (4%)

Query: 53  ECAVCLSHIEEGEE-IRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100
            C +CL  I         L C HL H  C +  +   Y  CP+C    +
Sbjct: 7   GCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYR-CPLCSGPSS 54

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

 Score = 48.9 bits (117), Expect = 3e-09
 Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 5/54 (9%)

Query: 49  AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102
            +  EC +C+    +G     L C H F   C+D W   +   CP+C   +  +
Sbjct: 13  TDEEECCICM----DGRADLILPCAHSFCQKCIDKWSDRH-RNCPICRLQMTGA 61

>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 = 44.9 bits (106), Expect = 3e-07
 Identities = 16/82 (19%), Positives = 28/82 (34%), Gaps = 7/82 (8%)

Query: 49  AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVC-----HDSIAPSR 103
           AE   C +C+  + +        C  L    C+  W++   A CP C        +   R
Sbjct: 20  AEVFRCFICMEKLRDARLC--PHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVNCR 77

Query: 104 WLTGHGEEVLVLKFRCFNSRTE 125
           W     +++  L+        E
Sbjct: 78  WAEEVTQQLDTLQLCSLTKHEE 99

>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 = 46.3 bits (109), Expect = 4e-07
 Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 8/76 (10%)

Query: 28  RINASEQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN 87
            I  +++   ++ +            C +C    E  ++++   C HL    CL +W  +
Sbjct: 314 HIKVTQEQYELYCEMGS-----TFQLCKICA---ENDKDVKIEPCGHLMCTSCLTSWQES 365

Query: 88  NYAICPVCHDSIAPSR 103
               CP C   I  + 
Sbjct: 366 EGQGCPFCRCEIKGTE 381

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

 Score = 46.4 bits (109), Expect = 4e-07
 Identities = 16/68 (23%), Positives = 26/68 (38%), Gaps = 15/68 (22%)

Query: 50  EAVECAVCLSHIEEGEEIRE-----LSCHHLFHAVCLDTWISNN----------YAICPV 94
           E + C +C ++  +G E+         C    HAVCL+ W              +  CP 
Sbjct: 307 EELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPF 366

Query: 95  CHDSIAPS 102
           C   ++ S
Sbjct: 367 CKAKLSTS 374

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

 Score = 43.2 bits (102), Expect = 6e-07
 Identities = 15/43 (34%), Positives = 18/43 (41%), Gaps = 3/43 (6%)

Query: 53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVC 95
           C +CL           L C H F  VC+  WI  N   CP+C
Sbjct: 7  RCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQN-PTCPLC 46

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

 Score = 42.2 bits (99), Expect = 1e-06
 Identities = 16/58 (27%), Positives = 22/58 (37%), Gaps = 5/58 (8%)

Query: 46 GSRAEAVECAVCLSHIEE----GEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99
             +  V C +C+    E    G  I    C H+F + CL   + N    CP C   I
Sbjct: 10 LRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA-NTCPTCRKKI 66

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

 Score = 42.6 bits (100), Expect = 1e-06
 Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 2/43 (4%)

Query: 54 CAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVC 95
          C  C +  ++ + +     C+H FH  C+  W+  N   CP+C
Sbjct: 29 CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQN-NRCPLC 70

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

 Score = 40.1 bits (94), Expect = 8e-06
 Identities = 17/59 (28%), Positives = 22/59 (37%), Gaps = 5/59 (8%)

Query: 49  AEAVECAVCLSHIEE----GEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR 103
              V C +C+    E    G  I    C H+F + CL   + N    CP C   I   R
Sbjct: 1   GAMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA-NTCPTCRKKINHKR 58

>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 = 39.4 bits (92), Expect = 1e-05
 Identities = 17/59 (28%), Positives = 23/59 (38%), Gaps = 5/59 (8%)

Query: 49  AEAVECAVCLSHIEE----GEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR 103
           +  V C +C+    E    G  I    C H+F + CL   + N    CP C   I   R
Sbjct: 8   SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA-NTCPTCRKKINHKR 65

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1 Length = 114

 Score = 39.8 bits (92), Expect = 3e-05
 Identities = 13/62 (20%), Positives = 18/62 (29%), Gaps = 19/62 (30%)

Query: 53 ECAVCLSHIEEGEE---------------IRELSCHHLFHAVCLDTWISN----NYAICP 93
          +C +C+  +                     R   C H FH +CL     N        CP
Sbjct: 27 DCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCP 86

Query: 94 VC 95
           C
Sbjct: 87 SC 88

>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 = 38.0 bits (88), Expect = 5e-05
 Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 3/48 (6%)

Query: 53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWI-SNNYAICPVCHDSI 99
           C +C S + +G+     +C    H  C+  +  SN    CP C+D  
Sbjct: 17 ICNICHSLLIQGQSCE--TCGIRMHLPCVAKYFQSNAEPRCPHCNDYW 62

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

 Score = 38.9 bits (90), Expect = 1e-04
 Identities = 17/94 (18%), Positives = 33/94 (35%), Gaps = 10/94 (10%)

Query: 5   LIRFLRCLKWACNLLLHFSFFGHRINASEQLVNIWEDRFELGSRAEAVECAVCLSHIEEG 64
           +++     KW   L+     F     A  ++     + +          C +C S + +G
Sbjct: 141 VLQKFVQNKW---LIEKEGEFTLHGRAILEMEQYIRETYP----DAVKICNICHSLLIQG 193

Query: 65  EEIRELSCHHLFHAVCLDTWISNNYAI-CPVCHD 97
           +      C    H  C+  +  +N    CP C+D
Sbjct: 194 QSCET--CGIRMHLPCVAKYFQSNAEPRCPHCND 225

>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 = 36.9 bits (85), Expect = 6e-04
 Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 2/66 (3%)

Query: 40  EDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99
           E      S    + C +CL  ++     +E  C H F A C+ T + +    CP C   +
Sbjct: 43  EIVVSPRSLHSELMCPICLDMLKNTMTTKE--CLHRFCADCIITALRSGNKECPTCRKKL 100

Query: 100 APSRWL 105
              R L
Sbjct: 101 VSKRSL 106

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

 Score = 36.3 bits (83), Expect = 7e-04
 Identities = 18/82 (21%), Positives = 29/82 (35%), Gaps = 5/82 (6%)

Query: 49  AEAVECAVCLSHIEEGEEIRE----LSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW 104
           +  V C +C+    E  +         C H+F + CL   + N    CP C   I   R+
Sbjct: 5   SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT-CPTCRKKINHKRY 63

Query: 105 LTGHGEEVLVLKFRCFNSRTER 126
              +     V    C +  +E 
Sbjct: 64  HPIYIGSGTVSCPICMDGYSEI 85

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	132
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.71
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.7
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.64
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.64
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.63
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.63
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.59
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.57
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.55
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.54
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.52
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.51
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.51
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.49
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.49
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.49
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.49
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.48
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.48
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.45
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.45
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.44
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.44
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.42
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.42
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.41
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.41
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.4
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.4
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.39
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.38
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.37
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.36
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.35
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.35
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.34
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.33
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.32
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.32
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.3
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.3
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.29
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.29
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.29
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.28
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.28
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.28
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.23
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.18
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.18
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.15
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.13
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.12
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.12
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.1
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.09
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.09
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.08
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.04
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.98
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.93
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.92
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.91
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.91
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.88
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.83
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.83
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.63
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.59
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.51
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.46
3nw0_A	238	Non-structural maintenance of chromosomes element	98.27
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	96.54
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	95.54
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	94.68
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	90.38
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	89.22
2yt5_A	66	Metal-response element-binding transcription facto	89.04
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	88.7
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	87.95
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	87.31
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	86.98
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	86.85
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	85.88
1we9_A	64	PHD finger family protein; structural genomics, PH	85.64
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	85.51
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	85.34
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	84.03
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	83.68
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	83.56
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	83.15
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	82.0
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	81.37
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	81.14

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

Probab=99.71  E-value=1.4e-17  Score=101.40  Aligned_cols=68  Identities=29%  Similarity=0.682  Sum_probs=56.1

Q ss_pred             cccccceecccccCCCCcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112           33 EQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS  102 (132)
Q Consensus        33 ~~~~~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  102 (132)
                      ...++..++...... .++.+|+||++.+..++.+..++|+|.||..|+..|++. +.+||+||+++.+.
T Consensus         6 i~~lp~~~~~~~~~~-~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A            6 SGQLPSYRFNPNNHQ-SEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKA-NRTCPICRADSGPS   73 (75)
T ss_dssp             CSSCCCEEBCSSSCS-SSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHH-CSSCTTTCCCCCCC
T ss_pred             HhhCCcEEecCcccc-CCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHc-CCcCcCcCCcCCCC
Confidence            456677777654433 567899999999999888888999999999999999975 47999999998754

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

Probab=99.70  E-value=1.9e-17  Score=104.59  Aligned_cols=68  Identities=28%  Similarity=0.656  Sum_probs=55.9

Q ss_pred             cccccceecccccCCCCcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112           33 EQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAP  101 (132)
Q Consensus        33 ~~~~~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  101 (132)
                      .+.++...+........++..|+||++.+..++.+..++|+|.||..||..|++. +.+||+||.++..
T Consensus        22 i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           22 IDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQK-SGTCPVCRCMFPP   89 (91)
T ss_dssp             HHTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTT-TCBCTTTCCBSSC
T ss_pred             HHhCCCeeecccccccCCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHc-CCcCcCcCccCCC
Confidence            4456666666555444677899999999999888888999999999999999975 5799999998864

>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=99.64  E-value=3.4e-16  Score=93.69  Aligned_cols=54  Identities=43%  Similarity=1.021  Sum_probs=46.8

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR  103 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  103 (132)
                      .++..|+||++.+..++.+..++|+|.||..|+..|++. +.+||+||.++....
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~   65 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLIT-NKKCPICRVDIEAQL   65 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHH-CSBCTTTCSBSCSCC
T ss_pred             CCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHc-CCCCcCcCccccCcC
Confidence            467789999999988777888999999999999999975 468999999986544

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

Probab=99.64  E-value=3.4e-16  Score=95.79  Aligned_cols=59  Identities=36%  Similarity=0.840  Sum_probs=50.4

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGH  108 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~  108 (132)
                      .++.+|+||++.+..++.+..++|+|.||..||..|++. +.+||+||.++.......++
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~~~~   71 (78)
T 2ect_A           13 GSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQ-HDSCPVCRKSLTGQNTATNP   71 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTT-TCSCTTTCCCCCCSCSCCCC
T ss_pred             CCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHc-CCcCcCcCCccCCcccCCCC
Confidence            457799999999998877788899999999999999975 47999999999876655543

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

Probab=99.63  E-value=4.6e-16  Score=94.29  Aligned_cols=55  Identities=29%  Similarity=0.694  Sum_probs=47.4

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      .++..|+||++.+..+.....++|+|.||..||.+|++.+ .+||+||.++.....
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~-~~CP~Cr~~~~~~~~   67 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVR-KVCPLCNMPVLQLAQ   67 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHC-SBCTTTCCBCSSCCS
T ss_pred             CCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcC-CcCCCcCcccccccc
Confidence            4577899999999988888888999999999999999754 699999999865443

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

Probab=99.63  E-value=1.5e-16  Score=91.10  Aligned_cols=51  Identities=47%  Similarity=1.073  Sum_probs=44.9

Q ss_pred             CcccccccccccccCCCceEEeC-CCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELS-CHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      +++.+|+||++++..++.+..++ |+|.||..|+.+|++. +.+||+||+++.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~-~~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGS-HSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTT-CCSCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHc-CCcCcCCCCEeE
Confidence            45678999999999888888886 9999999999999975 579999999874

>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=99.59  E-value=1.3e-15  Score=99.45  Aligned_cols=62  Identities=21%  Similarity=0.477  Sum_probs=47.1

Q ss_pred             cccccccccccccCCC---------------ceEEeCCCCcccHHhHHHHHh----cCCCCCCCCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGE---------------EIRELSCHHLFHAVCLDTWIS----NNYAICPVCHDSIAPSRWLTGHGE  110 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~---------------~~~~l~C~H~fh~~Ci~~wl~----~~~~~CP~Cr~~~~~~~~~~~~~~  110 (132)
                      .+.+|+||++.+..+.               ....++|+|.||..||..|+.    ..+.+||+||+.+.......+.+.
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~~g~qp~g~  103 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQPWGK  103 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSSSCTTSS
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCCCCCCCCCe
Confidence            4568999999996643               234569999999999999994    234689999999976655544444


