Citrus Sinensis ID: 027652

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220
Protein Sequence
MSTWELGQCLGRNARDSQRRRILPELDLNYPPTDGNIATNSQEYPFDGHSDSRGDIGDCVEVIDDDLAIINQRIFAEAKNNSRRNHSQVVDQLRHVLTDAGGLLDSLQEVTDLAILYVKQRRNRPDEATPDNCCINVDTSNNNKNDAAPLQLPQDPMAAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPTLS
Secondary Structure (PSIPRED)
cccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccHHHccccccccccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccccccccccEEccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHcccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccEEEEcccEEEcccHHHHHHHHHHcccccEEEEccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccccccccEcccccHHHHHHHHHHHHHcccccHHHHHccHcccccEEccccc
Coil and Loop (DISEMBL)
mstwelgqclgrnardsqrrrilpeldlnypptdgniatnsqeypfdghsdsrgdigdcvEVIDDDLAIINQRIFAEaknnsrrnHSQVVDQLRHVLTDAGGLLDSLQEVTDLAILYVKQrrnrpdeatpdnccinvdtsnnnkndaaplqlpqdpmaaaptfscpicmgplseatstkcghifCKDCIKGAIaaqgkcpncrqkvgkrgifrvylptls
Flexible Loop (DISEMBL)
mstwelgqclgrnardsqrrrilpeldlnypptdGNIATNSQEYPFDGHSDSRGDIGDCVEVIDDDLAIINQRIFaeaknnsrrnhSQVVDQLRHVLTDAGGLLDSLQEVTDLAILYVKqrrnrpdeatpdncCINVDTSNNNKNDAAPLQLPQDPMAAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIaaqgkcpncrqkvgkrgifrvylptls
Low Complexity Region (SEG)
MSTWELGQCLGRNARDSQRRRILPELDLNYPPTDGNIATNSQEYPFDGHSDSRGDIGDCVEVIDDDLAIINQRIFAEAKNNSRRNHSQVVDQLRHVLTDAGGLLDSLQEVTDLAILYVKQRRNRPDEATPDNCCINVDTSNNNKNDAAPLQLPQDPMAAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPTLS
Disordered region (IsUnstruct)
******************************************************DIGDCVEVIDDDLAIINQRIFAEA*********QVVDQLRHVLTDAGGLLDSLQEVTDLAILYVKQ************CCIN************************PTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLP***
Disordered Region (DISOPRED)
*************************************************************VIDDDL*************************************************************************************************CPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPTL*
Disordered Region (DISEMBL)
MSTWELGQCLGRNARDSQRRRILPELDLNYPPTDGNIATNSQEYPFDGHSDSRGDIGDCVEVIDDDLAIINQRIFAEAKNNSRRNHSQVVDQLRHVLTDAGGLLDSLQEVTDLAILYVKQRRNRPDEATPDNCCINVDTSNNNKNDAAPLQLPQDPMAAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPTLS
Disordered Region (DISPRO)
**TWELGQCLGRNARDSQRRRILPELDLNYPPT*********************DIGDCVEVIDDDLAIINQRIFAEAKNNSRRNHSQVVDQLR******************************************************************PTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPT**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSTWELGQCLGRNARDSQRRRILPELDLNYPPTDGNIATNSQEYPFDGHSDSRGDIGDCVEVIDDDLAIINQRIFAEAKNNSRRNHSQVVDQLRHVLTDAGGLLDSLQEVTDLAILYVKQRRNRPDEATPDNCCINVDTSNNNKNDAAPLQLPQDPMAAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPTLS
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	220	2.2.26 [Sep-21-2011]
Q9QZS2	194	E3 ubiquitin-protein liga	yes	no	0.345	0.391	0.314	1e-07
P78317	190	E3 ubiquitin-protein liga	yes	no	0.25	0.289	0.370	2e-07
O88846	194	E3 ubiquitin-protein liga	yes	no	0.25	0.283	0.370	2e-07
Q9CQ29	239	RING finger protein 151 O	no	no	0.236	0.217	0.442	3e-06
Q9R1A8	733	E3 ubiquitin-protein liga	no	no	0.2	0.060	0.454	8e-06
Q96EQ8	232	E3 ubiquitin-protein liga	no	no	0.295	0.280	0.318	1e-05
Q8NHY2	731	E3 ubiquitin-protein liga	no	no	0.2	0.060	0.454	1e-05
Q3U319	1001	E3 ubiquitin-protein liga	no	no	0.245	0.053	0.4	1e-05
Q8CJB9	1002	E3 ubiquitin-protein liga	no	no	0.245	0.053	0.4	1e-05
Q9P3U8	468	Uncharacterized RING fing	yes	no	0.204	0.096	0.4	1e-05

>sp|Q9QZS2|RNF4_MOUSE E3 ubiquitin-protein ligase RNF4 OS=Mus musculus GN=Rnf4 PE=1 SV=1

 Score = 56.2 bits (134), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 13/89 (14%)

Query: 135 INVDTSNNNKNDAAPLQLPQDPMAAAPTFSCPICMGPLSEAT-------STKCGHIFCKD 187
           +   T  + K+D A    P      + T SCPICM   SE         ST+CGH+FC  
Sbjct: 112 VTTHTPRSTKDDGATGPRP------SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQ 165

Query: 188 CIKGAIAAQGKCPNCRQKVGKRGIFRVYL 216
           C++ ++     CP CR+K+  +    +Y+
Sbjct: 166 CLRDSLKNANTCPTCRKKINHKRYHPIYI 194

E3 ubiquitin-protein ligase which binds polysumoylated chains covalently attached to proteins and mediates 'Lys-6'-, 'Lys-11'-, 'Lys-48'- and 'Lys-63'-linked polyubiquitination of those substrates and their subsequent targeting to the proteasome for degradation. Regulates the degradation of several proteins including PML and the transcriptional activator PEA3. Involved in chromosome alignment and spindle assembly, it regulates the kinetochore CENPH-CENPI-CENPK complex by targeting polysumoylated CENPI to proteasomal degradation. Regulates the cellular responses to hypoxia and heat shock through degradation of respectively EPAS1 and PARP1. Alternatively, it may also bind DNA/nucleosomes and have a more direct role in the regulation of transcription for instance enhancing basal transcription and steroid receptor-mediated transcriptional activation.
Mus musculus (taxid: 10090)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|P78317|RNF4_HUMAN E3 ubiquitin-protein ligase RNF4 OS=Homo sapiens GN=RNF4 PE=1 SV=1

 Score = 55.8 bits (133), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 7/62 (11%)

Query: 162 TFSCPICMGPLSEAT-------STKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRV 214
           T SCPICM   SE         ST+CGH+FC  C++ ++     CP CR+K+  +    +
Sbjct: 129 TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPI 188

Query: 215 YL 216
           Y+
Sbjct: 189 YI 190

E3 ubiquitin-protein ligase which binds polysumoylated chains covalently attached to proteins and mediates 'Lys-6'-, 'Lys-11'-, 'Lys-48'- and 'Lys-63'-linked polyubiquitination of those substrates and their subsequent targeting to the proteasome for degradation. Regulates the degradation of several proteins including PML and the transcriptional activator PEA3. Involved in chromosome alignment and spindle assembly, it regulates the kinetochore CENPH-CENPI-CENPK complex by targeting polysumoylated CENPI to proteasomal degradation. Regulates the cellular responses to hypoxia and heat shock through degradation of respectively EPAS1 and PARP1. Alternatively, it may also bind DNA/nucleosomes and have a more direct role in the regulation of transcription for instance enhancing basal transcription and steroid receptor-mediated transcriptional activation.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|O88846|RNF4_RAT E3 ubiquitin-protein ligase RNF4 OS=Rattus norvegicus GN=Rnf4 PE=1 SV=1

 Score = 55.8 bits (133), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 7/62 (11%)

Query: 162 TFSCPICMGPLSEAT-------STKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRV 214
           T SCPICM   SE         ST+CGH+FC  C++ ++     CP CR+K+  +    +
Sbjct: 133 TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPI 192

Query: 215 YL 216
           Y+
Sbjct: 193 YI 194

E3 ubiquitin-protein ligase which binds polysumoylated chains covalently attached to proteins and mediates 'Lys-6'-, 'Lys-11'-, 'Lys-48'- and 'Lys-63'-linked polyubiquitination of those substrates and their subsequent targeting to the proteasome for degradation. Regulates the degradation of several proteins including PML and the transcriptional activator PEA3. Involved in chromosome alignment and spindle assembly, it regulates the kinetochore CENPH-CENPI-CENPK complex by targeting polysumoylated CENPI to proteasomal degradation. Regulates the cellular responses to hypoxia and heat shock through degradation of respectively EPAS1 and PARP1. Alternatively, it may also bind DNA/nucleosomes and have a more direct role in the regulation of transcription for instance enhancing basal transcription and steroid receptor-mediated transcriptional activation.

Rattus norvegicus (taxid: 10116)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9CQ29|RN151_MOUSE RING finger protein 151 OS=Mus musculus GN=Rnf151 PE=1 SV=1

 Score = 52.0 bits (123), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 23/52 (44%), Positives = 29/52 (55%)

Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRV 214
           F C +C G L   T   C HIFCK CI   +A Q  CP CR++V +R +  V
Sbjct: 18  FLCSVCHGVLKRPTRLPCSHIFCKKCIFRWLARQNTCPCCRKEVTRRKMVEV 69

May be involved in acrosome formation of spermatids.