Q ss_pred             c
Q 042112          111 E  111 (132)
Q Consensus       111 ~  111 (132)
                      .
T Consensus       104 m  104 (114)
T 1v87_A          104 M  104 (114)
T ss_dssp             C
T ss_pred             E
Confidence            3

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

Probab=99.57  E-value=1e-15  Score=94.70  Aligned_cols=52  Identities=25%  Similarity=0.753  Sum_probs=41.0

Q ss_pred             cccccccccccccC-----------CCceEEe-CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEE-----------GEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAPS  102 (132)
Q Consensus        50 ~~~~C~IC~~~~~~-----------~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  102 (132)
                      ++++|+||++++.+           ++.++.+ +|+|.||..||.+|++. +.+||+||+++..+
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~~   77 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQ-NNRCPLCQQDWVVQ   77 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTT-CCBCTTTCCBCCEE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHh-CCCCCCcCCCcchh
Confidence            45678888888854           3435555 69999999999999985 47999999988644

>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=99.55  E-value=4.4e-15  Score=84.86  Aligned_cols=51  Identities=25%  Similarity=0.708  Sum_probs=42.7

Q ss_pred             CcccccccccccccCCC-ceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGE-EIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~-~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      .++.+|+||++.+.+++ .+..++|+|.||..|+.+|++.+ .+||+||+++.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~   54 (55)
T 2ecm_A            3 SGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEG-YRCPLCSGPSS   54 (55)
T ss_dssp             SCCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHT-CCCTTSCCSSC
T ss_pred             CCCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcC-CcCCCCCCcCC
Confidence            35678999999986644 45667999999999999999764 89999999875

>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=4.9e-15  Score=88.85  Aligned_cols=56  Identities=29%  Similarity=0.656  Sum_probs=46.0

Q ss_pred             CcccccccccccccCC----CceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEG----EEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWL  105 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~----~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~  105 (132)
                      +++.+|+||++.+.+.    +....++|||.||..|+.+|++. +.+||+||.++...+..
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~   67 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-ANTCPTCRKKINHKRYH   67 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHH-CSBCTTTCCBCCCCSCC
T ss_pred             CCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHc-CCCCCCCCCccChhhee
Confidence            5677899999998763    34466799999999999999975 47999999999766544

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

Probab=99.52  E-value=1.7e-14  Score=89.14  Aligned_cols=62  Identities=23%  Similarity=0.569  Sum_probs=48.0

Q ss_pred             cCCCCcccccccccccccCCCceEEeCCC-----CcccHHhHHHHHhcC-CCCCCCCCCCCCCCCCCCC
Q 042112           45 LGSRAEAVECAVCLSHIEEGEEIRELSCH-----HLFHAVCLDTWISNN-YAICPVCHDSIAPSRWLTG  107 (132)
Q Consensus        45 ~~~~~~~~~C~IC~~~~~~~~~~~~l~C~-----H~fh~~Ci~~wl~~~-~~~CP~Cr~~~~~~~~~~~  107 (132)
                      .....++..|.||++++.+++.. .+||+     |.||..||++|+..+ +.+||+||.++.......+
T Consensus         9 s~~~~~~~~C~IC~~~~~~~~~l-~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~~~~P   76 (80)
T 2d8s_A            9 SITPSSQDICRICHCEGDDESPL-ITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMETKLSG   76 (80)
T ss_dssp             CCCCTTSCCCSSSCCCCCSSSCE-ECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCCCSCC
T ss_pred             CCCCCCCCCCeEcCccccCCCee-EeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCcccCC
Confidence            33445678999999999876655 47996     999999999999643 3589999999976554433

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

Probab=99.51  E-value=3.7e-14  Score=85.53  Aligned_cols=56  Identities=20%  Similarity=0.505  Sum_probs=46.4

Q ss_pred             CcccccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGH  108 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~  108 (132)
                      ++...|+||++.+.+   +..+ +|+|.||..||..|++. +..||+||.++.........
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~~~~   69 (72)
T 2djb_A           13 TPYILCSICKGYLID---ATTITECLHTFCKSCIVRHFYY-SNRCPKCNIVVHQTQPLSGP   69 (72)
T ss_dssp             CGGGSCTTTSSCCSS---CEECSSSCCEECHHHHHHHHHH-CSSCTTTCCCCCSSCSCCCC
T ss_pred             CCCCCCCCCChHHHC---cCEECCCCCHHHHHHHHHHHHc-CCcCCCcCcccCcccccccC
Confidence            567899999999886   4455 99999999999999975 47999999999876665543

>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=2e-14  Score=85.54  Aligned_cols=52  Identities=29%  Similarity=0.662  Sum_probs=43.2

Q ss_pred             CcccccccccccccCC----CceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEG----EEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAP  101 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~----~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  101 (132)
                      .+...|+||++.+.+.    ..+..++|+|.||..|+..|+.. +..||+||.++..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-ANTCPTCRKKINH   68 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHH-CSSCTTTCCCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHc-CCCCCCCCCccCc
Confidence            4677899999998763    23466799999999999999975 5799999998854

>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=99.49  E-value=1.9e-14  Score=93.28  Aligned_cols=51  Identities=25%  Similarity=0.602  Sum_probs=41.9

Q ss_pred             cccccccccccccCCC---------------ceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGE---------------EIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAP  101 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~---------------~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  101 (132)
                      +++.|+||++.+...-               .+..++|+|.||..||..|+.. +.+||+||+++..
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~-~~~CP~Cr~~~~~  101 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-RQVCPLDNREWEF  101 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTT-CSBCSSSCSBCCE
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHc-CCcCcCCCCccee
Confidence            5678999999987541               2455799999999999999985 5799999998753

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

Probab=99.49  E-value=3.1e-14  Score=84.42  Aligned_cols=52  Identities=21%  Similarity=0.584  Sum_probs=43.3

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR  103 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  103 (132)
                      .++..|+||++.+.++   ..++|||.||..|+..|++.++..||+||+++...+
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   64 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCSP---KQTECGHRFCESCMAALLSSSSPKCTACQESIVKDK   64 (66)
T ss_dssp             CCCEECTTTCCEESSC---CCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTT
T ss_pred             CcCCCCCCCChHhcCe---eECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChhh
Confidence            4578899999998873   447999999999999999544578999999987543

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

Probab=99.49  E-value=1.5e-14  Score=84.90  Aligned_cols=53  Identities=30%  Similarity=0.669  Sum_probs=43.8

Q ss_pred             cccccccccccccCC----CceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEG----EEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR  103 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~----~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  103 (132)
                      ++.+|+||++.+.++    +.+..++|||.||..|+.+|++. +.+||+||+++...+
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~   58 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-ANTCPTCRKKINHKR   58 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHH-CSBCTTTCCBCTTTC
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHc-CCCCCCCCccCCccc
Confidence            456899999998753    33466799999999999999975 579999999987654

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

Probab=99.49  E-value=5.7e-14  Score=84.60  Aligned_cols=52  Identities=25%  Similarity=0.643  Sum_probs=43.5

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhc--CCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN--NYAICPVCHDSIAPSR  103 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~--~~~~CP~Cr~~~~~~~  103 (132)
                      .++..|+||++.+.+   +..++|||.||..|+..|++.  ++..||+||.++....
T Consensus        18 ~~~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           18 QEEVICPICLDILQK---PVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCCBCTTTCSBCSS---EEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             ccCCEeccCCcccCC---eEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            567799999999886   666799999999999999962  3468999999987554

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

Probab=99.48  E-value=1.1e-14  Score=87.56  Aligned_cols=52  Identities=25%  Similarity=0.494  Sum_probs=43.8

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      .++..|+||++.+.+   ...++|+|.||..|+..|+.. +..||+||.++.....
T Consensus        13 ~~~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~~~~~-~~~CP~Cr~~~~~~~~   64 (71)
T 2d8t_A           13 LTVPECAICLQTCVH---PVSLPCKHVFCYLCVKGASWL-GKRCALCRQEIPEDFL   64 (71)
T ss_dssp             SSCCBCSSSSSBCSS---EEEETTTEEEEHHHHHHCTTC-SSBCSSSCCBCCHHHH
T ss_pred             CCCCCCccCCcccCC---CEEccCCCHHHHHHHHHHHHC-CCcCcCcCchhCHhhc
Confidence            456789999999876   566899999999999999975 4789999999875443

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

Probab=99.48  E-value=8.1e-14  Score=86.70  Aligned_cols=54  Identities=24%  Similarity=0.604  Sum_probs=45.1

Q ss_pred             CcccccccccccccCCCc-eEEeCCCCcccHHhHHHHHhcC--CCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEE-IRELSCHHLFHAVCLDTWISNN--YAICPVCHDSIAPS  102 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~-~~~l~C~H~fh~~Ci~~wl~~~--~~~CP~Cr~~~~~~  102 (132)
                      .+..+|+||++.+.+.+. +..++|||.||..|+..|+..+  ...||+||.++...
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           13 REVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             cCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            456789999999987664 6667999999999999999653  36899999988654

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

Probab=99.45  E-value=9e-14  Score=84.87  Aligned_cols=55  Identities=13%  Similarity=0.392  Sum_probs=45.9

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT  106 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~  106 (132)
                      .++..|+||++.+.+   +..++|||.||..||..|+..++..||+||.++.......
T Consensus         6 ~~~~~C~IC~~~~~~---Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~l~~   60 (78)
T 1t1h_A            6 PEYFRCPISLELMKD---PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTP   60 (78)
T ss_dssp             SSSSSCTTTSCCCSS---EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEE
T ss_pred             cccCCCCCccccccC---CEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChhhCcc
Confidence            457799999999887   6668999999999999999754678999999987654433

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

Probab=99.45  E-value=7.9e-14  Score=82.40  Aligned_cols=55  Identities=18%  Similarity=0.427  Sum_probs=43.5

Q ss_pred             cccccccccc-cccCCCce-EEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLS-HIEEGEEI-RELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        50 ~~~~C~IC~~-~~~~~~~~-~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      ++..|+||++ .+.++... ..++|||.||..|+.+|+..++..||+||.++.....
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   58 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNF   58 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCC
T ss_pred             CCCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccccc
Confidence            4568999999 77665433 3469999999999999986555789999999875543

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

Probab=99.44  E-value=6.7e-14  Score=83.26  Aligned_cols=50  Identities=30%  Similarity=0.749  Sum_probs=41.7

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAP  101 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  101 (132)
                      +++..|+||++.+.++  ...++|||.||..|+..|++. +.+||+||.++..
T Consensus         3 ~~~~~C~IC~~~~~~~--~~~~~C~H~fc~~Ci~~~~~~-~~~CP~Cr~~~~~   52 (68)
T 1chc_A            3 TVAERCPICLEDPSNY--SMALPCLHAFCYVCITRWIRQ-NPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCCSSCCSCCCSC--EEETTTTEEESTTHHHHHHHH-SCSTTTTCCCCCC
T ss_pred             CCCCCCeeCCccccCC--cEecCCCCeeHHHHHHHHHhC-cCcCcCCChhhHh
Confidence            4567899999998652  466799999999999999975 4799999998863

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

Probab=99.44  E-value=1.7e-13  Score=83.11  Aligned_cols=52  Identities=17%  Similarity=0.539  Sum_probs=42.6

Q ss_pred             CcccccccccccccCCCceEEeC-CCCcccHHhHHHHHhcC-CCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELS-CHHLFHAVCLDTWISNN-YAICPVCHDSIAPSR  103 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~wl~~~-~~~CP~Cr~~~~~~~  103 (132)
                      .++..|+||++.+.+   +..++ |+|.||..||..|++.+ ...||+||+++...+
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2yur_A           13 PDELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD   66 (74)
T ss_dssp             CGGGSCSSSCCCCTT---CEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTT
T ss_pred             CCCCCCcCCChHHhC---CeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCcc
Confidence            467899999999887   56688 99999999999999643 258999999865443

>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=84.58  Aligned_cols=50  Identities=26%  Similarity=0.745  Sum_probs=42.7

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR  103 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  103 (132)
                      .++..|+||++.+.+    ..++|+|.||..|+..|+.. +..||+||.++....
T Consensus        13 ~~~~~C~IC~~~~~~----~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~   62 (70)
T 2ecn_A           13 TDEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDR-HRNCPICRLQMTGAN   62 (70)
T ss_dssp             CCCCCCSSSCCSCCS----EEETTTEEECHHHHHHSSCC-CSSCHHHHHCTTCCC
T ss_pred             CCCCCCeeCCcCccC----cccCCCCcccHHHHHHHHHC-cCcCCCcCCcccCCC
Confidence            456789999999876    56899999999999999974 589999999987544

>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=99.42  E-value=6.4e-14  Score=89.72  Aligned_cols=56  Identities=23%  Similarity=0.661  Sum_probs=45.8

Q ss_pred             CcccccccccccccCCCceEE-eCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRE-LSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTG  107 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~-l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~  107 (132)
                      .++..|+||++.+.+   +.. ++|||.||..||..|+..+...||+||.++........
T Consensus        20 ~~~~~C~IC~~~~~~---p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~l~~~   76 (100)
T 3lrq_A           20 AEVFRCFICMEKLRD---ARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVNC   76 (100)
T ss_dssp             HHHTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEEC
T ss_pred             CCCCCCccCCccccC---ccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHHHhHhh
Confidence            356789999999986   666 79999999999999997544689999999976554433

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

Probab=99.41  E-value=4.6e-14  Score=86.19  Aligned_cols=56  Identities=27%  Similarity=0.530  Sum_probs=45.3

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC------CCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN------YAICPVCHDSIAPSRWLTG  107 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~------~~~CP~Cr~~~~~~~~~~~  107 (132)
                      .++..|+||++.+.+   +..++|||.||..|+..|+...      ...||+||.++.......+
T Consensus        10 ~~~~~C~IC~~~~~~---p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~n   71 (79)
T 2egp_A           10 QEEVTCPICLELLTE---PLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEHLQAN   71 (79)
T ss_dssp             CCCCEETTTTEECSS---CCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSGGGTC
T ss_pred             ccCCCCcCCCcccCC---eeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhhCCcC
Confidence            467789999999877   4557999999999999999642      4689999999976554443

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

Probab=99.41  E-value=2.5e-13  Score=83.55  Aligned_cols=48  Identities=17%  Similarity=0.448  Sum_probs=41.6

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      .+...|+||++.+.+   +..++|+|.||..|+..|++. ...||+||.++.
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~-~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQN---PVVTKCRHYFCESCALEHFRA-TPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCCS---EEECTTSCEEEHHHHHHHHHH-CSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhcC---eeEccCCCHhHHHHHHHHHHC-CCcCCCcCcccc
Confidence            456789999999876   566899999999999999975 578999999985

>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=1.1e-13  Score=93.41  Aligned_cols=48  Identities=27%  Similarity=0.812  Sum_probs=41.4

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAP  101 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  101 (132)
                      ++..|+||++.+.+   +..++|||.||..||..|+.. +.+||+||.++..
T Consensus        52 ~~~~C~iC~~~~~~---~~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           52 NELQCIICSEYFIE---AVTLNCAHSFCSYCINEWMKR-KIECPICRKDIKS   99 (138)
T ss_dssp             HHSBCTTTCSBCSS---EEEETTSCEEEHHHHHHHTTT-CSBCTTTCCBCCC
T ss_pred             ccCCCcccCcccCC---ceECCCCCCccHHHHHHHHHc-CCcCCCCCCcCCC
Confidence            34579999999876   677899999999999999974 5789999998854

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

Probab=99.40  E-value=2.7e-13  Score=83.56  Aligned_cols=55  Identities=27%  Similarity=0.574  Sum_probs=44.7

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC-----CCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN-----YAICPVCHDSIAPSRWLT  106 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~-----~~~CP~Cr~~~~~~~~~~  106 (132)
                      .++..|+||++.+.+   +..++|+|.||..|+..|+...     ...||+||.++.......
T Consensus        17 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~   76 (85)
T 2ecw_A           17 KEEVTCPICLELLKE---PVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLKP   76 (85)
T ss_dssp             CTTTSCTTTCSCCSS---CEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTCCEE
T ss_pred             ccCCCCcCCChhhCc---ceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHhCCc
Confidence            456789999999877   4568999999999999999652     468999999987654433

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

Probab=99.39  E-value=3.4e-13  Score=83.08  Aligned_cols=56  Identities=30%  Similarity=0.620  Sum_probs=45.4

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhc-----CCCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN-----NYAICPVCHDSIAPSRWLTG  107 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~-----~~~~CP~Cr~~~~~~~~~~~  107 (132)
                      .+...|+||++.+.+   +..++|+|.||..|+..|+..     +...||+||..+.......+
T Consensus        17 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~n   77 (85)
T 2ecv_A           17 KEEVTCPICLELLTQ---PLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRPN   77 (85)
T ss_dssp             CCCCCCTTTCSCCSS---CBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSSCCCS
T ss_pred             cCCCCCCCCCcccCC---ceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHhcCcc
Confidence            457799999999876   455799999999999999964     24789999999986555444

>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=99.38  E-value=4.1e-13  Score=88.90  Aligned_cols=49  Identities=22%  Similarity=0.493  Sum_probs=42.6

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAP  101 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  101 (132)
                      ++..|+||++.+.+   +..++|||.||..||..|+..+...||+||.++..
T Consensus        51 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           51 ETFQCICCQELVFR---PITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHTBCTTTSSBCSS---EEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             cCCCCCcCChHHcC---cEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            46689999999886   66689999999999999997555689999999975

>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=99.37  E-value=5.1e-14  Score=92.74  Aligned_cols=52  Identities=29%  Similarity=0.658  Sum_probs=1.1

Q ss_pred             cccccccccccccCC-------------Cc--eEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEG-------------EE--IRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS  102 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~-------------~~--~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  102 (132)
                      +++.|+||++++.+.             +.  +..++|+|.||..||.+|+.. +.+||+||+++..+
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~-~~~CP~Cr~~~~~~  113 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-RQVCPLDNREWEFQ  113 (117)
T ss_dssp             CC------------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHc-CCcCCCCCCeeeee
Confidence            467899999999752             22  222489999999999999985 57999999987544

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

Probab=99.36  E-value=7.9e-13  Score=77.51  Aligned_cols=44  Identities=27%  Similarity=0.721  Sum_probs=37.4

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhc--CCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN--NYAICPVC   95 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~--~~~~CP~C   95 (132)
                      +++..|+||++.+.+   +..++|||.||..||.+|++.  ++..||+|
T Consensus        18 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           18 QEEVICPICLDILQK---PVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCBCTTTCSBCSS---CEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             ccCCCCCcCCchhCC---eEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            567899999999886   566799999999999999963  34689998

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

Probab=99.35  E-value=4.4e-13  Score=88.95  Aligned_cols=55  Identities=29%  Similarity=0.680  Sum_probs=45.2

Q ss_pred             CcccccccccccccCC----CceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEG----EEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~----~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      .++.+|+||++.+.++    +.+..++|||.||..||.+|++. +.+||+||+.+.....
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~l   63 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-ANTCPTCRKKINHKRY   63 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTT-CSBCTTTCCBCTTTCE
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHh-CCCCCCCCCcCccccc
Confidence            4567899999998763    33477899999999999999975 4799999999876544

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

Probab=99.35  E-value=1.7e-12  Score=81.49  Aligned_cols=49  Identities=18%  Similarity=0.577  Sum_probs=41.4

Q ss_pred             CcccccccccccccCCCceEEeC-CCCcccHHhHHHHHhc-CCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELS-CHHLFHAVCLDTWISN-NYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~wl~~-~~~~CP~Cr~~~~  100 (132)
                      .++..|+||++.+.+   +..++ |||.||..||..|+.. ++..||+||.++.
T Consensus        11 ~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           11 PDELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CTTTEETTTTEECSS---CEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CcCCCCCCCChhhcC---ceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            567899999999886   56688 9999999999999953 3368999999873

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

Probab=99.34  E-value=1.2e-12  Score=79.50  Aligned_cols=53  Identities=23%  Similarity=0.548  Sum_probs=42.4

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC-CCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN-YAICPVCHDSIAPSR  103 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~-~~~CP~Cr~~~~~~~  103 (132)
                      +...+|+||.+.+..++...  .|+|.||..||.+|++.+ +.+||+||+++....
T Consensus        13 ~~i~~C~IC~~~i~~g~~C~--~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~   66 (74)
T 2ct0_A           13 DAVKICNICHSLLIQGQSCE--TCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEI   66 (74)
T ss_dssp             SSSCBCSSSCCBCSSSEECS--SSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCC
T ss_pred             CCCCcCcchhhHcccCCccC--CCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCC
Confidence            34578999999998765433  899999999999999643 268999999986443

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

Probab=99.33  E-value=1e-12  Score=75.61  Aligned_cols=44  Identities=32%  Similarity=0.795  Sum_probs=36.7

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhc--CCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN--NYAICPVC   95 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~--~~~~CP~C   95 (132)
                      .++..|+||++.+.+   +..++|+|.||..||..|+..  ++..||+|
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLKE---PVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCSS---CCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccCCCCccCCcccCc---cEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            457789999999987   455799999999999999743  45789998

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

Probab=99.32  E-value=6.5e-13  Score=84.63  Aligned_cols=50  Identities=18%  Similarity=0.650  Sum_probs=42.3

Q ss_pred             cccccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR  103 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  103 (132)
                      +...|+||++.+.+   +..+ +|||.||..|+..|+.. +..||+||.++....
T Consensus        21 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~-~~~CP~Cr~~~~~~~   71 (99)
T 2y43_A           21 DLLRCGICFEYFNI---AMIIPQCSHNYCSLCIRKFLSY-KTQCPTCCVTVTEPD   71 (99)
T ss_dssp             HHTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHTT-CCBCTTTCCBCCGGG
T ss_pred             CCCCcccCChhhCC---cCEECCCCCHhhHHHHHHHHHC-CCCCCCCCCcCChhh
Confidence            46789999999886   5556 89999999999999975 478999999887543

>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=99.32  E-value=1e-12  Score=86.34  Aligned_cols=53  Identities=25%  Similarity=0.535  Sum_probs=44.6

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      .++..|+||++.+.+   +..++|||.||..||..|+..++..||+||.++.....
T Consensus        16 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   68 (118)
T 3hct_A           16 ESKYECPICLMALRE---AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQL   68 (118)
T ss_dssp             CGGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGC
T ss_pred             CCCCCCCcCChhhcC---eEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHHhc
Confidence            567899999999887   56689999999999999996544589999999876543

>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=99.30  E-value=2.2e-12  Score=83.60  Aligned_cols=55  Identities=25%  Similarity=0.686  Sum_probs=44.2

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCC--CCCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNY--AICPVCHDSIAPSRWLTG  107 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~--~~CP~Cr~~~~~~~~~~~  107 (132)
                      +...|+||++.+.+   +..++|||.||..|+..|+..+.  ..||+||.++.......+
T Consensus        20 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~~~~   76 (112)
T 1jm7_A           20 KILECPICLELIKE---PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQES   76 (112)
T ss_dssp             HHTSCSSSCCCCSS---CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBCC
T ss_pred             CCCCCcccChhhcC---eEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhhcCcc
Confidence            45689999999876   44579999999999999997432  489999999987655444

>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=99.30  E-value=2.2e-12  Score=88.34  Aligned_cols=50  Identities=18%  Similarity=0.483  Sum_probs=43.1

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS  102 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  102 (132)
                      +...|+||++.+.+   +..++|||.||..||..|+..+...||+||.++...
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            45689999999887   666899999999999999976545899999999765

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

Probab=99.29  E-value=4.6e-12  Score=77.71  Aligned_cols=55  Identities=18%  Similarity=0.527  Sum_probs=42.8