Mus musculus (taxid: 10090)

>sp|Q9R1A8|RFWD2_MOUSE E3 ubiquitin-protein ligase RFWD2 OS=Mus musculus GN=Rfwd2 PE=1 SV=2

 Score = 50.4 bits (119), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 24/44 (54%)

Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKV 206
           F CPIC   + EA  TKCGH FC  CI  ++    +CP C   V
Sbjct: 136 FVCPICFDMIEEAYMTKCGHSFCYKCIHQSLEDNNRCPKCNYVV 179

E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Involved in JUN ubiquitination and degradation. Directly involved in p53 (TP53) ubiquitination and degradation, thereby abolishing p53-dependent transcription and apoptosis. Ubiquitinates p53 independently of MDM2 or RCHY1. Probably mediates E3 ubiquitin ligase activity by functioning as the essential RING domain subunit of larger E3 complexes. In contrast, it does not constitute the catalytic RING subunit in the DCX DET1-COP1 complex that negatively regulates JUN, the ubiquitin ligase activity being mediated by RBX1.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q96EQ8|RN125_HUMAN E3 ubiquitin-protein ligase RNF125 OS=Homo sapiens GN=RNF125 PE=1 SV=4

 Score = 50.1 bits (118), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 147 AAPLQLPQDPMAAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIA-AQGKCPNCRQK 205
           A  L+  +DP     +F C +C+  L +   T+CGH+FC+ CI  ++   +  CP CR  
Sbjct: 19  ARALERRRDPELPVTSFDCAVCLEVLHQPVRTRCGHVFCRSCIATSLKNNKWTCPYCRAY 78

Query: 206 VGKRGI 211
           +   G+
Sbjct: 79  LPSEGV 84

E3 ubiquitin-protein ligase that acts as a positive regulator of T-cell activation. E3 ligase proteins mediate ubiquitination and subsequent proteasomal degradation of target proteins.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q8NHY2|RFWD2_HUMAN E3 ubiquitin-protein ligase RFWD2 OS=Homo sapiens GN=RFWD2 PE=1 SV=1

 Score = 50.1 bits (118), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 24/44 (54%)

Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKV 206
           F CPIC   + EA  TKCGH FC  CI  ++    +CP C   V
Sbjct: 134 FVCPICFDMIEEAYMTKCGHSFCYKCIHQSLEDNNRCPKCNYVV 177

E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Involved in JUN ubiquitination and degradation. Directly involved in p53 (TP53) ubiquitination and degradation, thereby abolishing p53-dependent transcription and apoptosis. Ubiquitinates p53 independently of MDM2 or RCHY1. Probably mediates E3 ubiquitin ligase activity by functioning as the essential RING domain subunit of larger E3 complexes. In contrast, it does not constitute the catalytic RING subunit in the DCX DET1-COP1 complex that negatively regulates JUN, the ubiquitin ligase activity being mediated by RBX1.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q3U319|BRE1B_MOUSE E3 ubiquitin-protein ligase BRE1B OS=Mus musculus GN=Rnf40 PE=2 SV=2

 Score = 50.1 bits (118), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/55 (40%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 163  FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAA-QGKCPNCRQKVGKRGIFRVYL 216
             +CP C     +A  TKC H+FC +C++G   A Q KCP C    G     RVY+
Sbjct: 946  LTCPCCNTRKKDAVLTKCFHVFCFECVRGRYEARQRKCPKCNAAFGAHDFHRVYI 1000

Component of the RNF20/40 E3 ubiquitin-protein ligase complex that mediates monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1). H2BK120ub1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation (H3K4me and H3K79me, respectively). It thereby plays a central role in histone code and gene regulation. The RNF20/40 complex forms a H2B ubiquitin ligase complex in cooperation with the E2 enzyme UBE2A or UBE2B; reports about the cooperation with UBE2E1/UBCH are contradictory. Required for transcriptional activation of Hox genes.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q8CJB9|BRE1B_RAT E3 ubiquitin-protein ligase BRE1B OS=Rattus norvegicus GN=Rnf40 PE=1 SV=1

 Score = 50.1 bits (118), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/55 (40%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 163  FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAA-QGKCPNCRQKVGKRGIFRVYL 216
             +CP C     +A  TKC H+FC +C++G   A Q KCP C    G     RVY+
Sbjct: 947  LTCPCCNTRKKDAVLTKCFHVFCFECVRGRYEARQRKCPKCNAAFGAHDFHRVYI 1001

Component of the RNF20/40 E3 ubiquitin-protein ligase complex that mediates monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1). H2BK120ub1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation (H3K4me and H3K79me, respectively). It thereby plays a central role in histone code and gene regulation. The RNF20/40 complex forms a H2B ubiquitin ligase complex in cooperation with the E2 enzyme UBE2A or UBE2B; reports about the cooperation with UBE2E1/UBCH are contradictory. Required for transcriptional activation of Hox genes.

Rattus norvegicus (taxid: 10116)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9P3U8|YJ95_SCHPO Uncharacterized RING finger protein C548.05c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPCC548.05c PE=4 SV=1

 Score = 50.1 bits (118), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 18/45 (40%), Positives = 24/45 (53%)

Query: 162 TFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKV 206
           T  CPIC   L    +T CGH +C +C+   +     CP CRQK+
Sbjct: 82  TLECPICTEALQRPFTTHCGHTYCYECLLNWLKESKSCPTCRQKL 126

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

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	220
225468779	209	PREDICTED: uncharacterized protein LOC10	0.913	0.961	0.394	5e-25
255584000	224	RING finger protein, putative [Ricinus c	0.945	0.928	0.367	6e-24
449453284	206	PREDICTED: E3 ubiquitin-protein ligase R	0.877	0.936	0.393	2e-23
217070974	247	unknown [Medicago truncatula]	0.677	0.603	0.419	2e-23
225433465	220	PREDICTED: uncharacterized protein LOC10	0.813	0.813	0.37	2e-23
356538599	205	PREDICTED: uncharacterized protein LOC10	0.845	0.907	0.369	2e-23
351725147	205	uncharacterized protein LOC100306616 [Gl	0.845	0.907	0.369	2e-23
217075410	242	unknown [Medicago truncatula] gi|3884945	0.654	0.595	0.419	5e-23
224075260	242	predicted protein [Populus trichocarpa]	0.872	0.793	0.333	1e-21
296080870	163	unnamed protein product [Vitis vinifera]	0.677	0.914	0.403	4e-21

>gi|225468779|ref|XP_002262663.1| PREDICTED: uncharacterized protein LOC100246586 [Vitis vinifera]

 Score =  120 bits (300), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 90/228 (39%), Positives = 118/228 (51%), Gaps = 27/228 (11%)

Query: 1   MSTWELGQCLGRNARDSQRRRILPELDLN-YPPTDGNIATNSQEYPFDGHSDSRGDIGDC 59
           MS   + +   R AR S+RR+ +  LDLN  PPTD    T  QE P            D 
Sbjct: 1   MSASGVREVPLRYARSSRRRKTVLNLDLNDTPPTD----TRDQEGPSIRTMPVPPAAID- 55

Query: 60  VEVIDDDLAIINQRIFAEAKNNSRRNHSQVVDQLRHVLTDAGGLLDSLQEVTDLAILYVK 119
           VE IDD++   +   FA A+NNSRR   + V             +D   EV     L  +
Sbjct: 56  VEAIDDEVVESSATAFAAARNNSRRIRGRTV-------------VDVDLEVQTTRPLNNR 102

Query: 120 QRRNR--PDEAT-PDNCCINVDTSNN----NKNDAAPLQLPQDPMAAAPTFSCPICMGPL 172
            +R R  P++    D+  IN+++SN+    NK       +P  P    PTF+CPICMG L
Sbjct: 103 NKRRRAPPNQTIINDDRYINLESSNSLLRENKPPEQTWHVPPLP-PKEPTFNCPICMGQL 161

Query: 173 SEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPTLS 220
            +  STKCGHIFCK CIK AI+AQGKCP CR++V  +   R+YLP  S
Sbjct: 162 VDEMSTKCGHIFCKMCIKAAISAQGKCPTCRKRVTMKDTIRIYLPAAS 209

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255584000|ref|XP_002532746.1| RING finger protein, putative [Ricinus communis] gi|223527523|gb|EEF29648.1| RING finger protein, putative [Ricinus communis]

 Score =  116 bits (291), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 86/234 (36%), Positives = 120/234 (51%), Gaps = 26/234 (11%)

Query: 1   MSTWELGQCLGRNARDSQRRRILPELDLNYPPTDG--NIATNSQEYPFDGHSDSRGDIGD 58
           MST   G   G   R  +RR+ +  LDLN PP++      T+SQ    D H   +     
Sbjct: 1   MSTQTQG-VRGPPLRGYRRRKTM--LDLNVPPSESRDQEGTSSQ----DAHRGGQTTQQG 53

Query: 59  C---------VEVIDDDLAIINQRIFAEAKNNSRRNHSQVVDQLRHVLTDAGGLLDSLQE 109
                     VE ++DD+   + R FAEAKNN++RN+ Q     R   T    ++  +  
Sbjct: 54  QQSVPLTTIDVEALEDDVVESSPRAFAEAKNNAQRNNLQRNHAQR---TRGSTVIVDVDS 110

Query: 110 VTDLAILYVKQRRNR-PDEATPDNC--CINVDTSNNNKNDAAPLQLPQDPMAAAPTFSCP 166
                + Y + +R R     T  NC   +N+++S+++  D   +Q    P    PTF+CP
Sbjct: 111 GRTTRLTYAQNKRRRVSSNQTIINCDHYVNLESSSSSMRDN--IQPRPPPPPKEPTFNCP 168

Query: 167 ICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPTLS 220
           ICMGP  E TSTKCGHIFCK CIK AI  Q KCP CR++V  + + RV+LP  S
Sbjct: 169 ICMGPFIEETSTKCGHIFCKACIKTAIGVQSKCPTCRKRVTIKELIRVFLPATS 222

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449453284|ref|XP_004144388.1| PREDICTED: E3 ubiquitin-protein ligase RNF4-like [Cucumis sativus] gi|449523007|ref|XP_004168516.1| PREDICTED: E3 ubiquitin-protein ligase RNF4-like [Cucumis sativus]