Q ss_pred             CcccccccccccccCCCceEEe--CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIREL--SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l--~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      +++.+|+||++++...+. ..+  +|||.||..|+..+....+..||.||+++.....
T Consensus         9 ~~~~~CpICle~~~~~d~-~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~   65 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDI-NFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPA   65 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTT-TCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSS
T ss_pred             ccCCcCCccCccCccccc-cccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCch
Confidence            567789999998865332 233  4999999999999885455789999999876544

>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=99.29  E-value=2.7e-12  Score=82.97  Aligned_cols=50  Identities=18%  Similarity=0.594  Sum_probs=42.7

Q ss_pred             CcccccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAPS  102 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  102 (132)
                      .++..|+||++.+.+   +..+ +|||.||..||..|+.. +..||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~-~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           13 NPHLMCVLCGGYFID---ATTIIECLHSFCKTCIVRYLET-SKYCPICDVQVHKT   63 (108)
T ss_dssp             GGGTBCTTTSSBCSS---EEEETTTCCEEEHHHHHHHHTS-CSBCTTTCCBSCSS
T ss_pred             CCcCCCccCChHHhC---cCEeCCCCChhhHHHHHHHHHh-CCcCcCCCcccccc
Confidence            456789999999876   5666 99999999999999975 47899999998754

>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=99.29  E-value=1.7e-12  Score=84.89  Aligned_cols=54  Identities=24%  Similarity=0.600  Sum_probs=45.0

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT  106 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~  106 (132)
                      ++..|+||++.+.+   +..++|||.||..||..|+...+..||+||.++.......
T Consensus        22 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~   75 (116)
T 1rmd_A           22 KSISCQICEHILAD---PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLES   75 (116)
T ss_dssp             HHTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCBC
T ss_pred             CCCCCCCCCcHhcC---cEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhhccc
Confidence            46789999999876   5668999999999999999754578999999987655443

>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=99.28  E-value=4.9e-13  Score=87.39  Aligned_cols=49  Identities=20%  Similarity=0.648  Sum_probs=42.4

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      .++..|+||++.+.+   +..++|||.||..|+..|+..++..||+||..+.
T Consensus        13 ~~~~~C~iC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   61 (115)
T 3l11_A           13 LSECQCGICMEILVE---PVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVS   61 (115)
T ss_dssp             HHHHBCTTTCSBCSS---CEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCH
T ss_pred             CCCCCCccCCcccCc---eeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccC
Confidence            457789999999886   5667999999999999999654578999999885

>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=99.28  E-value=2.1e-12  Score=89.42  Aligned_cols=50  Identities=24%  Similarity=0.618  Sum_probs=42.3

Q ss_pred             CcccccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAP  101 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  101 (132)
                      .+...|+||++.+.+   +..+ +|||.||..||..|+..++..||+||.++..
T Consensus        52 ~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           52 HSELMCPICLDMLKN---TMTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHHHBCTTTSSBCSS---EEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCCcccChHhhC---cCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            356699999999887   5555 9999999999999998546789999999853

>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=99.28  E-value=1.5e-13  Score=93.34  Aligned_cols=51  Identities=18%  Similarity=0.412  Sum_probs=43.4

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS  102 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  102 (132)
                      +++..|+||++.+.+   +..++|||.||..||..|+..+...||+||.++...
T Consensus        29 ~~~~~C~IC~~~~~~---pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   79 (141)
T 3knv_A           29 EAKYLCSACRNVLRR---PFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYE   79 (141)
T ss_dssp             CGGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHGGGSCEECHHHHHTTCCC
T ss_pred             CcCcCCCCCChhhcC---cEECCCCCccCHHHHHHHHhcCCCCCCCCCCccccc
Confidence            567899999999887   566899999999999999975545899999987544

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

Probab=99.23  E-value=5.6e-12  Score=83.53  Aligned_cols=54  Identities=30%  Similarity=0.667  Sum_probs=44.2

Q ss_pred             CcccccccccccccCC----CceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEG----EEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR  103 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~----~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  103 (132)
                      ++...|+||++.+.+.    .....++|||.||..|+.+|+.. +.+||+||.++...+
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~  127 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-ANTCPTCRKKINHKR  127 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHH-CSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHc-CCCCCCCCCcCChhc
Confidence            4567899999998752    33466799999999999999975 479999999987554

>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=6.3e-12  Score=72.23  Aligned_cols=48  Identities=21%  Similarity=0.503  Sum_probs=39.5

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR  103 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  103 (132)
                      .+...|+||++.+.+   +..++|+|.||..|+..|    ...||+||+++....
T Consensus         4 ~~~~~C~IC~~~~~~---p~~l~CgH~fC~~Ci~~~----~~~CP~Cr~~~~~~~   51 (56)
T 1bor_A            4 FQFLRCQQCQAEAKC---PKLLPCLHTLCSGCLEAS----GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CCCSSCSSSCSSCBC---CSCSTTSCCSBTTTCSSS----SSSCSSCCSSSSCCS
T ss_pred             ccCCCceEeCCccCC---eEEcCCCCcccHHHHccC----CCCCCcCCcEeecCC
Confidence            456789999999887   566899999999999873    468999999886543

>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=99.18  E-value=1.8e-11  Score=72.21  Aligned_cols=48  Identities=21%  Similarity=0.418  Sum_probs=39.9

Q ss_pred             CcccccccccccccCCCceEEe--CCCCc-ccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIREL--SCHHL-FHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l--~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      +++.+|+||++...+   ...+  ||||. |+..|+..|.+. +..||+||+++.
T Consensus         6 ~~~~~C~IC~~~~~~---~~~~~~pCgH~~~C~~C~~~~~~~-~~~CPiCR~~i~   56 (64)
T 2vje_A            6 NAIEPCVICQGRPKN---GCIVHGKTGHLMACFTCAKKLKKR-NKPCPVCRQPIQ   56 (64)
T ss_dssp             GGGSCCTTTSSSCSC---EEEEETTEEEEEECHHHHHHHHHT-TCCCTTTCCCCC
T ss_pred             CCcCCCCcCCCCCCC---EEEECCCCCChhhHHHHHHHHHHc-CCcCCCcCcchh
Confidence            456789999998665   4555  99999 899999999975 478999999884

>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=99.15  E-value=2.9e-11  Score=93.77  Aligned_cols=49  Identities=24%  Similarity=0.643  Sum_probs=42.0

Q ss_pred             ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS  102 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  102 (132)
                      ...|+||++.+.+   +..+||||.||..|+..|+..++..||+||.++...
T Consensus       332 ~~~C~ICle~~~~---pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          332 FQLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             SSBCTTTSSSBCC---EEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCCccCcCCCC---eEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            4689999998866   677899999999999999974457899999988654

>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=99.13  E-value=5.1e-11  Score=76.27  Aligned_cols=54  Identities=7%  Similarity=0.056  Sum_probs=46.1

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT  106 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~  106 (132)
                      .+...|+||++.|.+   +..++|||.|+..||..|+.. +.+||+||.++......+
T Consensus        27 p~~~~CpI~~~~m~d---PV~~~cGhtf~r~~I~~~l~~-~~~cP~~~~~l~~~~L~p   80 (100)
T 2kre_A           27 PDEFRDPLMDTLMTD---PVRLPSGTIMDRSIILRHLLN-SPTDPFNRQTLTESMLEP   80 (100)
T ss_dssp             STTTBCTTTCSBCSS---EEEETTTEEEEHHHHHHHTTS-CSBCSSSCCBCCTTSSEE
T ss_pred             cHhhCCcCccCcccC---CeECCCCCEEchHHHHHHHHc-CCCCCCCCCCCChhhceE
Confidence            457899999999998   777899999999999999974 589999999987654443

>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=99.12  E-value=3.2e-11  Score=83.71  Aligned_cols=53  Identities=25%  Similarity=0.535  Sum_probs=44.8

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      ++...|+||++.+.+   +..++|||.||..|+..|+..++..||+||.++.....
T Consensus        16 ~~~~~C~IC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   68 (170)
T 3hcs_A           16 ESKYECPICLMALRE---AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQL   68 (170)
T ss_dssp             CGGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGC
T ss_pred             CCCCCCCCCChhhcC---cEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchhhh
Confidence            567899999999887   56689999999999999996544589999999876543

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

Probab=99.12  E-value=5.1e-11  Score=74.06  Aligned_cols=52  Identities=8%  Similarity=0.050  Sum_probs=44.8

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      .+...|+||++.|++   +..++|||.|+..||..|+.. +.+||+||.++.....
T Consensus        12 p~~~~CpI~~~~m~d---PV~~~cGhtf~r~~I~~~l~~-~~~cP~~~~~l~~~~l   63 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTD---PVRLPSGTVMDRSIILRHLLN-SPTDPFNRQMLTESML   63 (85)
T ss_dssp             CTTTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHH-CSBCTTTCCBCCGGGC
T ss_pred             chheECcccCchhcC---CeECCCCCEECHHHHHHHHhc-CCCCCCCcCCCChHhc
Confidence            457899999999998   777899999999999999975 5799999998865443

>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=99.10  E-value=9.8e-11  Score=74.68  Aligned_cols=54  Identities=4%  Similarity=-0.027  Sum_probs=45.9

Q ss_pred             CcccccccccccccCCCceEEeCCC-CcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCH-HLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT  106 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~-H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~  106 (132)
                      .++..|+||++.|++   +..++|| |.|+..||..|+.. +.+||+||.++......+
T Consensus        20 p~~~~CpI~~~~m~d---PV~~~cG~htf~r~cI~~~l~~-~~~cP~~~~~l~~~~L~p   74 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLS-DQTDPFNRSPLTMDQIRP   74 (98)
T ss_dssp             CTTTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTT-SCBCTTTCSBCCTTTSEE
T ss_pred             cHhcCCcCccccccC---CeECCCCCeEECHHHHHHHHHh-CCCCCCCCCCCChhhceE
Confidence            457799999999998   7778999 99999999999975 578999999987654443

>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=99.09  E-value=6.2e-11  Score=69.68  Aligned_cols=48  Identities=21%  Similarity=0.390  Sum_probs=39.4

Q ss_pred             CcccccccccccccCCCceEEe--CCCCc-ccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIREL--SCHHL-FHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l--~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      +.+..|+||++...+   ...+  ||||. ||..|+..|.+. +..||+||+++.
T Consensus         5 ~~~~~C~IC~~~~~~---~~~~~~pCgH~~~C~~C~~~~~~~-~~~CPiCR~~i~   55 (63)
T 2vje_B            5 NLLKPCSLCEKRPRD---GNIIHGRTGHLVTCFHCARRLKKA-GASCPICKKEIQ   55 (63)
T ss_dssp             GGGSBCTTTSSSBSC---EEEEETTEEEEEECHHHHHHHHHT-TCBCTTTCCBCC
T ss_pred             CcCCCCcccCCcCCC---eEEEecCCCCHhHHHHHHHHHHHh-CCcCCCcCchhh
Confidence            356789999998665   4445  99998 999999999875 478999999884

>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=1.8e-11  Score=80.19  Aligned_cols=50  Identities=26%  Similarity=0.575  Sum_probs=41.6

Q ss_pred             cccccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWL  105 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~  105 (132)
                      +...|+||++.+.+   +..+ +|||.||..||..|+.   ..||+||.++......
T Consensus        21 ~~~~C~IC~~~~~~---pv~~~~CgH~fC~~Ci~~~~~---~~CP~Cr~~~~~~~~~   71 (117)
T 1jm7_B           21 KLLRCSRCTNILRE---PVCLGGCEHIFCSNCVSDCIG---TGCPVCYTPAWIQDLK   71 (117)
T ss_dssp             HTTSCSSSCSCCSS---CBCCCSSSCCBCTTTGGGGTT---TBCSSSCCBCSCSSCC
T ss_pred             hCCCCCCCChHhhC---ccEeCCCCCHHHHHHHHHHhc---CCCcCCCCcCcccccc
Confidence            46789999999877   5557 9999999999999986   5799999998654433

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=99.08  E-value=3.3e-11  Score=72.94  Aligned_cols=44  Identities=27%  Similarity=0.608  Sum_probs=37.8

Q ss_pred             CcccccccccccccCCCceEEeCCCCc-ccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHL-FHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      +++..|+||++.+.+   +..+||||. ||..|+..|     ..||+||+++.
T Consensus        22 ~~~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~-----~~CP~Cr~~i~   66 (74)
T 4ic3_A           22 QEEKLCKICMDRNIA---IVFVPCGHLVTCKQCAEAV-----DKCPMCYTVIT   66 (74)
T ss_dssp             HHHTBCTTTSSSBCC---EEEETTCCBCCCHHHHTTC-----SBCTTTCCBCS
T ss_pred             ccCCCCCCCCCCCCC---EEEcCCCChhHHHHhhhcC-----ccCCCcCcCcc
Confidence            346789999998776   677899999 999999987     57999999875

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

Probab=99.04  E-value=1.3e-10  Score=85.70  Aligned_cols=55  Identities=5%  Similarity=0.082  Sum_probs=45.6

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT  106 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~  106 (132)
                      .+...|+||++.+.+   +..++|||.||..||..|+..++.+||+||.++......+
T Consensus       206 ~~~~~c~i~~~~~~d---Pv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~l~~  260 (281)
T 2c2l_A          206 PDYLCGKISFELMRE---PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIP  260 (281)
T ss_dssp             CSTTBCTTTCSBCSS---EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEE
T ss_pred             CcccCCcCcCCHhcC---CeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCchhcCcc
Confidence            457789999999988   7778999999999999999754456999999997554433

>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=98.98  E-value=2.8e-10  Score=71.90  Aligned_cols=54  Identities=19%  Similarity=0.449  Sum_probs=42.7

Q ss_pred             CcccccccccccccCCCceEEeC-CCCcccHHhHHHHHhcC-----CCCCCC--CCCC-CCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELS-CHHLFHAVCLDTWISNN-----YAICPV--CHDS-IAPSRWL  105 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~wl~~~-----~~~CP~--Cr~~-~~~~~~~  105 (132)
                      .++..|+||++.|.+   +..++ |||.|++.||..|+..+     ...||+  |+.. +......
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            456789999999987   67785 99999999999999642     358999  9876 6544433

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=98.93  E-value=5.4e-10  Score=78.42  Aligned_cols=55  Identities=5%  Similarity=0.076  Sum_probs=45.5

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT  106 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~  106 (132)
                      .+...|+||++.|.+   +..++|||.|+..||..|+..+..+||+|+.++......+
T Consensus       104 p~~f~CPI~~elm~D---PV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~L~p  158 (179)
T 2f42_A          104 PDYLCGKISFELMRE---PCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIP  158 (179)
T ss_dssp             CGGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEE
T ss_pred             cHhhcccCccccCCC---CeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChhhCcc
Confidence            567899999999998   7778999999999999999653347999999887554433

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.92  E-value=1.1e-09  Score=65.31  Aligned_cols=45  Identities=22%  Similarity=0.635  Sum_probs=37.4

Q ss_pred             CcccccccccccccCCCceEEeCCCCc-ccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHL-FHAVCLDTWISNNYAICPVCHDSIAP  101 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~~  101 (132)
                      .++..|.||++...+   +..+||+|. ||..|+..     ...||+||.++..
T Consensus        13 ~~~~~C~IC~~~~~~---~v~~pCgH~~~C~~C~~~-----~~~CP~CR~~i~~   58 (68)
T 2ea5_A           13 ENSKDCVVCQNGTVN---WVLLPCRHTCLCDGCVKY-----FQQCPMCRQFVQE   58 (68)
T ss_dssp             CCSSCCSSSSSSCCC---CEETTTTBCCSCTTHHHH-----CSSCTTTCCCCCC
T ss_pred             CCCCCCCCcCcCCCC---EEEECCCChhhhHHHHhc-----CCCCCCCCcchhc
Confidence            456789999998665   677899999 99999984     3689999998864

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=98.91  E-value=1.2e-09  Score=63.67  Aligned_cols=50  Identities=22%  Similarity=0.541  Sum_probs=37.9

Q ss_pred             CcccccccccccccCCCceEEeCCC--C---cccHHhHHHHHhc-CCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCH--H---LFHAVCLDTWISN-NYAICPVCHDSIAP  101 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~--H---~fh~~Ci~~wl~~-~~~~CP~Cr~~~~~  101 (132)
                      ++...|.||+++..  +.. .+||.  +   .||..|+.+|+.. ++.+||+|+.++..
T Consensus         4 ~~~~~CrIC~~~~~--~~l-~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            4 EDVPVCWICNEELG--NER-FRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEECS--CCC-CCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCEeEEeecCCC--Cce-ecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            46678999999732  333 46865  4   9999999999953 35789999998753

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.91  E-value=4.9e-10  Score=67.83  Aligned_cols=44  Identities=27%  Similarity=0.592  Sum_probs=36.5

Q ss_pred             cccccccccccccCCCceEEeCCCCc-ccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHL-FHAVCLDTWISNNYAICPVCHDSIAP  101 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~~  101 (132)
                      ++..|+||++.+.+   +..+||||. ||..|+..     ...||+||.++..
T Consensus        24 ~~~~C~IC~~~~~~---~~~~pCgH~~~C~~C~~~-----~~~CP~Cr~~i~~   68 (75)
T 2ecg_A           24 EEKLCKICMDRNIA---IVFVPCGHLVTCKQCAEA-----VDKCPMCYTVITF   68 (75)
T ss_dssp             HHHSCSSSCSSCCC---BCCSSSCCCCBCHHHHHH-----CSBCTTTCCBCCC
T ss_pred             CCCCCCcCCCCCCC---EEEecCCCHHHHHHHhhC-----CCCCccCCceecC
Confidence            46689999998766   566799999 99999964     3689999998854

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

Probab=98.88  E-value=2.2e-10  Score=87.32  Aligned_cols=54  Identities=30%  Similarity=0.735  Sum_probs=40.8

Q ss_pred             CcccccccccccccCCCc-e----EEeCCCCcccHHhHHHHHhcCC----------CCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEE-I----RELSCHHLFHAVCLDTWISNNY----------AICPVCHDSIAPS  102 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~-~----~~l~C~H~fh~~Ci~~wl~~~~----------~~CP~Cr~~~~~~  102 (132)
                      ++..+|+||++.+.++.. +    ...+|+|.||..|+.+|++...          .+||+||+++..+
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~s  374 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTS  374 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCcc
Confidence            467799999999877332 2    1247999999999999995311          3699999988643

>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=98.83  E-value=1.3e-09  Score=68.56  Aligned_cols=50  Identities=20%  Similarity=0.572  Sum_probs=38.6

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhc----C---CCCCCC--CCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN----N---YAICPV--CHDS   98 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~----~---~~~CP~--Cr~~   98 (132)
                      .+..+|+||++.+..++.....+|+|.||..|+..++..    +   ...||.  |+..
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            3 SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            346689999999876544443489999999999999842    1   247999  9987

>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=98.83  E-value=8.2e-10  Score=67.67  Aligned_cols=44  Identities=27%  Similarity=0.561  Sum_probs=37.0

Q ss_pred             cccccccccccccCCCceEEeCCCCc-ccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHL-FHAVCLDTWISNNYAICPVCHDSIAP  101 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~~  101 (132)
                      ++..|+||++...+   +..+||||. ||..|+..|     ..||+||.++..
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            45689999998766   777899999 999999865     389999998863

>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=98.63  E-value=6e-09  Score=79.90  Aligned_cols=43  Identities=28%  Similarity=0.683  Sum_probs=37.5

Q ss_pred             cccccccccccccCCCceEEeCCCCc-ccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHL-FHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      ++..|+||++.+.+   +..+||||. ||..|+..|     ..||+||.++.
T Consensus       294 ~~~~C~IC~~~~~~---~v~lpCgH~~fC~~C~~~~-----~~CP~CR~~i~  337 (345)
T 3t6p_A          294 EERTCKVCMDKEVS---VVFIPCGHLVVCQECAPSL-----RKCPICRGIIK  337 (345)
T ss_dssp             TTCBCTTTSSSBCC---EEEETTCCEEECTTTGGGC-----SBCTTTCCBCC
T ss_pred             CCCCCCccCCcCCc---eEEcCCCChhHhHHHHhcC-----CcCCCCCCCcc
Confidence            46789999999876   777899999 999999987     57999999885

>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=98.59  E-value=1.3e-08  Score=75.11  Aligned_cols=55  Identities=15%  Similarity=0.399  Sum_probs=43.4

Q ss_pred             CcccccccccccccCCCceEEe-CCCCcccHHhHHHHHhcC-CCCCCC--CCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNN-YAICPV--CHDSIAPSRWLT  106 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~-~~~CP~--Cr~~~~~~~~~~  106 (132)
                      ..+..|+||++.|.+   +... .|||.|++.||..|+..+ ...||+  |++.+.......
T Consensus       179 ~~el~CPIcl~~f~D---PVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL~p  237 (267)
T 3htk_C          179 KIELTCPITCKPYEA---PLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFVR  237 (267)
T ss_dssp             BCCSBCTTTSSBCSS---EEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGEEE
T ss_pred             ceeeECcCccCcccC---CeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhCCc
Confidence            457799999999987   4444 999999999999999642 357999  999876554433

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

Probab=98.51  E-value=1e-07  Score=60.32  Aligned_cols=46  Identities=26%  Similarity=0.504  Sum_probs=37.5

Q ss_pred             ccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        53 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      -|.+|--++..  ..+.+||+|+||.+|+..|.+++...||.|+.++.
T Consensus         3 fC~~C~~Pi~i--ygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~   48 (101)
T 3vk6_A            3 FCDKCGLPIKV--YGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQ   48 (101)
T ss_dssp             BCTTTCSBCSE--EEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCS
T ss_pred             ecCccCCCeEE--EeeeccccccHHHHHHHHHHhccCCCCcCcCCeee
Confidence            37788777654  35666999999999999998766689999999875

>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=98.46  E-value=6.5e-08  Score=56.31  Aligned_cols=51  Identities=10%  Similarity=0.206  Sum_probs=42.9

Q ss_pred             cccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCC
Q 042112           52 VECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT  106 (132)
Q Consensus        52 ~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~  106 (132)
                      ..|+|+++.+++   +..+ ++||.|.+.||.+|+.. +.+||+.+.++...+..+
T Consensus         4 ~~CpIs~~~m~d---PV~~~~sG~~yer~~I~~~l~~-~~~cP~t~~~L~~~~Lip   55 (61)
T 2bay_A            4 MLCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKD-TGNDPITNEPLSIEEIVE   55 (61)
T ss_dssp             CCCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHH-HSBCTTTCCBCCGGGCEE
T ss_pred             EEecCCCCCCCC---CEEeCCCCcEEcHHHHHHHHHh-CCCCcCCcCCCChhhcEE
Confidence            579999999987   6667 89999999999999975 467999999987665543

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

Probab=98.27  E-value=6e-07  Score=65.54  Aligned_cols=53  Identities=23%  Similarity=0.519  Sum_probs=41.9

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC-CCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN-YAICPVCHDSIAPSRW  104 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~-~~~CP~Cr~~~~~~~~  104 (132)
                      .-..|.||.+....+..+.  .|+|.||..|+..|++.+ +..||.|+.+++...+
T Consensus       179 ~i~~C~iC~~iv~~g~~C~--~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~~~  232 (238)
T 3nw0_A          179 AVKICNICHSLLIQGQSCE--TCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIP  232 (238)
T ss_dssp             TCCBCTTTCSBCSSCEECS--SSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSCCC
T ss_pred             CCCcCcchhhHHhCCcccC--ccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCC
Confidence            4678999999988764333  499999999999999543 3589999998876543

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=95.54  E-value=0.0077  Score=37.47  Aligned_cols=35  Identities=20%  Similarity=0.393  Sum_probs=25.8

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHH
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTW   84 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w   84 (132)
                      ++..|.||.+.+.......-+.|+|.||..|+..+
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETTTTEEECHHHHHHH
T ss_pred             CCCCCcCCCCCCCCCceEECCcCChHHhHHHCHHH
Confidence            35689999986433222334799999999999983

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=94.68  E-value=0.036  Score=32.16  Aligned_cols=48  Identities=23%  Similarity=0.418  Sum_probs=32.6