 Score =  115 bits (287), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 91/231 (39%), Positives = 122/231 (52%), Gaps = 38/231 (16%)

Query: 1   MSTWELGQCLGRNARDSQRRRILPELDLN-YPPTDG-NIATNSQEYPFDGHSDSRGDIGD 58
           MST  +    G   R   RR+ L +LDLN  PPT+  +    SQ    D   + +  +  
Sbjct: 1   MSTQAMR---GHTTRGYHRRKSL-DLDLNSMPPTENRDQGETSQLRLQDAQVNQQQPVQP 56

Query: 59  C---VEVIDDDLAIINQRIFAEAKNNSRRN-HSQVVDQLRHVLTDAGGLLDSLQEVTDLA 114
               +E IDDD+   + R FAEAKN SRRN    VVD       DA       +E + ++
Sbjct: 57  AMIDIEAIDDDVIESSARAFAEAKNKSRRNARKNVVD------VDA-------EERSRVS 103

Query: 115 ILYVKQRR----NRPDEATPDNCCINVDTSNNN-KNDAAPLQLPQDPMAAAPTFSCPICM 169
                +RR    NRP  +   +  IN++ SN++ K   AP   P++P      FSCPICM
Sbjct: 104 NNNRSKRRRDVSNRP--SVNSDLLINLEASNSSMKVKPAP---PKEP-----KFSCPICM 153

Query: 170 GPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPTLS 220
           GPL E TST+CGHIFCK CI+ AI  Q KCP CR++V  + + RV+LP  S
Sbjct: 154 GPLVEETSTRCGHIFCKACIRAAIGVQSKCPTCRKRVTAKELIRVFLPGTS 204

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217070974|gb|ACJ83847.1| unknown [Medicago truncatula]

 Score =  115 bits (287), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 68/162 (41%), Positives = 93/162 (57%), Gaps = 13/162 (8%)

Query: 60  VEVIDDDLAIINQ-RIFAEAKNNSRRNHSQVVDQLRHVLTDAGGLLDSLQEVTDLAILYV 118
           VE IDDD  +++  R FAEAKNNSRRN  + V        D   ++   +E   L+    
Sbjct: 94  VEAIDDDDVVLSSPRAFAEAKNNSRRNRGRTV-------VDVDLVMFFAEEQIRLSNNNR 146

Query: 119 KQRRNRPDEATPDNC--CINVDTSNNNKNDAAPLQLPQDPMAAAPTFSCPICMGPLSEAT 176
            +RR    + +  NC   IN+D S++N  ++             P F+CPICMGP+ E  
Sbjct: 147 NKRRRESPKRSIFNCDLYINLDASSSNTMESVKKP---PEPPKEPVFTCPICMGPMVEEM 203

Query: 177 STKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPT 218
           ST+CGHIFCK CIK AI+AQ KCP CR+K+  + + RV+LPT
Sbjct: 204 STRCGHIFCKSCIKAAISAQAKCPTCRKKITVKELIRVFLPT 245

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225433465|ref|XP_002263351.1| PREDICTED: uncharacterized protein LOC100262402 [Vitis vinifera] gi|298205213|emb|CBI17272.3| unnamed protein product [Vitis vinifera]

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 74/200 (37%), Positives = 109/200 (54%), Gaps = 21/200 (10%)

Query: 29  NYPPTDGNIA---TNSQEYPFDGHSD----SRGDIGDCVEVIDDDLAIINQ-RIFAEAKN 80
           NYPP   N+A   T +   P + ++     S     + V+  DDD+ I++  R F EA+ 
Sbjct: 28  NYPPPSDNVALESTFTSSSPLELYAKDQRWSNPQATNNVDASDDDVVILSSPRSFLEARK 87

Query: 81  NSRRNHSQVV--DQLRHVLTDAGGLLDSLQEVTDLAILYVKQRRNRPDEATPDNCCINVD 138
           NSRRN   ++  D    +    G + D ++      I     ++N+ D  T    C+ + 
Sbjct: 88  NSRRNAEVIMVNDNDIEMPGHLGIVFDDIEMQGHQEIA----QQNKID--TDLKLCLEL- 140

Query: 139 TSNNNKNDAAPLQLPQD-PMAAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG 197
               NK +   +Q+P + P    PTF+CPICM  L+E TSTKCGHIFCK+CI+GA+A   
Sbjct: 141 ---FNKTETENVQIPTEVPSPETPTFTCPICMDQLTEETSTKCGHIFCKECIEGAMAVSQ 197

Query: 198 KCPNCRQKVGKRGIFRVYLP 217
           +CP CR+K+ K+ I RVYLP
Sbjct: 198 RCPTCRKKLKKKDIIRVYLP 217

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538599|ref|XP_003537790.1| PREDICTED: uncharacterized protein LOC100792853 [Glycine max]

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 82/222 (36%), Positives = 111/222 (50%), Gaps = 36/222 (16%)

Query: 11  GRNARDSQRRRILPELDLNYPPTDGNI---ATNSQEYPFDGHSDSRGDIGDC----VEVI 63
           G   R  +RR+   +LDLN  P   N      ++Q  P +   + +  +       VE I
Sbjct: 8   GPAIRSYRRRKTALDLDLNRLPAGENREQEGPSTQAVPQEIQLEQQPQVTQPPMIDVEAI 67

Query: 64  DDDLAIINQRIFAEAKNNSRRNHSQVVDQLRHVLTDAGGLLDSLQEVTDLAILYVKQRRN 123
           DDD+     R FAEAKNNSRR   + V  +             L++ T         RRN
Sbjct: 68  DDDVVECTPRAFAEAKNNSRRIRRRTVVDI------------DLEDQT---------RRN 106

Query: 124 RPDEATPDNCCINVDTSNNNKNDAAPL-----QLPQDPMAAAPTFSCPICMGPLSEATST 178
           +     P N  IN D   N +  ++ +     + P+ P      F+CPICMGP+    ST
Sbjct: 107 KRRRELP-NLIINCDKYINLEGSSSSMGGSVKKTPEPPKEL--VFNCPICMGPMVHEMST 163

Query: 179 KCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPTLS 220
           +CGHIFCKDCIK AI+AQGKCP CR+KV  + + RVYLP+ S
Sbjct: 164 RCGHIFCKDCIKAAISAQGKCPTCRKKVVAKDLIRVYLPSTS 205

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351725147|ref|NP_001237594.1| uncharacterized protein LOC100306616 [Glycine max] gi|255629089|gb|ACU14889.1| unknown [Glycine max]

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 82/222 (36%), Positives = 108/222 (48%), Gaps = 36/222 (16%)

Query: 11  GRNARDSQRRRILPELDLNYPPTDGNI---ATNSQEYPFDGHSDSRGDIGDC----VEVI 63
           G   R  +RR+   +LDLN  P   N      ++Q  P +   + +          VE I
Sbjct: 8   GPAVRSYRRRKTALDLDLNRVPAGENREQEGPSTQSVPREVQVEQQQQATQPPMIDVEAI 67

Query: 64  DDDLAIINQRIFAEAKNNSRRNHSQVVDQLRHVLTDAGGLLDSLQEVTDLAILYVKQRRN 123
           DDD+     R FAEAKNNSRR         R  + D                L  + RRN
Sbjct: 68  DDDVVECTPRAFAEAKNNSRRVR-------RRTIVDVD--------------LEDQTRRN 106

Query: 124 RPDEATPDNCCINVDTSNNNKNDAAPLQL-----PQDPMAAAPTFSCPICMGPLSEATST 178
           +     P N  IN D   N +  ++ ++      P+ P      F+CPICMGP+    ST
Sbjct: 107 KRRRELP-NLIINCDKYINLEGGSSSMEQSFKKPPEPPKEL--VFNCPICMGPMVHEMST 163

Query: 179 KCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPTLS 220
           +CGHIFCKDCIK AI+AQGKCP CR+KV  + + RVYLP+ S
Sbjct: 164 RCGHIFCKDCIKAAISAQGKCPTCRKKVVAKDLIRVYLPSTS 205

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217075410|gb|ACJ86065.1| unknown [Medicago truncatula] gi|388494518|gb|AFK35325.1| unknown [Medicago truncatula]

 Score =  113 bits (283), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 68/162 (41%), Positives = 92/162 (56%), Gaps = 18/162 (11%)

Query: 60  VEVIDDDLAIINQ-RIFAEAKNNSRRNHSQVVDQLRHVLTDAGGLLDSLQEVTDLAILYV 118
           VE IDDD  +++  R FAEAKNNSRRN  + V  +             L+E   L+    
Sbjct: 94  VEAIDDDDVVLSSPRAFAEAKNNSRRNRGRTVVDV------------DLEEQIRLSNNNR 141

Query: 119 KQRRNRPDEATPDNC--CINVDTSNNNKNDAAPLQLPQDPMAAAPTFSCPICMGPLSEAT 176
            +RR    + +  NC   IN+D S++N  ++             P F+CPICMGP+ E  
Sbjct: 142 NKRRRESPKRSIFNCDLYINLDASSSNTMESVKKP---PEPPKEPVFTCPICMGPMVEEM 198

Query: 177 STKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPT 218
           ST+CGHIFCK CIK AI+AQ KCP CR+K+  + + RV+LPT
Sbjct: 199 STRCGHIFCKSCIKAAISAQAKCPTCRKKITVKELIRVFLPT 240

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224075260|ref|XP_002304583.1| predicted protein [Populus trichocarpa] gi|222842015|gb|EEE79562.1| predicted protein [Populus trichocarpa]

 Score =  108 bits (271), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 71/213 (33%), Positives = 99/213 (46%), Gaps = 21/213 (9%)