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC---CCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN---YAICPVCHDSI   99 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~---~~~CP~Cr~~~   99 (132)
                      ..+..|.||.+.   ++.+.--.|...||..|+...+...   .=.||.|+..-
T Consensus        10 ~~~~~C~vC~~~---~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           10 APGARCGVCGDG---TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             CTTCCCTTTSCC---TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCCcCCCCCC---CeEEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            456789999753   2322222789999999998877432   12699997643

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1

Probab=90.38  E-value=1.1  Score=27.37  Aligned_cols=51  Identities=18%  Similarity=0.322  Sum_probs=38.0

Q ss_pred             cccccccccccccCCCc--eEE--eCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEE--IRE--LSCHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~--~~~--l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      ....|.||-+++.....  +..  ..|+--.|+.|...=.+..+..||.|++.+.
T Consensus        15 ~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCktrYk   69 (93)
T 1weo_A           15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYK   69 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCC
T ss_pred             CCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhccCccccccCCccc
Confidence            45689999998643322  221  2677788999998877767789999999886

>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=89.22  E-value=0.3  Score=29.67  Aligned_cols=35  Identities=23%  Similarity=0.427  Sum_probs=23.1

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHH
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTW   84 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w   84 (132)
                      ..++.|.||-. +..++....--|+-+||..|+.+-
T Consensus        13 ~~D~~C~VC~~-~t~~~l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           13 VNDEMCDVCEV-WTAESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTTCC-CCSSCCSSCSSSSSCCCHHHHHHH
T ss_pred             CCCcccCcccc-ccccceeccccccccccHhhcccc
Confidence            35778999963 222222111248899999999996

>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=89.04  E-value=0.21  Score=28.45  Aligned_cols=51  Identities=18%  Similarity=0.463  Sum_probs=33.2

Q ss_pred             CcccccccccccccCCCceEEe--CCCCcccHHhHHHHHh------cCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIREL--SCHHLFHAVCLDTWIS------NNYAICPVCHDSI   99 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l--~C~H~fh~~Ci~~wl~------~~~~~CP~Cr~~~   99 (132)
                      .++..|.+|......++...++  .|...||..|+..=+.      ...=.||.|+...
T Consensus         4 ~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~   62 (66)
T 2yt5_A            4 GSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFAT   62 (66)
T ss_dssp             CCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTT
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCcc
Confidence            5677899999865433333333  8899999999875331      1234688886543

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=88.70  E-value=0.22  Score=26.90  Aligned_cols=45  Identities=29%  Similarity=0.601  Sum_probs=28.0

Q ss_pred             ccccccccccCCCceEEeCCCCcccHHhHHHHHhc---CCCCCCCCCC
Q 042112           53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN---NYAICPVCHD   97 (132)
Q Consensus        53 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~   97 (132)
                      .|.||...-..++.+.--.|...||..|+..=+..   +.-.||.|+.
T Consensus         2 ~C~vC~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCCEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            58888865333222222278899999999753321   1235999965

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=87.95  E-value=0.1  Score=30.65  Aligned_cols=50  Identities=20%  Similarity=0.476  Sum_probs=32.8

Q ss_pred             CcccccccccccccCCCceEEe-CCCCcccHHhHHHHHhc---CCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISN---NYAICPVCHDSI   99 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~~~   99 (132)
                      .+...|.+|..... ++....- .|..-||..|+..-...   ..-.||.|+..+
T Consensus        16 ~~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~   69 (75)
T 2k16_A           16 NQIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKI   69 (75)
T ss_dssp             CEEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHH
T ss_pred             CCCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCch
Confidence            45667999987643 3323322 78899999999754421   134699997654

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=87.31  E-value=0.67  Score=28.18  Aligned_cols=51  Identities=18%  Similarity=0.440  Sum_probs=31.9

Q ss_pred             CcccccccccccccCCCceEEe--CCCCcccHHhHHHHH-hcCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIREL--SCHHLFHAVCLDTWI-SNNYAICPVCHDSI   99 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l--~C~H~fh~~Ci~~wl-~~~~~~CP~Cr~~~   99 (132)
                      +++..|.||...-..+....++  .|.-.||..|+..-. -.+.=.||.|....
T Consensus        23 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~   76 (88)
T 2l43_A           23 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSR   76 (88)
T ss_dssp             CCCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHT
T ss_pred             CCCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCcc
Confidence            4678899998754222222323  788999999997532 11223588886543

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=86.98  E-value=0.3  Score=27.58  Aligned_cols=46  Identities=33%  Similarity=0.626  Sum_probs=30.5

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhc---CCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN---NYAICPVCHD   97 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~   97 (132)
                      ..+..|.+|.+.   ++.+.--.|...||..|+..-+..   +.-.||.|+.
T Consensus         9 ~~~~~C~vC~~~---g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A            9 DHQDYCEVCQQG---GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             CCCSSCTTTSCC---SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCCCCCccCCCC---CcEEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            456789999863   222222278899999999875421   1236999964

>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=86.85  E-value=0.2  Score=31.63  Aligned_cols=48  Identities=27%  Similarity=0.562  Sum_probs=30.7

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhc---CCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN---NYAICPVCH   96 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~---~~~~CP~Cr   96 (132)
                      ..++.|.+|.+.-...+.+.--.|...||..|+......   ..-.||.|+
T Consensus         5 ~~~~~C~~C~~~g~~~~ll~C~~C~~~~H~~Cl~~~~~~~~~~~W~C~~C~   55 (111)
T 2ysm_A            5 SSGANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPECK   55 (111)
T ss_dssp             CCCSCBTTTCCCCCTTTSEECSSSCCEECTTTTTCCCCTTTSTTCCCTTTC
T ss_pred             CCCCCCcCCCCCCCCcCCeECCCCCCCcChHHhCCccccccccCccCCcCC
Confidence            457789999876332222333378999999999876531   223566664

>1wep_A PHF8; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: g.50.1.2

Probab=85.88  E-value=3.7  Score=24.07  Aligned_cols=50  Identities=22%  Similarity=0.467  Sum_probs=32.0

Q ss_pred             cccccccccccccCCCceEEe-CCCCcccHHhHHHHH----hcCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWI----SNNYAICPVCHDSIA  100 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl----~~~~~~CP~Cr~~~~  100 (132)
                      +...| ||.....++...++- .|..=||..|+.--.    ......||.|+..-.
T Consensus        11 ~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~~   65 (79)
T 1wep_A           11 VPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFG   65 (79)
T ss_dssp             CCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSC
T ss_pred             CccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCcccccC
Confidence            34456 898877543333333 788999999995321    113467999987653

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=85.64  E-value=0.47  Score=26.81  Aligned_cols=50  Identities=20%  Similarity=0.410  Sum_probs=34.2

Q ss_pred             CcccccccccccccCCCceEEe-CCCCcccHHhHHHHHh----cCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWIS----NNYAICPVCHDS   98 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~----~~~~~CP~Cr~~   98 (132)
                      +++..|++|...+.++...++- .|..=||..|+.--..    .....||.|+..
T Consensus         4 ~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            5667899999887654444433 7889999999864321    134579999653

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=85.51  E-value=0.55  Score=28.71  Aligned_cols=49  Identities=24%  Similarity=0.460  Sum_probs=32.4

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhc---CCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN---NYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~~~~  100 (132)
                      ..+..|.+|.+.   ++-+.--.|.-.||..|+.+=+..   +.-.||.|+..-.
T Consensus        23 ~n~~~C~vC~~~---g~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~~   74 (88)
T 1fp0_A           23 DSATICRVCQKP---GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   74 (88)
T ss_dssp             SSSSCCSSSCSS---SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             CCCCcCcCcCCC---CCEEECCCCCCceecccCCCCCCCCcCCCcCCccccCCCc
Confidence            456789999864   222222278899999999775532   1226999986543

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=85.34  E-value=1.2  Score=28.05  Aligned_cols=47  Identities=28%  Similarity=0.459  Sum_probs=29.0

Q ss_pred             cccccccccccccC-----CCc-eEEeCCCCcccHHhHHH------HHhcCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEE-----GEE-IRELSCHHLFHAVCLDT------WISNNYAICPVCH   96 (132)
Q Consensus        50 ~~~~C~IC~~~~~~-----~~~-~~~l~C~H~fh~~Ci~~------wl~~~~~~CP~Cr   96 (132)
                      ....|.+|+..-..     ++. +.-..|+..||..|+..      -.....-.||.|+
T Consensus         4 p~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   62 (112)
T 3v43_A            4 PIPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLKFSPELTVRVKALRWQCIECK   62 (112)
T ss_dssp             CCSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHTCCHHHHHHHHTSCCCCTTTC
T ss_pred             cCccccccCCchhhCcCCCchhceEhhhcCCCCCCchhcCCHHHHHHhhccccccccCC
Confidence            45679999875321     112 22237999999999952      2233344677775

>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=84.03  E-value=0.27  Score=27.78  Aligned_cols=48  Identities=25%  Similarity=0.510  Sum_probs=30.8

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhc---CCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN---NYAICPVCHDSI   99 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~~~   99 (132)
                      ..+..|.+|.+.   ++.+.--.|...||..|+..-+..   +.-.||.|+...
T Consensus         7 ~~~~~C~vC~~~---g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            7 HHMEFCRVCKDG---GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC---SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCCcCCCCCCC---CCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            456789999853   222222268899999999864422   123599997643

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=83.68  E-value=0.37  Score=33.46  Aligned_cols=50  Identities=16%  Similarity=0.413  Sum_probs=34.2

Q ss_pred             ccccccccccccCCCc---eEEe-CCCCcccHHhHHHH------Hh----cCCCCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEGEE---IREL-SCHHLFHAVCLDTW------IS----NNYAICPVCHDSIA  100 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~~---~~~l-~C~H~fh~~Ci~~w------l~----~~~~~CP~Cr~~~~  100 (132)
                      +..|+||...+.+++.   .++- .|..=||..|+.--      +.    .....||.|+..-+
T Consensus         2 G~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~~   65 (183)
T 3lqh_A            2 GNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHP   65 (183)
T ss_dssp             CCBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSSS
T ss_pred             cCcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCCC
Confidence            3469999999988762   3333 78899999998421      11    01468999987543

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=83.56  E-value=0.22  Score=34.30  Aligned_cols=47  Identities=32%  Similarity=0.571  Sum_probs=31.3

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhc---CCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN---NYAICPVCHDSI   99 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~~~   99 (132)
                      .++.|.+|...   ++-+..-.|...||..|+.+-+..   +.-.||.|+..-
T Consensus         3 ~~~~C~~C~~~---g~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A            3 NEDWCAVCQNG---GELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             SCSSCTTTCCC---SSCEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCccccCCCC---CeeeecCCCCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            45779999854   332222278899999998775532   123699998654

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*

Probab=83.15  E-value=1.1  Score=25.68  Aligned_cols=34  Identities=21%  Similarity=0.673  Sum_probs=24.6

Q ss_pred             CcccccccccccccCCCceEEe--CCCCcccHHhHH
Q 042112           49 AEAVECAVCLSHIEEGEEIREL--SCHHLFHAVCLD   82 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l--~C~H~fh~~Ci~   82 (132)
                      ++...|++|..++.+++..+.-  .|.--||..|+.
T Consensus         6 ~~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvg   41 (65)
T 2vpb_A            6 DPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTG   41 (65)
T ss_dssp             ---CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHT
T ss_pred             CCcCcCccCCCccCCCCCeEecccCccccCchhccC
Confidence            4567899999998776555443  688999999983

>2dar_A PDZ and LIM domain protein 5; enigma homolog protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=82.00  E-value=1.4  Score=26.26  Aligned_cols=42  Identities=19%  Similarity=0.286  Sum_probs=30.2

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS  102 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  102 (132)
                      .....|+.|-+.+.. +.  +..-+..||..|         ..|-.|+.+|...
T Consensus        23 ~~~~~C~~C~~~I~~-~~--v~a~~~~~H~~C---------F~C~~C~~~L~~~   64 (90)
T 2dar_A           23 KRTPMCAHCNQVIRG-PF--LVALGKSWHPEE---------FNCAHCKNTMAYI   64 (90)
T ss_dssp             TCCCBBSSSCCBCCS-CE--EEETTEEECTTT---------CBCSSSCCBCSSS
T ss_pred             CCCCCCccCCCEecc-eE--EEECCccccccC---------CccCCCCCCCCCC
Confidence            345789999998853 32  234678899866         6799999888643