Query: 19  RRRILPELDLNYP-PTDGNIATNSQEYPFD---------GHSDSRGDIGDCVEVIDDDLA 68
            R      DLN+P P + NI      +P           G +  RG   D VEVIDDD+A
Sbjct: 38  ERSYYQHFDLNFPVPVENNIPPCGPWFPAQPQIFQAEAYGLTRQRGTARD-VEVIDDDIA 96

Query: 69  IINQRIFAEAKNNSRRNHSQVVDQLRHVLTDAGGL--LDSLQEVTDLAILYVKQRRNRPD 126
           II+   F +A+  +RRN    V +  ++   AG +  L    +    +      +   P 
Sbjct: 97  IISPNTFDQARKKARRNPDAEVRENINMANQAGSVPQLPGSSQAVPPSQFPGSSQTVPPP 156

Query: 127 EATPDNCCINVDTSNNNKNDAAPLQLPQDPMAAAPTFSCPICMGPLSEATSTKCGHIFCK 186
           + +  +  +     +     A P          AP F CPICM  + EATSTKCGH+FCK
Sbjct: 157 QLSGLSLTVPPPHFSGLSQTAPP--------PPAPMFCCPICMDEMKEATSTKCGHVFCK 208

Query: 187 DCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPTL 219
            CI+ A+A Q KCP CR K   + IFR++LP  
Sbjct: 209 SCIEKALAVQKKCPTCRMKCIAKSIFRIFLPAF 241

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296080870|emb|CBI18799.3| unnamed protein product [Vitis vinifera]

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 67/166 (40%), Positives = 93/166 (56%), Gaps = 17/166 (10%)

Query: 60  VEVIDDDLAIINQRIFAEAKNNSRRNHSQVVDQLRHVLTDAGGLLDSLQEVTDLAILYVK 119
           VE IDD++   +   FA A+NNSRR   + V        D    + + + + +      K
Sbjct: 10  VEAIDDEVVESSATAFAAARNNSRRIRGRTV-------VDVDLEVQTTRPLNNRN----K 58

Query: 120 QRRNRPDEATP-DNCCINVDTSNN----NKNDAAPLQLPQDPMAAAPTFSCPICMGPLSE 174
           +RR  P++    D+  IN+++SN+    NK       +P  P    PTF+CPICMG L +
Sbjct: 59  RRRAPPNQTIINDDRYINLESSNSLLRENKPPEQTWHVPPLP-PKEPTFNCPICMGQLVD 117

Query: 175 ATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPTLS 220
             STKCGHIFCK CIK AI+AQGKCP CR++V  +   R+YLP  S
Sbjct: 118 EMSTKCGHIFCKMCIKAAISAQGKCPTCRKRVTMKDTIRIYLPAAS 163

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	220
TAIR|locus:2098505	182	AT3G07200 [Arabidopsis thalian	0.359	0.434	0.476	4.3e-23
TAIR|locus:505006682	203	AT5G48655 [Arabidopsis thalian	0.845	0.916	0.361	4.8e-23
FB|FBgn0037384	319	dgrn "degringolade" [Drosophil	0.245	0.169	0.535	1.5e-12
MGI|MGI:1201691	194	Rnf4 "ring finger protein 4" [	0.427	0.484	0.321	2.5e-10
UNIPROTKB|F1ND52	190	RNF4 "Uncharacterized protein"	0.4	0.463	0.316	5.2e-10
UNIPROTKB|F6RV66	186	RNF4 "Uncharacterized protein"	0.422	0.5	0.339	5.2e-10
UNIPROTKB|F1S8Q2	190	RNF4 "Uncharacterized protein"	0.427	0.494	0.321	5.2e-10
UNIPROTKB|J9NS55	191	RNF4 "Uncharacterized protein"	0.427	0.492	0.321	6.6e-10
UNIPROTKB|F1PF91	195	RNF4 "Uncharacterized protein"	0.427	0.482	0.321	1.1e-09
UNIPROTKB|F1PC91	189	RNF4 "Uncharacterized protein"	0.422	0.492	0.324	1.1e-09

TAIR|locus:2098505 AT3G07200 [Arabidopsis thaliana (taxid:3702)]

 Score = 219 (82.2 bits), Expect = 4.3e-23, Sum P(2) = 4.3e-23
 Identities = 40/84 (47%), Positives = 53/84 (63%)

Query:   140 SNNNKNDAAPLQLPQDPMAAAPT-----FSCPICMGPLSEATSTKCGHIFCKDCIKGAIA 194
             S+    D+  L  P+   A AP      FSCPIC+ P ++  STKCGHIFCK CIK A++
Sbjct:    97 SDQTSVDSVELNKPRKSKAVAPPVEEPKFSCPICLCPFTQEVSTKCGHIFCKKCIKNALS 156

Query:   195 AQGKCPNCRQKVGKRGIFRVYLPT 218
              Q KCP CR+K+  + + RV+LPT
Sbjct:   157 LQAKCPTCRKKITVKDLIRVFLPT 180

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:505006682 AT5G48655 [Arabidopsis thaliana (taxid:3702)]

 Score = 266 (98.7 bits), Expect = 4.8e-23, P = 4.8e-23
 Identities = 78/216 (36%), Positives = 112/216 (51%)

Query:    12 RNARDSQRRRILPELDLNYPPTD--GNIAT-NSQEYPFDGHSDSRGDIGDCVEVIDDDLA 68
             R  R ++RR+ +  +DLN  P D  G  A+  +   P      +   I   V+ I+DD+ 
Sbjct:     7 RVPRGNRRRKAV--IDLNAVPVDQEGTSASVRTLTVPITPSQPAPTMID--VDAIEDDVI 62

Query:    69 IINQRIFAEAKNNSR--RNHSQVVDQLRHVLTDAGGLLDSLQEVTDLAILYVKQRRNRPD 126
               +   FAEAK+ SR  R    +VD       ++GG       +++      K+RR    
Sbjct:    63 ESSASAFAEAKSKSRNARRRPLMVD------VESGGTTRFPANISN------KRRRIPSS 110

Query:   127 EATPD--NCCIN--VDTSNNNKNDAAPLQLPQDPMAAAPTFSCPICMGPLSEATSTKCGH 182
             E+  D  +  +N  V+ S+      AP   P++P      F+CPICM P +E  STKCGH
Sbjct:   111 ESVIDCEHASVNDEVNMSSRVSRSKAPAPPPEEPK-----FTCPICMCPFTEEMSTKCGH 165

Query:   183 IFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPT 218
             IFCK CIK AI+ QGKCP CR+KV  + + RV+LPT
Sbjct:   166 IFCKGCIKMAISRQGKCPTCRKKVTAKELIRVFLPT 201

GO:0005634 "nucleus" evidence=ISM

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

GO:0010200 "response to chitin" evidence=IEP

FB|FBgn0037384 dgrn "degringolade" [Drosophila melanogaster (taxid:7227)]

 Score = 171 (65.3 bits), Expect = 1.5e-12, P = 1.5e-12
 Identities = 30/56 (53%), Positives = 39/56 (69%)

Query:   163 FSCPICMGPLS--EATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL 216
             + CPICM  +S  E  STKCGH+FC++CI+ AI A  KCP C +K+  R  FR+YL
Sbjct:   264 YKCPICMDSVSKREPVSTKCGHVFCRECIETAIRATHKCPICNKKLTARQFFRIYL 319

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032183 "SUMO binding" evidence=IPI

GO:0016567 "protein ubiquitination" evidence=IDA

GO:0001103 "RNA polymerase II repressing transcription factor binding" evidence=IPI

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

GO:0005634 "nucleus" evidence=IDA

GO:0033768 "SUMO-targeted ubiquitin ligase complex" evidence=IC

GO:0070201 "regulation of establishment of protein localization" evidence=IDA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

GO:0043393 "regulation of protein binding" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0007530 "sex determination" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

GO:0022008 "neurogenesis" evidence=IGI

MGI|MGI:1201691 Rnf4 "ring finger protein 4" [Mus musculus (taxid:10090)]

 Score = 146 (56.5 bits), Expect = 2.5e-10, P = 2.5e-10
 Identities = 36/112 (32%), Positives = 54/112 (48%)

Query:   121 RRNRPDEATPDNCCINVDTS--NNNKNDAAPLQLPQ---DPMAAAP----TFSCPICMGP 171
             RR R D A  D+C ++ D    + +K+       P+   D  A  P    T SCPICM  
Sbjct:    85 RRLRQDHA--DSCVVSSDDEELSRDKDVYVTTHTPRSTKDDGATGPRPSGTVSCPICMDG 142

Query:   172 LSEAT-------STKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL 216
              SE         ST+CGH+FC  C++ ++     CP CR+K+  +    +Y+
Sbjct:   143 YSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI 194

GO:0003677 "DNA binding" evidence=ISO

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005654 "nucleoplasm" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO;IDA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0008134 "transcription factor binding" evidence=IPI

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=ISO

GO:0016605 "PML body" evidence=ISO

GO:0016874 "ligase activity" evidence=IEA

GO:0030331 "estrogen receptor binding" evidence=ISO

GO:0031491 "nucleosome binding" evidence=ISO

GO:0032184 "SUMO polymer binding" evidence=ISO

GO:0033142 "progesterone receptor binding" evidence=ISO

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=ISO

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISO

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO;IDA

GO:0046685 "response to arsenic-containing substance" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

GO:0050681 "androgen receptor binding" evidence=ISO

GO:0051865 "protein autoubiquitination" evidence=ISO

GO:0070534 "protein K63-linked ubiquitination" evidence=ISO

GO:0070936 "protein K48-linked ubiquitination" evidence=ISO

GO:0070979 "protein K11-linked ubiquitination" evidence=ISO

GO:0085020 "protein K6-linked ubiquitination" evidence=ISO

GO:0090169 "regulation of spindle assembly" evidence=ISO

GO:0090234 "regulation of kinetochore assembly" evidence=ISO

UNIPROTKB|F1ND52 RNF4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 143 (55.4 bits), Expect = 5.2e-10, P = 5.2e-10
 Identities = 31/98 (31%), Positives = 48/98 (48%)

Query:   126 DEATPDNCCINVDTSNNNKNDAAPLQLPQDPMAAAPTFSCPICMGPLSEAT-------ST 178
             ++ T DN   +V  ++    +  PL+        + T SCPICM   SE         ST
Sbjct:    96 EDETRDN---DVYVTDKVSRELGPLEDETASSKPSGTVSCPICMDGYSEIVQSGRLIVST 152

Query:   179 KCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL 216
             KCGH+FC  C++ ++     CP CR+K+  R    +Y+
Sbjct:   153 KCGHVFCSQCLRDSLRNANSCPTCRKKLTHRQYHPIYI 190

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F6RV66 RNF4 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 143 (55.4 bits), Expect = 5.2e-10, P = 5.2e-10
 Identities = 37/109 (33%), Positives = 52/109 (47%)

Query:   121 RRNRPDEATPDNCCINVDTSNNNKNDAAPLQLPQDPMAAA----P--TFSCPICMGPLSE 174
             RR R D A  D+C ++ D     + D         P +AA    P  T SCPICM   SE
Sbjct:    81 RRLRQDHA--DSCVVSSDEEELAR-DKDVYVTTHSPRSAATGFRPSGTVSCPICMDGYSE 137

Query:   175 AT-------STKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL 216
                      ST+CGHIFC  C++ ++     CP CR+K+  +    +Y+
Sbjct:   138 IVQNGRLIVSTECGHIFCSQCLRDSLKNANTCPTCRKKMSHKRYHPIYI 186

GO:0090234 "regulation of kinetochore assembly" evidence=IEA

GO:0090169 "regulation of spindle assembly" evidence=IEA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0015630 "microtubule cytoskeleton" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1S8Q2 RNF4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 143 (55.4 bits), Expect = 5.2e-10, P = 5.2e-10
 Identities = 36/112 (32%), Positives = 55/112 (49%)

Query:   121 RRNRPDEATPDNCCINVDTSNNNKN-DA-APLQLPQDPMAAA-----P--TFSCPICMGP 171
             RR R D A  D+C ++ D    +++ D     Q P++    A     P  T SCPICM  
Sbjct:    81 RRLRQDHA--DSCVVSSDDEELSRDRDVYVTTQTPRNAREEAATGLRPSGTVSCPICMDG 138

Query:   172 LSEAT-------STKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL 216
              SE         ST+CGH+FC  C++ ++     CP CR+K+  +    +Y+
Sbjct:   139 YSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI 190

GO:0090234 "regulation of kinetochore assembly" evidence=IEA

GO:0090169 "regulation of spindle assembly" evidence=IEA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0015630 "microtubule cytoskeleton" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|J9NS55 RNF4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 142 (55.0 bits), Expect = 6.6e-10, P = 6.6e-10
 Identities = 36/112 (32%), Positives = 54/112 (48%)

Query:   121 RRNRPDEATPDNCCINVDTSNNNKN-DA-APLQLPQDPMAAA-----P--TFSCPICMGP 171
             RR R D A  D+C ++ D    +++ D       P++    A     P  T SCPICM  
Sbjct:    82 RRPRQDHA--DSCVVSSDDEELSRDRDVYVTTHTPRNTREEAATGLRPSGTVSCPICMDG 139

Query:   172 LSEAT-------STKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL 216
              SE         ST+CGH+FC  C++ A+     CP CR+K+  +    +Y+
Sbjct:   140 YSEIVQNGRLIVSTECGHVFCSQCLRDALKNANTCPTCRKKINHKRYHPIYI 191

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1PF91 RNF4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 142 (55.0 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 36/112 (32%), Positives = 54/112 (48%)

Query:   121 RRNRPDEATPDNCCINVDTSNNNKN-DA-APLQLPQDPMAAA-----P--TFSCPICMGP 171
             RR R D A  D+C ++ D    +++ D       P++    A     P  T SCPICM  
Sbjct:    86 RRPRQDHA--DSCVVSSDDEELSRDRDVYVTTHTPRNTREEAATGLRPSGTVSCPICMDG 143

Query:   172 LSEAT-------STKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL 216
              SE         ST+CGH+FC  C++ A+     CP CR+K+  +    +Y+
Sbjct:   144 YSEIVQNGRLIVSTECGHVFCSQCLRDALKNANTCPTCRKKINHKRYHPIYI 195

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1PC91 RNF4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 140 (54.3 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 36/111 (32%), Positives = 53/111 (47%)

Query:   121 RRNRPDEATPDNCCINVDTSNNNKN-DA-APLQLPQDPMAAA-----P--TFSCPICMGP 171
             RR R D A  D+C ++ D    +++ D       P++    A     P  T SCPICM  
Sbjct:    81 RRPRQDHA--DSCVVSSDDEELSRDRDVYVTTHTPRNTREEAATGLRPSGTVSCPICMDG 138

Query:   172 LSEAT-------STKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVY 215
              SE         ST+CGH+FC  C++ A+     CP CR+K+  +    +Y
Sbjct:   139 YSEIVQNGRLIVSTECGHVFCSQCLRDALKNANTCPTCRKKINHKRYHPIY 189

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	6.3.2	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh4_pg.C_LG_III001250 hypothetical protein (242 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	220
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	1e-09
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	2e-09
COG5574	271	COG5574, PEX10, RING-finger-containing E3 ubiquiti	3e-09
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	2e-08
smart00184	40	smart00184, RING, Ring finger	5e-06
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	1e-05
pfam13920	49	pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RI	3e-05
TIGR00599	397	TIGR00599, rad18, DNA repair protein rad18	3e-04
COG5222	427	COG5222, COG5222, Uncharacterized conserved protei	7e-04
pfam13445	55	pfam13445, zf-RING_LisH, RING-type zinc-finger, Li	0.001
COG5432	391	COG5432, RAD18, RING-finger-containing E3 ubiquiti	0.002

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

 Score = 51.7 bits (124), Expect = 1e-09
 Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 1/43 (2%)

Query: 163 FSCPICMGPLSEA-TSTKCGHIFCKDCIKGAIAAQGKCPNCRQ 204
             CPIC+  L +    T CGH+FC++CI   +  + KCP CR 
Sbjct: 3   LECPICLDLLRDPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 51.2 bits (123), Expect = 2e-09
 Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 3/46 (6%)

Query: 163 FSCPICMGPLS---EATSTKCGHIFCKDCIKGAIAAQGKCPNCRQK 205
             CPIC+       E     CGH+F K+C+   + +   CP CR  
Sbjct: 1   DECPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

 Score = 54.9 bits (132), Expect = 3e-09
 Identities = 36/172 (20%), Positives = 67/172 (38%), Gaps = 11/172 (6%)

Query: 39  TNSQEYPFDGHSDSRGDIGDCVEVI-DDDLAIINQRIFAEAKNNSRRNHSQVVDQLRHVL 97
           T S EY  + + D  G++     +        I      +  N    + SQ++  L  + 
Sbjct: 97  TLSIEYSRETNIDKEGEVLYPCGIFFCIGCDYIWSIDLKQTANTHEASPSQLLKFLPTIR 156

Query: 98  TDAGGLLDSLQEVTDLAILYVKQRRNR-PDEATPDNCCINVDTSNNNKNDAAPLQLPQDP 156
                + + + ++T +A+   + R       +   +    V T    +N +    LP  P
Sbjct: 157 LAMN-IPEVISDLTAVALSLDESRLQPILQPSNNLHTLFQVITK---ENLSKKNGLPFIP 212

Query: 157 MAAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQ--GKCPNCRQKV 206
           +A    + C +C+      + T CGH+FC  C+  +   +    CP CR KV
Sbjct: 213 LA---DYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKV 261

Length = 271

>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 = 48.6 bits (116), Expect = 2e-08
 Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 2/44 (4%)

Query: 165 CPICMGPLSEATST-KCGHIFCKDCIKGAI-AAQGKCPNCRQKV 206
           CPIC+    E      CGH+FC+ CI   + + +  CP CR  +
Sbjct: 2   CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 42.1 bits (99), Expect = 5e-06
 Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 2/40 (5%)

Query: 165 CPICMGPLSEAT-STKCGHIFCKDCIKGAIAAQG-KCPNC 202
           CPIC+    +      CGH FC+ CI+  + +    CP C
Sbjct: 1   CPICLEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 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 = 40.5 bits (95), Expect = 1e-05
 Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 2/40 (5%)

Query: 165 CPICMGPLSEA-TSTKCGHIFCKDCIKGAI-AAQGKCPNC 202
           CPIC+    +  T   CGH+FC  CI   + +    CP C
Sbjct: 1   CPICLEEPKDPVTILPCGHLFCSKCILSWLESGNVTCPLC 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|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger)

 Score = 40.1 bits (94), Expect = 3e-05
 Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 2/43 (4%)

Query: 165 CPICMGPLSEATSTKCGH-IFCKDCIKGAIAAQGKCPNCRQKV 206
           C IC+          CGH   C++C K  + ++ KCP CRQ +
Sbjct: 5   CVICLERPRNVVFLPCGHLCLCEECAK-RLRSKKKCPICRQPI 46

Length = 49

>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18

 Score = 40.8 bits (95), Expect = 3e-04
 Identities = 16/41 (39%), Positives = 19/41 (46%)

Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCR 203
             C IC         T C H FC  CI+  ++ Q KCP CR
Sbjct: 27  LRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCR 67

All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 397

>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

 Score = 39.7 bits (92), Expect = 7e-04
 Identities = 19/43 (44%), Positives = 23/43 (53%), Gaps = 2/43 (4%)