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=81.37  E-value=1.9  Score=25.09  Aligned_cols=48  Identities=17%  Similarity=0.462  Sum_probs=29.5

Q ss_pred             CcccccccccccccCCCceEEe--CCCCcccHHhHHHHH-hcCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIREL--SCHHLFHAVCLDTWI-SNNYAICPVCH   96 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l--~C~H~fh~~Ci~~wl-~~~~~~CP~Cr   96 (132)
                      .++..|.||.+.-..++...++  .|.-.||..|+..-. -.+.=.||.|+
T Consensus        14 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~   64 (71)
T 2ku3_A           14 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCL   64 (71)
T ss_dssp             CSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCc
Confidence            4577899998764222222333  888999999987422 11123577774

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A

Probab=81.14  E-value=1.6  Score=37.49  Aligned_cols=57  Identities=4%  Similarity=-0.029  Sum_probs=45.8

Q ss_pred             CCCcccccccccccccCCCceEEeCCC-CcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCCC
Q 042112           47 SRAEAVECAVCLSHIEEGEEIRELSCH-HLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTG  107 (132)
Q Consensus        47 ~~~~~~~C~IC~~~~~~~~~~~~l~C~-H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~  107 (132)
                      ...+.-.|||-.+-+.+   +..+|-| +.|=+..|.+|+.. +.+||+=|.++......++
T Consensus       887 ~iP~~F~cPIs~~lM~D---PVilpsG~~TydR~~I~~wl~~-~~tdP~Tr~~L~~~~liPN  944 (968)
T 3m62_A          887 DVPDEFLDPLMYTIMKD---PVILPASKMNIDRSTIKAHLLS-DSTDPFNRMPLKLEDVTPN  944 (968)
T ss_dssp             CSCGGGBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHTT-CCBCTTTCCBCCGGGCEEC
T ss_pred             CCcHHhCCcchhhHHhC---CeEcCCCCEEECHHHHHHHHhc-CCCCCCCCCCCCccccccc
Confidence            33567789999999998   7778887 68999999999975 5799999998876544433

---

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	132
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	7e-10
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-07
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	3e-07
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	1e-06
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	3e-05
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	6e-05
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	2e-04
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	2e-04
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	3e-04
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	8e-04
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	0.001

>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 = 49.1 bits (117), Expect = 7e-10
 Identities = 24/51 (47%), Positives = 36/51 (70%), Gaps = 2/51 (3%)

Query: 50 EAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSI 99
          + VECAVCL+ +E+GEE R L  C H FHA C+D W+ ++ + CP+C  ++
Sbjct: 4  DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSH-STCPLCRLTV 53

>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 = 43.8 bits (103), Expect = 1e-07
 Identities = 14/67 (20%), Positives = 29/67 (43%), Gaps = 1/67 (1%)

Query: 33 EQLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAIC 92
          +  + + ++++EL     +    +C    E  ++++   C HL    CL +W  +    C
Sbjct: 3  QDHIKVTQEQYELYCEMGS-TFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGC 61

Query: 93 PVCHDSI 99
          P C   I
Sbjct: 62 PFCRCEI 68

>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 = 42.8 bits (100), Expect = 3e-07
 Identities = 9/52 (17%), Positives = 16/52 (30%), Gaps = 2/52 (3%)

Query: 50 EAVECAVCLSHIEEGEEIREL--SCHHLFHAVCLDTWISNNYAICPVCHDSI 99
          +   C  C +       ++ +   C H     C+D         CP C   +
Sbjct: 2  DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 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 = 41.1 bits (96), Expect = 1e-06
 Identities = 15/47 (31%), Positives = 19/47 (40%), Gaps = 3/47 (6%)

Query: 53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99
           C +CL           L C H F  VC+  WI  N   CP+C   +
Sbjct: 7  RCPICLEDPSNY--SMALPCLHAFCYVCITRWIRQN-PTCPLCKVPV 50

>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 = 37.4 bits (86), Expect = 3e-05
 Identities = 10/49 (20%), Positives = 19/49 (38%), Gaps = 1/49 (2%)

Query: 52 VECAVCLSHIEEGE-EIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99
          VEC +C+  +E  +      +C +     C     ++   +CP C    
Sbjct: 1  VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPY 49

>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 = 36.4 bits (84), Expect = 6e-05
 Identities = 11/53 (20%), Positives = 18/53 (33%), Gaps = 7/53 (13%)

Query: 50  EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102
           + + C  C     E +  + L C H   + CL+         CP+C       
Sbjct: 5   QFLRCQQCQ---AEAKCPKLLPCLHTLCSGCLEASGMQ----CPICQAPWPLG 50

>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 = 35.8 bits (82), Expect = 2e-04
 Identities = 19/95 (20%), Positives = 36/95 (37%), Gaps = 5/95 (5%)

Query: 36  VNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWI--SNNYAICP 93
           + + E +  + +  + +EC +CL  I+E        C H+F   C+   +      + CP
Sbjct: 6   LRVEEVQNVINAMQKILECPICLELIKE---PVSTKCDHIFCKFCMLKLLNQKKGPSQCP 62

Query: 94  VCHDSIAPSRWLTGHGEEVLVLKFRCFNSRTERDT 128
           +C + I             LV +        + DT
Sbjct: 63  LCKNDITKRSLQESTRFSQLVEELLKIICAFQLDT 97

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.8 bits (82), Expect = 2e-04
 Identities = 7/39 (17%), Positives = 15/39 (38%)

Query: 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN 87
          + +  C +CL      +      C  +F  +CL  ++  
Sbjct: 3  SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVEL 41

>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 = 35.3 bits (81), Expect = 3e-04
 Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 3/53 (5%)

Query: 50  EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102
           +++ C +C   + +     E SC HLF  +C+   +    + CP C     P+
Sbjct: 22  KSISCQICEHILAD---PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPT 71

>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 = 34.3 bits (78), Expect = 8e-04
 Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 16/58 (27%)

Query: 53 ECAVCLSHIEEGE---------------EIRELSCHHLFHAVCLDTWISNNYAICPVC 95
           CA+C +HI +                  +    C+H FH  C+  W+     +CP+ 
Sbjct: 23 NCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTR-QVCPLD 79

>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 = 33.9 bits (76), Expect = 0.001
 Identities = 13/57 (22%), Positives = 16/57 (28%), Gaps = 4/57 (7%)

Query: 43 FELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN----NYAICPVC 95
           E  + A           +      R   C H FH +CL     N        CP C
Sbjct: 32 MEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSC 88

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	132
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.73
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.65
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.6
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.6
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.58
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.57
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.53
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.5
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.38
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.37
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.35
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.32
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.3
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.3
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.15
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.88
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.77
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	93.89
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	92.68
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	92.48
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	89.43
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	88.32
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	88.02
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	87.84
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	87.57

>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=99.73  E-value=7.5e-19  Score=100.04  Aligned_cols=51  Identities=47%  Similarity=1.069  Sum_probs=44.9

Q ss_pred             CcccccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      +++.+|+||++++..++.+..+ +|+|.||..|+.+|++. +.+||+||+++.
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~-~~~CP~CR~~i~   54 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGS-HSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTT-CCSCSSSCCCSC
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHh-CCcCCCCCCEeE
Confidence            4567899999999998888777 69999999999999985 579999999874

>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=99.65  E-value=1.8e-17  Score=93.15  Aligned_cols=49  Identities=18%  Similarity=0.531  Sum_probs=41.0

Q ss_pred             ccccccccccCCCce-EEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112           53 ECAVCLSHIEEGEEI-RELSCHHLFHAVCLDTWISNNYAICPVCHDSIAP  101 (132)
Q Consensus        53 ~C~IC~~~~~~~~~~-~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  101 (132)
                      +|+||++++..++.. ..++|||.||..|+.+|++..+.+||+||+++.+
T Consensus         2 eCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            699999999776543 4459999999999999997555679999999864

>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=99.60  E-value=3.2e-16  Score=91.86  Aligned_cols=53  Identities=19%  Similarity=0.445  Sum_probs=41.8

Q ss_pred             cccccccccccccCCC--ceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGE--EIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS  102 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~--~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  102 (132)
                      ++.+|+||++++..+.  ....++|||.||..||..|++.++.+||+||+++...
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~   56 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCcccc
Confidence            4678999999864432  2344599999999999999965556899999988543

>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=99.60  E-value=5e-16  Score=94.32  Aligned_cols=52  Identities=23%  Similarity=0.576  Sum_probs=43.7

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      ....|+||++.+.+   ++.++|||.||..||..|+..++.+||+||.++...+.
T Consensus        22 ~~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~   73 (79)
T d1fbva4          22 TFQLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP   73 (79)
T ss_dssp             CTTBCTTTSSSBCC---EECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCC
T ss_pred             CCCCCccCCCcCCC---eEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCce
Confidence            34579999998776   77789999999999999997555789999999975543

>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=6.4e-16  Score=91.27  Aligned_cols=48  Identities=31%  Similarity=0.782  Sum_probs=40.8

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA  100 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  100 (132)
                      ..++|+||++.+.+  ..+.++|+|.||..|+.+|++. +.+||+||+++.
T Consensus         4 ~~d~C~IC~~~~~~--~~~~~~C~H~Fc~~Ci~~w~~~-~~~CP~CR~~i~   51 (68)
T d1chca_           4 VAERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQ-NPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETTTTEEESTTHHHHHHHH-SCSTTTTCCCCC
T ss_pred             CCCCCccCCcCccC--CcEEeCCCCcCcHHHHHHHHHh-CCcCCCCCcchH
Confidence            45679999999865  3566799999999999999985 479999999875

>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=99.57  E-value=1.3e-15  Score=98.27  Aligned_cols=62  Identities=24%  Similarity=0.498  Sum_probs=46.0

Q ss_pred             CcccccccccccccCC---------------CceEEeCCCCcccHHhHHHHHhcC----CCCCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEG---------------EEIRELSCHHLFHAVCLDTWISNN----YAICPVCHDSIAPSRWLTGHG  109 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~---------------~~~~~l~C~H~fh~~Ci~~wl~~~----~~~CP~Cr~~~~~~~~~~~~~  109 (132)
                      ..++.|+||++++..+               ..+..++|+|.||..||..|++.+    +.+||+||+.+..+....+.+
T Consensus        23 ~~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~~~~qP~~  102 (114)
T d1v87a_          23 APEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQPWG  102 (114)
T ss_dssp             CCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSSSCTTS
T ss_pred             cccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccCcCCCCCC
Confidence            3466899999998542               224556999999999999999643    247999999987765544443


Q ss_pred             C
Q 042112          110 E  110 (132)
Q Consensus       110 ~  110 (132)
                      .
T Consensus       103 ~  103 (114)
T d1v87a_         103 K  103 (114)
T ss_dssp             S
T ss_pred             c
Confidence            3

>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=99.53  E-value=3.6e-15  Score=92.17  Aligned_cols=51  Identities=25%  Similarity=0.602  Sum_probs=41.1

Q ss_pred             cccccccccccccCCC---------------ceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGE---------------EIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAP  101 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~---------------~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  101 (132)
                      .++.|+||++++.+..               .+..++|+|.||..||.+|++. +.+||+||+++..
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~   85 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-RQVCPLDNREWEF   85 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTT-CSBCSSSCSBCCE
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHH-CCcCCCCCCcccc
Confidence            4556999999886532               2455799999999999999986 5789999998753

>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=99.50  E-value=5.4e-15  Score=90.95  Aligned_cols=54  Identities=24%  Similarity=0.600  Sum_probs=45.1

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT  106 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~  106 (132)
                      +...|+||++.+.+   +..++|||.||..||.+|++.++.+||+||.++.+.....
T Consensus        22 ~~l~C~IC~~~~~~---pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l~~   75 (86)
T d1rmda2          22 KSISCQICEHILAD---PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLES   75 (86)
T ss_dssp             HHTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCBC
T ss_pred             cCcCCccCCcchhc---ceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChhhccC
Confidence            34689999999887   7778999999999999999655678999999987655443

>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=99.38  E-value=1.6e-13  Score=86.85  Aligned_cols=56  Identities=25%  Similarity=0.672  Sum_probs=44.4