Query: 165 CPICMGPLSEATSTK-CGHIFCKDCIKGAIAAQG-KCPNCRQK 205
           CP+C   L     T  CGH FC +CI  A+     KCPNC +K
Sbjct: 277 CPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRK 319

Length = 427

>gnl|CDD|222135 pfam13445, zf-RING_LisH, RING-type zinc-finger, LisH dimerisation motif

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 6/44 (13%)

Query: 163 FSCPICMGPLSEAT----STKCGHIFCKDCIK--GAIAAQGKCP 200
           F CPI    +++         CGH++ +  ++       + KCP
Sbjct: 11  FVCPISKEVMTDEENPPVMLPCGHVYSRKALEKLAKNGGKFKCP 54

This zinc-finger is the dimerisation motif for LisH proteins, and is also a typical RING-type of plant ubiquitin ligases. Length = 55

>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

 Score = 38.5 bits (89), Expect = 0.002
 Identities = 17/39 (43%), Positives = 20/39 (51%)

Query: 165 CPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCR 203
           C IC   +S    T CGH FC  CI+  +  Q  CP CR
Sbjct: 28  CRICDCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCR 66

Length = 391

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	220
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.49
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.31
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.28
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.21
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.16
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.15
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	99.13
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.08
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.06
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.0
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.96
PHA02929	238	N1R/p28-like protein; Provisional	98.89
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.89
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.88
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.86
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.83
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.79
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.76
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.66
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.65
PF14634	44	zf-RING_5: zinc-RING finger domain	98.64
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.63
PHA02926	242	zinc finger-like protein; Provisional	98.58
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	98.52
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.44
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	98.41
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.38
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.34
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	98.33
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.3
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.26
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.18
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	98.18
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.02
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.94
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.91
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.89
KOG3039	303	consensus Uncharacterized conserved protein [Funct	97.84
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	97.8
KOG2660	331	consensus Locus-specific chromosome binding protei	97.77
COG5152	259	Uncharacterized conserved protein, contains RING a	97.73
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.56
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	97.53
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.53
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	97.46
PF04641	260	Rtf2: Rtf2 RING-finger	97.42
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.38
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	97.34
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.24
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.06
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.05
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.01
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.0
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	96.97
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	96.79
KOG1002	791	consensus Nucleotide excision repair protein RAD16	96.74
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	96.68
COG5222	427	Uncharacterized conserved protein, contains RING Z	96.59
KOG0825	1134	consensus PHD Zn-finger protein [General function	96.57
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	96.48
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	96.42
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	96.4
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	96.36
COG5219	1525	Uncharacterized conserved protein, contains RING Z	96.3
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.27
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	96.24
KOG1001	674	consensus Helicase-like transcription factor HLTF/	96.07
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	95.79
COG5236	493	Uncharacterized conserved protein, contains RING Z	95.34
KOG4367	699	consensus Predicted Zn-finger protein [Function un	95.31
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	95.26
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	95.25
KOG4739	233	consensus Uncharacterized protein involved in syna	95.21
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.11
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	95.07
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.04
KOG3002	299	consensus Zn finger protein [General function pred	94.26
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	93.73
COG5109	396	Uncharacterized conserved protein, contains RING Z	93.62
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	93.57
KOG4445	368	consensus Uncharacterized conserved protein, conta	93.53
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	93.16
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	93.06
KOG1941	518	consensus Acetylcholine receptor-associated protei	92.15
KOG3579	352	consensus Predicted E3 ubiquitin ligase [Posttrans	91.51
KOG0298	1394	consensus DEAD box-containing helicase-like transc	91.11
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	90.86
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	90.56
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	90.5
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	90.32
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	90.22
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	90.02
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	89.56
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	89.45
PHA03096	284	p28-like protein; Provisional	89.09
KOG3113	293	consensus Uncharacterized conserved protein [Funct	89.07
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	88.78
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	88.18
PHA02825	162	LAP/PHD finger-like protein; Provisional	88.0
KOG3039	303	consensus Uncharacterized conserved protein [Funct	87.93
KOG1940	276	consensus Zn-finger protein [General function pred	87.52
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	87.11
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	87.01
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	86.4
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	84.92
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	83.77
PHA02862	156	5L protein; Provisional	81.38

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

Probab=99.49  E-value=1.3e-14  Score=118.42  Aligned_cols=58  Identities=48%  Similarity=1.138  Sum_probs=53.1

Q ss_pred             CCCCccccccCCCCCC--ceEecccCccchhHHHHHHhcCCCCCCCCccccCCCceeecC
Q 027652          159 AAPTFSCPICMGPLSE--ATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL  216 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~--pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iyl  216 (220)
                      .+..+.||||++.+.+  |+.+.|||+||+.||+..++...+||+|+++++.+++++|||
T Consensus       128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~~~rI~L  187 (187)
T KOG0320|consen  128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQFHRIYL  187 (187)
T ss_pred             cccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchhhheeccC
Confidence            4556899999998876  456899999999999999999999999999999999999997

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.31  E-value=2.2e-12  Score=107.39  Aligned_cols=60  Identities=32%  Similarity=0.753  Sum_probs=52.5

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhc----------------CCCCCCCCccccCCCceeecCCC
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAA----------------QGKCPNCRQKVGKRGIFRVYLPT  218 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~----------------~~~CP~Cr~~v~~~~l~~iylp~  218 (220)
                      ....+.|+||++.+.+|+.++|||.||+.||.+|+..                ...||+|+..+...+++++|--+
T Consensus        15 ~~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiygrg   90 (193)
T PLN03208         15 SGGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIYGRG   90 (193)
T ss_pred             CCCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEeeccC
Confidence            3456899999999999999999999999999999752                24799999999999999999543

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

Probab=99.28  E-value=4.5e-12  Score=107.49  Aligned_cols=58  Identities=28%  Similarity=0.721  Sum_probs=53.1

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhcC---CCCCCCCccccCCCceeecC
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQ---GKCPNCRQKVGKRGIFRVYL  216 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~---~~CP~Cr~~v~~~~l~~iyl  216 (220)
                      ....|.|-||++..++||.+.|||.||+.||.+|+...   ..||+|+..++.+.+++||=
T Consensus        44 ~~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlYG  104 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLYG  104 (230)
T ss_pred             CCCceeeeeeccccCCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEeeec
Confidence            46689999999999999999999999999999999853   36899999999999999993

>smart00504 Ubox Modified RING finger domain

Probab=99.21  E-value=1.3e-11  Score=84.57  Aligned_cols=53  Identities=17%  Similarity=0.374  Sum_probs=49.2

Q ss_pred             ccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCccccCCCceeec
Q 027652          163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVY  215 (220)
Q Consensus       163 ~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iy  215 (220)
                      +.||||.+.+.+|+.++|||+||+.||.+|++....||.|+.++..+++++++
T Consensus         2 ~~Cpi~~~~~~~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~~   54 (63)
T smart00504        2 FLCPISLEVMKDPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPNL   54 (63)
T ss_pred             cCCcCCCCcCCCCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeCH
Confidence            67999999999999999999999999999999888999999999888887754

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

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

Probab=99.16  E-value=2.2e-11  Score=106.19  Aligned_cols=57  Identities=32%  Similarity=0.732  Sum_probs=52.1

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCccccCCCceeec
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVY  215 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iy  215 (220)
                      .+....|.+|++...+|..++|||+||+.||..|......||+||.+++..+++-++
T Consensus       236 ~~a~~kC~LCLe~~~~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskvi~Lr  292 (293)
T KOG0317|consen  236 PEATRKCSLCLENRSNPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKVICLR  292 (293)
T ss_pred             CCCCCceEEEecCCCCCCcCcCcchHHHHHHHHHHccccCCCcccccCCCcceeeec
Confidence            345679999999999999999999999999999999888999999999999888665

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

Probab=99.15  E-value=1.9e-11  Score=78.19  Aligned_cols=38  Identities=37%  Similarity=1.068  Sum_probs=30.7

Q ss_pred             ccccCCCCCCceEecccCccchhHHHHHHhcC----CCCCCC
Q 027652          165 CPICMGPLSEATSTKCGHIFCKDCIKGAIAAQ----GKCPNC  202 (220)
Q Consensus       165 CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~----~~CP~C  202 (220)
                      ||||++.+.+|++++|||+||..||.++.+..    ..||.|
T Consensus         1 CpiC~~~~~~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999999999999999999999998754    369987

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

Probab=99.13  E-value=3.8e-11  Score=111.61  Aligned_cols=97  Identities=30%  Similarity=0.577  Sum_probs=69.4

Q ss_pred             ccCCCCCCC--CCcceeeecCCCCccccCCCCCCCCCCCC-----CCCCccccccCCCCCCceEecccCccchhHHHHHH
Q 027652          121 RRNRPDEAT--PDNCCINVDTSNNNKNDAAPLQLPQDPMA-----AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAI  193 (220)
Q Consensus       121 ~r~~~~~~~--~~~c~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l  193 (220)
                      ++....+++  .++..|.+. ..++......+..+.+...     ...+..||||++...-|+.+.|||+||..||.+++
T Consensus       139 ~~~~~~~q~f~~any~fvv~-~gd~~~qn~dpD~p~~~e~i~qv~~~t~~~CPICL~~~~~p~~t~CGHiFC~~CiLqy~  217 (513)
T KOG2164|consen  139 RRRDEREQTFLNANYRFVVD-EGDYVLQNTDPDAPVDWEDIFQVYGSTDMQCPICLEPPSVPVRTNCGHIFCGPCILQYW  217 (513)
T ss_pred             ccccccchhhhccchheeec-ccchhhhccCCccccchHHhhhhhcCcCCcCCcccCCCCcccccccCceeeHHHHHHHH
Confidence            333334444  567778777 4444333333333322211     01178999999999999999999999999999998


Q ss_pred             hcC-----CCCCCCCccccCCCceeecCCC
Q 027652          194 AAQ-----GKCPNCRQKVGKRGIFRVYLPT  218 (220)
Q Consensus       194 ~~~-----~~CP~Cr~~v~~~~l~~iylp~  218 (220)
                      ...     ..||+|+..+..++|..++++.
T Consensus       218 ~~s~~~~~~~CPiC~s~I~~kdl~pv~~e~  247 (513)
T KOG2164|consen  218 NYSAIKGPCSCPICRSTITLKDLLPVFIED  247 (513)
T ss_pred             hhhcccCCccCCchhhhccccceeeeeecc
Confidence            744     4799999999999999999864

>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=99.08  E-value=6.1e-11  Score=74.39  Aligned_cols=38  Identities=47%  Similarity=1.208  Sum_probs=33.8

Q ss_pred             ccccCCCCCCc-eEecccCccchhHHHHHHhcCCCCCCC
Q 027652          165 CPICMGPLSEA-TSTKCGHIFCKDCIKGAIAAQGKCPNC  202 (220)
Q Consensus       165 CpIC~~~~~~p-v~l~CgH~fC~~Ci~~~l~~~~~CP~C  202 (220)
                      |+||++.+.+| +.++|||+||+.|+.+|++...+||.|
T Consensus         1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence            89999999999 678999999999999999998899987

>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=99.06  E-value=9.7e-11  Score=77.29  Aligned_cols=46  Identities=35%  Similarity=0.930  Sum_probs=41.3

Q ss_pred             CccccccCCCCCCceEecccCc-cchhHHHHHHhcCCCCCCCCcccc
Q 027652          162 TFSCPICMGPLSEATSTKCGHI-FCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       162 ~~~CpIC~~~~~~pv~l~CgH~-fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      +..|.||++...+.+.++|||. ||..|+.+|++....||+||+++.
T Consensus         2 ~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            4689999999999999999999 999999999998889999999886

...

>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=99.00  E-value=1.3e-10  Score=74.59  Aligned_cols=40  Identities=38%  Similarity=1.036  Sum_probs=35.1

Q ss_pred             cccccCCCCC---CceEecccCccchhHHHHHHhcCCCCCCCC
Q 027652          164 SCPICMGPLS---EATSTKCGHIFCKDCIKGAIAAQGKCPNCR  203 (220)
Q Consensus       164 ~CpIC~~~~~---~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr  203 (220)
                      .|+||++.+.   ..+.++|||.||..||.+|++....||+||
T Consensus         2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence            6999999884   456779999999999999999999999996

...

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.96  E-value=3.9e-10  Score=103.59  Aligned_cols=58  Identities=28%  Similarity=0.647  Sum_probs=51.1

Q ss_pred             CCCCCccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCccccCCCceeec
Q 027652          158 AAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVY  215 (220)
Q Consensus       158 ~~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iy  215 (220)
                      .....+.|+||++.+.+|+.++|||.||..||..|+.....||+|+..+...++...+
T Consensus        22 ~Le~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~N~   79 (397)
T TIGR00599        22 PLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRSNW   79 (397)
T ss_pred             ccccccCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccccCccch
Confidence            3567789999999999999999999999999999998888899999998876665544

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

>PHA02929 N1R/p28-like protein; Provisional

Probab=98.89  E-value=1.2e-09  Score=94.33  Aligned_cols=47  Identities=30%  Similarity=0.737  Sum_probs=40.9

Q ss_pred             CCccccccCCCCCCc--------eEecccCccchhHHHHHHhcCCCCCCCCcccc
Q 027652          161 PTFSCPICMGPLSEA--------TSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       161 ~~~~CpIC~~~~~~p--------v~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      .+..|+||++.+.++        +.++|||.||..||.+|+.....||+||..+.
T Consensus       173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~  227 (238)
T PHA02929        173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI  227 (238)
T ss_pred             CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence            456899999987653        45689999999999999998899999999886

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

Probab=98.89  E-value=8.9e-10  Score=78.45  Aligned_cols=55  Identities=20%  Similarity=0.356  Sum_probs=45.0

Q ss_pred             CCccccccCCCCCCceEecccCccchhHHHHHHhc-CCCCCCCCccccCCCceeec
Q 027652          161 PTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAA-QGKCPNCRQKVGKRGIFRVY  215 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~-~~~CP~Cr~~v~~~~l~~iy  215 (220)
                      +.|.|||+.+.+.+|+.+++||+|++.||.+|+.. ...||+|+..+...++++.+
T Consensus         3 ~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn~   58 (73)
T PF04564_consen    3 DEFLCPITGELMRDPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPNR   58 (73)
T ss_dssp             GGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-H
T ss_pred             cccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceECH
Confidence            56899999999999999999999999999999998 77999999999988887653

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

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

Probab=98.88  E-value=3.2e-10  Score=100.95  Aligned_cols=58  Identities=24%  Similarity=0.580  Sum_probs=52.9

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCccccCCCceeecC
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL  216 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iyl  216 (220)
                      .+..+.|-||+++|..|+.++|+|+||..||..++..+..||.|+.++...+|...+|
T Consensus        20 lD~lLRC~IC~eyf~ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n~i   77 (442)
T KOG0287|consen   20 LDDLLRCGICFEYFNIPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNNRI   77 (442)
T ss_pred             hHHHHHHhHHHHHhcCceeccccchHHHHHHHHHhccCCCCCceecccchhhhhhhhH
Confidence            3456899999999999999999999999999999999999999999999888876654

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

Probab=98.86  E-value=6.2e-10  Score=107.68  Aligned_cols=57  Identities=33%  Similarity=0.869  Sum_probs=52.8

Q ss_pred             CCCccccccCCCCCCceEecccCccchhHHHHHHh-cCCCCCCCCccccCCCceeecC
Q 027652          160 APTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIA-AQGKCPNCRQKVGKRGIFRVYL  216 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~-~~~~CP~Cr~~v~~~~l~~iyl  216 (220)
                      ...+.||+|...+.+.+++.|||+||..|+.+.+. ++.+||.|...|..+|+++|||
T Consensus       641 K~~LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I~l  698 (698)
T KOG0978|consen  641 KELLKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHRIHL  698 (698)
T ss_pred             HhceeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccccccCC
Confidence            45679999999999999999999999999998877 6789999999999999999997

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

Probab=98.83  E-value=2.1e-09  Score=67.74  Aligned_cols=38  Identities=42%  Similarity=1.199  Sum_probs=34.6

Q ss_pred             ccccCCCCCCce-EecccCccchhHHHHHHh--cCCCCCCC
Q 027652          165 CPICMGPLSEAT-STKCGHIFCKDCIKGAIA--AQGKCPNC  202 (220)
Q Consensus       165 CpIC~~~~~~pv-~l~CgH~fC~~Ci~~~l~--~~~~CP~C  202 (220)
                      |+||++.+.+++ .++|||.||..|+.+|+.  ....||+|
T Consensus         1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            899999999998 889999999999999998  44589987

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 ....

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

Probab=98.79  E-value=5.2e-09  Score=65.69  Aligned_cols=43  Identities=37%  Similarity=1.069  Sum_probs=37.0

Q ss_pred             cccccCCCCCCceEec-ccCccchhHHHHHHhc-CCCCCCCCccc
Q 027652          164 SCPICMGPLSEATSTK-CGHIFCKDCIKGAIAA-QGKCPNCRQKV  206 (220)
Q Consensus       164 ~CpIC~~~~~~pv~l~-CgH~fC~~Ci~~~l~~-~~~CP~Cr~~v  206 (220)
                      .|+||++.+.+++.+. |||.||..|+..|+.. ...||.|+..+
T Consensus         1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            4999999997777665 9999999999999987 66899998753

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

Probab=98.76  E-value=3.3e-09  Score=91.66  Aligned_cols=52  Identities=29%  Similarity=0.687  Sum_probs=46.7

Q ss_pred             CCCccccccCCCCCCceEecccCccchhHHHH-HHhcCC-CCCCCCccccCCCc
Q 027652          160 APTFSCPICMGPLSEATSTKCGHIFCKDCIKG-AIAAQG-KCPNCRQKVGKRGI  211 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~-~l~~~~-~CP~Cr~~v~~~~l  211 (220)
                      +.++.|+||++.+..|..++|||+||..||.. |-++.. .||+||+.+..+++
T Consensus       213 ~~d~kC~lC~e~~~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v  266 (271)
T COG5574         213 LADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV  266 (271)
T ss_pred             ccccceeeeecccCCcccccccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence            56899999999999999999999999999998 766655 59999999988776

>smart00184 RING Ring finger

Probab=98.66  E-value=2.2e-08  Score=60.65  Aligned_cols=38  Identities=39%  Similarity=1.147  Sum_probs=34.4

Q ss_pred             ccccCCCCCCceEecccCccchhHHHHHHh-cCCCCCCC
Q 027652          165 CPICMGPLSEATSTKCGHIFCKDCIKGAIA-AQGKCPNC  202 (220)
Q Consensus       165 CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~-~~~~CP~C  202 (220)
                      |+||++....++.++|||.||..|+..|+. ....||.|
T Consensus         1 C~iC~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            789999988999999999999999999998 55679987

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

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

Probab=98.65  E-value=8e-09  Score=90.49  Aligned_cols=52  Identities=33%  Similarity=0.749  Sum_probs=46.6

Q ss_pred             CCCccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCccccCCCc
Q 027652          160 APTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGI  211 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l  211 (220)
                      ...+.|-||...+..|+.++|||+||+.||..++..+..||+||......-+
T Consensus        23 Ds~lrC~IC~~~i~ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~esrl   74 (391)
T COG5432          23 DSMLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCESRL   74 (391)
T ss_pred             hhHHHhhhhhheeecceecccccchhHHHHHHHhcCCCCCccccccHHhhhc
Confidence            4457999999999999999999999999999999999999999998765433