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCC--CCCCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNY--AICPVCHDSIAPSRWLTGH  108 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~--~~CP~Cr~~~~~~~~~~~~  108 (132)
                      +...|+||++.+.+   +..++|||.||..||..|++.+.  ..||+||.++.......+.
T Consensus        20 ~~l~CpIC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l~~n~   77 (103)
T d1jm7a_          20 KILECPICLELIKE---PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQEST   77 (103)
T ss_dssp             HHTSCSSSCCCCSS---CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBCCC
T ss_pred             cCcCCCccCchhCC---eEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhCCcCH
Confidence            34579999999877   45579999999999999995432  4799999999766654443

>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=99.37  E-value=5e-14  Score=79.89  Aligned_cols=48  Identities=21%  Similarity=0.483  Sum_probs=39.2

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      +..+|+||++.+.+   ++.++|||.||..|+.+|    +.+||+||+++.....
T Consensus         5 ~~l~C~IC~~~~~~---p~~lpCgH~fC~~Ci~~~----~~~CP~Cr~~~~~~~~   52 (56)
T d1bora_           5 QFLRCQQCQAEAKC---PKLLPCLHTLCSGCLEAS----GMQCPICQAPWPLGAD   52 (56)
T ss_dssp             CCSSCSSSCSSCBC---CSCSTTSCCSBTTTCSSS----SSSCSSCCSSSSCCSS
T ss_pred             CCCCCcccCcccCC---CEEecCCCHHhHHHHHcC----CCcCcCCCCcccCCCC
Confidence            34589999999887   566899999999999764    4689999999975543

>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=99.35  E-value=1.1e-13  Score=78.45  Aligned_cols=48  Identities=10%  Similarity=0.196  Sum_probs=40.9

Q ss_pred             ccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112           53 ECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW  104 (132)
Q Consensus        53 ~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  104 (132)
                      .|+||++.+++   +..+ .|||.||++||.+|++. +.+||+||+++..++.
T Consensus         2 ~C~Ic~~~~~~---Pv~~~~cGh~fc~~cI~~~l~~-~~~CP~c~~~l~~~dL   50 (56)
T d2baya1           2 LCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKD-TGNDPITNEPLSIEEI   50 (56)
T ss_dssp             CCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHH-HSBCTTTCCBCCGGGC
T ss_pred             CCccCCchHHh---cCccCCCCCcccHHHHHHHHhh-ccCCCccCCcCCHHhc
Confidence            59999999887   5556 69999999999999975 4789999999876554

>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=99.32  E-value=4.6e-13  Score=76.81  Aligned_cols=52  Identities=17%  Similarity=0.386  Sum_probs=38.3

Q ss_pred             CcccccccccccccCCCce--EEeCCCCcccHHhHHHHHhc-CCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEI--RELSCHHLFHAVCLDTWISN-NYAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~--~~l~C~H~fh~~Ci~~wl~~-~~~~CP~Cr~~~~  100 (132)
                      ++...|+||++++.+....  ....|+|.||..|+.+|+.. ++.+||+||+++.
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            5677899999987653221  11134599999999999943 4568999999875

>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=99.30  E-value=8.6e-13  Score=79.79  Aligned_cols=55  Identities=5%  Similarity=0.082  Sum_probs=45.8

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT  106 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~  106 (132)
                      .++..|+||++.|.+   +..++|||.|+..||.+|+..++..||.||.++.......
T Consensus         5 P~~l~CpIc~~l~~d---Pv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~l~p   59 (80)
T d2c2la2           5 PDYLCGKISFELMRE---PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIP   59 (80)
T ss_dssp             CSTTBCTTTCSBCSS---EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEE
T ss_pred             CccccCcCcCchhhh---hcccCCcCeecHHHHHHHHhcCCccCCCcccccccccccc
Confidence            466789999999988   6678999999999999999655578999999887554443

>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=99.30  E-value=1.2e-12  Score=78.76  Aligned_cols=56  Identities=13%  Similarity=0.387  Sum_probs=47.3

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTG  107 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~  107 (132)
                      .++..|+||++.|.+   +..++|||.|++.||..|+..++..||.|+.++......++
T Consensus         6 P~~l~CpIc~~~m~d---PV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~l~pN   61 (78)
T d1t1ha_           6 PEYFRCPISLELMKD---PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPN   61 (78)
T ss_dssp             SSSSSCTTTSCCCSS---EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEEC
T ss_pred             CccCCCcCcCchhhC---ceEccCCCcchHHHHHHHHHHCCCCCCcccccCCcccccch
Confidence            467889999999988   67789999999999999997655789999999876655544

>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=99.15  E-value=2.5e-12  Score=80.34  Aligned_cols=53  Identities=23%  Similarity=0.515  Sum_probs=41.2

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTG  107 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~  107 (132)
                      +...|+||++.+.++  +...+|||.||..||.+|+.   ..||+||.++.......+
T Consensus        21 ~~l~C~IC~~~~~~p--v~~~~CgH~fC~~Ci~~~~~---~~CP~Cr~~~~~~~l~~n   73 (97)
T d1jm7b_          21 KLLRCSRCTNILREP--VCLGGCEHIFCSNCVSDCIG---TGCPVCYTPAWIQDLKIN   73 (97)
T ss_dssp             HTTSCSSSCSCCSSC--BCCCSSSCCBCTTTGGGGTT---TBCSSSCCBCSCSSCCCC
T ss_pred             hcCCCccCCchhhcC--ceeCCCCCchhHHHHHHHHh---ccccccCCcCchhhCccc
Confidence            345899999999873  23348999999999999984   359999998876555443

>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=98.88  E-value=1.1e-09  Score=68.23  Aligned_cols=55  Identities=4%  Similarity=-0.024  Sum_probs=45.4

Q ss_pred             CcccccccccccccCCCceEEeCCC-CcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCH-HLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTG  107 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~-H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~  107 (132)
                      .++..|+||.+.|.+   +..++|+ |.|++.||..|+.. +..||+|+.++......++
T Consensus        20 P~~f~CPI~~~lm~d---PV~~~~~~~ty~r~~I~~~l~~-~~~~P~~~~~l~~~~L~pN   75 (98)
T d1wgma_          20 CDEFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLS-DQTDPFNRSPLTMDQIRPN   75 (98)
T ss_dssp             CTTTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTT-SCBCTTTCSBCCTTTSEEC
T ss_pred             cHHhCCcCchhHHHH---HHhcccccchhhHHHHHHHHHh-cCCcccccccccchhhcch
Confidence            457899999999998   7778776 57999999999975 5789999999876655544

>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=98.77  E-value=8.8e-10  Score=67.91  Aligned_cols=48  Identities=19%  Similarity=0.508  Sum_probs=37.1

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC----C---CCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN----Y---AICPVCH   96 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~----~---~~CP~Cr   96 (132)
                      ....+|+||++++...+.+..++|+|.||.+|+..|+..+    .   ..||.|+
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           3 SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            3567899999998776656656999999999999999321    1   2599864

>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=93.89  E-value=0.012  Score=30.83  Aligned_cols=45  Identities=29%  Similarity=0.582  Sum_probs=28.7

Q ss_pred             ccccccccccCCCceEEeCCCCcccHHhHHHHHhcC---CCCCCCCCC
Q 042112           53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN---YAICPVCHD   97 (132)
Q Consensus        53 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~---~~~CP~Cr~   97 (132)
                      .|.||...-..+..+.--.|...||..|+..-+...   .-.||.||.
T Consensus         2 ~C~vC~~~~~~~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            588897654332222212789999999998765321   125999975

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=92.68  E-value=0.011  Score=32.54  Aligned_cols=51  Identities=20%  Similarity=0.365  Sum_probs=34.5

Q ss_pred             CcccccccccccccCCCceEE-eCCCCcccHHhHHHHH----hcCCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRE-LSCHHLFHAVCLDTWI----SNNYAICPVCHDSI   99 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~-l~C~H~fh~~Ci~~wl----~~~~~~CP~Cr~~~   99 (132)
                      .....|.+|.+...+++..+. -.|+.-||..|+..-.    ......||.|+..-
T Consensus         4 ~~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~~   59 (64)
T d1we9a_           4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKS   59 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTTT
T ss_pred             CCCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCcC
Confidence            356689999987766554433 2899999999995321    11235799997543

>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=92.48  E-value=0.046  Score=31.65  Aligned_cols=35  Identities=23%  Similarity=0.446  Sum_probs=25.0

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHH
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTW   84 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w   84 (132)
                      ..+..|.|| +.+...+....--|+.+||..|+.+-
T Consensus        13 ~~D~mC~vC-~v~t~~~l~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          13 VNDEMCDVC-EVWTAESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTT-CCCCSSCCSSCSSSSSCCCHHHHHHH
T ss_pred             CcCcccccc-CcccccceecceeecchhhHHHHHHh
Confidence            457889999 66655443221247899999999987

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=89.43  E-value=0.73  Score=26.54  Aligned_cols=53  Identities=17%  Similarity=0.284  Sum_probs=38.4

Q ss_pred             cccccccccccccCCCc--eE--EeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEE--IR--ELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS  102 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~--~~--~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  102 (132)
                      ....|.||-+++.....  +.  .-.|+--.|+.|..-=.+..+..||.|++++...
T Consensus        15 ~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Ykr~   71 (93)
T d1weoa_          15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKRL   71 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCCC
T ss_pred             ccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhhhh
Confidence            46789999998754322  21  1257777899999876766778999999988543

>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=88.32  E-value=0.039  Score=29.92  Aligned_cols=48  Identities=25%  Similarity=0.510  Sum_probs=30.8

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhc---CCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN---NYAICPVCHDSI   99 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~~~   99 (132)
                      ..++.|.+|.+.   ++.+.--.|.-.||..|+..-+..   ..-.||.|+..-
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            445679999753   222222278899999998765432   123699997543

>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=88.02  E-value=0.13  Score=28.49  Aligned_cols=49  Identities=24%  Similarity=0.439  Sum_probs=30.7

Q ss_pred             CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC---CCCCCCCCCCCC
Q 042112           49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN---YAICPVCHDSIA  100 (132)
Q Consensus        49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~---~~~CP~Cr~~~~  100 (132)
                      +....|.+|.+.   ++.+.--.|...||..|+...+...   .-.||.|+..-.
T Consensus         5 d~c~~C~~C~~~---~~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   56 (70)
T d1fp0a1           5 DSATICRVCQKP---GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   56 (70)
T ss_dssp             SSSSCCSSSCSS---SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             CCCCCCCCCCCc---CEEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCc
Confidence            345567777643   3322222788999999998766321   235999976543

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {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 8
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.84  E-value=1  Score=25.10  Aligned_cols=50  Identities=18%  Similarity=0.362  Sum_probs=32.0

Q ss_pred             ccccccccccccCCCceEEe-CCCCcccHHhHHH--HH-h-cCCCCCCCCCCCCC
Q 042112           51 AVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDT--WI-S-NNYAICPVCHDSIA  100 (132)
Q Consensus        51 ~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~--wl-~-~~~~~CP~Cr~~~~  100 (132)
                      ...+.||.+....++..++= .|.--||..|+..  .- . .....||.|+....
T Consensus        11 ~pv~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~g   65 (79)
T d1wepa_          11 VPVYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFG   65 (79)
T ss_dssp             CCCCSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSC
T ss_pred             CCeEeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCcC
Confidence            34555999876554443333 7899999999942  21 1 12368999987544

>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=87.57  E-value=0.12  Score=27.86  Aligned_cols=45  Identities=18%  Similarity=0.361  Sum_probs=29.8

Q ss_pred             cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCC
Q 042112           50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVC   95 (132)
Q Consensus        50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~C   95 (132)
                      ....|.-|...+.+.....-..|++.|+.+|=.---. .--+||.|
T Consensus        14 ~~~~C~gC~~~l~~~~~y~C~~C~~~FC~dCD~fiHe-~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKDQHVYVCAVCQNVFCVDCDVFVHD-SLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTTSEEECCTTTTCCBCHHHHHTTTT-TSCSSSTT
T ss_pred             CCCCccCCCCcCCCCceEECcCCCCccccccchhhhh-hhcCCCCC
Confidence            3467999998886543333347999999999543222 22379988