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.64  E-value=1.8e-08  Score=64.83  Aligned_cols=41  Identities=41%  Similarity=0.995  Sum_probs=34.7

Q ss_pred             cccccCCCC---CCceEecccCccchhHHHHHHhcCCCCCCCCc
Q 027652          164 SCPICMGPL---SEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQ  204 (220)
Q Consensus       164 ~CpIC~~~~---~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~  204 (220)
                      .|++|++.+   ..+..++|||+||..|+.++......||+|++
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            489999988   24678899999999999998855668999975

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

Probab=98.63  E-value=1.5e-08  Score=65.13  Aligned_cols=35  Identities=46%  Similarity=1.095  Sum_probs=22.4

Q ss_pred             ccccCCCCCC----ceEecccCccchhHHHHHHhcC----CCCC
Q 027652          165 CPICMGPLSE----ATSTKCGHIFCKDCIKGAIAAQ----GKCP  200 (220)
Q Consensus       165 CpIC~~~~~~----pv~l~CgH~fC~~Ci~~~l~~~----~~CP  200 (220)
                      ||||.+ +.+    |+.|+|||+||..|+.++.+..    .+||
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 777    8999999999999999998854    2576

>PHA02926 zinc finger-like protein; Provisional

Probab=98.58  E-value=2.9e-08  Score=84.20  Aligned_cols=48  Identities=29%  Similarity=0.682  Sum_probs=38.3

Q ss_pred             CCCccccccCCCCCC---------ceEecccCccchhHHHHHHhcC------CCCCCCCcccc
Q 027652          160 APTFSCPICMGPLSE---------ATSTKCGHIFCKDCIKGAIAAQ------GKCPNCRQKVG  207 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~---------pv~l~CgH~fC~~Ci~~~l~~~------~~CP~Cr~~v~  207 (220)
                      ..+..|+||++...+         ++..+|+|.||..||..|....      ..||+||..+.
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            345689999997643         2455999999999999999742      35999999876

>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=98.52  E-value=7.5e-08  Score=68.60  Aligned_cols=40  Identities=40%  Similarity=0.942  Sum_probs=33.3

Q ss_pred             cccccCCCCCCc-------------eEecccCccchhHHHHHHhcCCCCCCCC
Q 027652          164 SCPICMGPLSEA-------------TSTKCGHIFCKDCIKGAIAAQGKCPNCR  203 (220)
Q Consensus       164 ~CpIC~~~~~~p-------------v~l~CgH~fC~~Ci~~~l~~~~~CP~Cr  203 (220)
                      .|+||++.+.++             +..+|||.|+..||.+|++....||+||
T Consensus        21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            599999988332             3348999999999999999999999997

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 ....

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

Probab=98.44  E-value=4.4e-08  Score=67.70  Aligned_cols=51  Identities=33%  Similarity=0.774  Sum_probs=27.1

Q ss_pred             CCccccccCCCCCCceEe-cccCccchhHHHHHHhcCCCCCCCCccccCCCcee
Q 027652          161 PTFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFR  213 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~  213 (220)
                      ..+.|++|.+.+.+|+.+ .|.|+||..|+...+  ...||+|+.+...+|++-
T Consensus         6 ~lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~--~~~CPvC~~Paw~qD~~~   57 (65)
T PF14835_consen    6 ELLRCSICFDILKEPVCLGGCEHIFCSSCIRDCI--GSECPVCHTPAWIQDIQI   57 (65)
T ss_dssp             HTTS-SSS-S--SS-B---SSS--B-TTTGGGGT--TTB-SSS--B-S-SS---
T ss_pred             HhcCCcHHHHHhcCCceeccCccHHHHHHhHHhc--CCCCCCcCChHHHHHHHh
Confidence            356899999999999865 999999999997644  346999999988777653

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

Probab=98.41  E-value=1.4e-07  Score=85.10  Aligned_cols=48  Identities=33%  Similarity=0.728  Sum_probs=41.3

Q ss_pred             CCCccccccCCCCC-C------------ceEecccCccchhHHHHHHhcCCCCCCCCcccc
Q 027652          160 APTFSCPICMGPLS-E------------ATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       160 ~~~~~CpIC~~~~~-~------------pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      ..+..|.||++.+. .            |..++|||.++..|++.|+.++..||+||.++.
T Consensus       285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~i  345 (491)
T COG5243         285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVI  345 (491)
T ss_pred             CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccc
Confidence            45668999999743 2            378899999999999999999999999999964

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

Probab=98.38  E-value=1.6e-07  Score=90.04  Aligned_cols=58  Identities=26%  Similarity=0.603  Sum_probs=49.5

Q ss_pred             CCCccccccCCCCCC-----ceEecccCccchhHHHHHHhcCCCCCCCCccccCCCceeecCC
Q 027652          160 APTFSCPICMGPLSE-----ATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLP  217 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~-----pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iylp  217 (220)
                      ..+..|+||.+.+..     +..++|||.||..|++.|++++..||+||..+..........+
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~~~~~~~~~~~  351 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLYDYVLWQIAAL  351 (543)
T ss_pred             hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhhccccccccCC
Confidence            346799999999998     7899999999999999999999999999997766665555444

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.34  E-value=3.6e-07  Score=81.36  Aligned_cols=57  Identities=23%  Similarity=0.642  Sum_probs=43.4

Q ss_pred             CccccccCCC-CCCce---Ee-cccCccchhHHHHHHhc-CCCCCCCCccccCCCceeecCCC
Q 027652          162 TFSCPICMGP-LSEAT---ST-KCGHIFCKDCIKGAIAA-QGKCPNCRQKVGKRGIFRVYLPT  218 (220)
Q Consensus       162 ~~~CpIC~~~-~~~pv---~l-~CgH~fC~~Ci~~~l~~-~~~CP~Cr~~v~~~~l~~iylp~  218 (220)
                      +..||+|... +.+|.   .+ +|||.||..|+..++.. ...||.|+..+..+++....++.
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr~q~F~D   65 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFRVQLFED   65 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhcccccccc
Confidence            4589999983 33332   22 79999999999997654 45899999999988877666654

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).

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

Probab=98.33  E-value=2.6e-07  Score=83.45  Aligned_cols=46  Identities=24%  Similarity=0.681  Sum_probs=40.0

Q ss_pred             ccccccCCCCCCc---eEecccCccchhHHHHHHhcCCC-CCCCCccccC
Q 027652          163 FSCPICMGPLSEA---TSTKCGHIFCKDCIKGAIAAQGK-CPNCRQKVGK  208 (220)
Q Consensus       163 ~~CpIC~~~~~~p---v~l~CgH~fC~~Ci~~~l~~~~~-CP~Cr~~v~~  208 (220)
                      ..|+||++.+...   ..|||+|.|+..||..|+...++ ||+|+..+..
T Consensus       230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~  279 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRT  279 (348)
T ss_pred             ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence            5899999999864   56799999999999999998865 9999987754

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

Probab=98.30  E-value=2e-07  Score=79.24  Aligned_cols=46  Identities=33%  Similarity=0.873  Sum_probs=40.5

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCc
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQ  204 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~  204 (220)
                      ..+.+.|+||++.+..|+.++|||.||..|+..+......||.||.
T Consensus        10 ~~~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   10 LQEELTCPICLEYFREPVLLPCGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             ccccccChhhHHHhhcCccccccchHhHHHHHHhcCCCcCCcccCC
Confidence            4567899999999999988899999999999998874458999994

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

Probab=98.26  E-value=1.2e-07  Score=63.40  Aligned_cols=51  Identities=27%  Similarity=0.699  Sum_probs=43.4

Q ss_pred             ccccccCCCCCCceEecccCc-cchhHHHHHHh-cCCCCCCCCccccCCCceeec
Q 027652          163 FSCPICMGPLSEATSTKCGHI-FCKDCIKGAIA-AQGKCPNCRQKVGKRGIFRVY  215 (220)
Q Consensus       163 ~~CpIC~~~~~~pv~l~CgH~-fC~~Ci~~~l~-~~~~CP~Cr~~v~~~~l~~iy  215 (220)
                      .+|.||++...+.+...|||. .|+.|-.+.++ ....||+||+++.  ++++-|
T Consensus         8 dECTICye~pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~--dvIkTY   60 (62)
T KOG4172|consen    8 DECTICYEHPVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK--DVIKTY   60 (62)
T ss_pred             cceeeeccCcchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH--HHHHhh
Confidence            689999999999999999998 89999888777 4668999999886  455544

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

Probab=98.18  E-value=6.9e-07  Score=78.75  Aligned_cols=51  Identities=29%  Similarity=0.529  Sum_probs=44.4

Q ss_pred             CCccccccCCCCCCceEecccCccchhHHHHHHhcCCC-CCCCCccccCCCc
Q 027652          161 PTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGK-CPNCRQKVGKRGI  211 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~-CP~Cr~~v~~~~l  211 (220)
                      -+-.|+||+....-|+.+.|+|.||+.||+......++ |++||.+|...-+
T Consensus         6 ~~~eC~IC~nt~n~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i~   57 (324)
T KOG0824|consen    6 KKKECLICYNTGNCPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTID   57 (324)
T ss_pred             cCCcceeeeccCCcCccccccchhhhhhhcchhhcCCCCCceecCCCCcchh
Confidence            34589999999999999999999999999988877665 9999999986433

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

Probab=98.18  E-value=1e-06  Score=77.83  Aligned_cols=47  Identities=28%  Similarity=0.673  Sum_probs=40.0

Q ss_pred             CccccccCCCCCCc---eEecccCccchhHHHHHHh-cCCCCCCCCccccC
Q 027652          162 TFSCPICMGPLSEA---TSTKCGHIFCKDCIKGAIA-AQGKCPNCRQKVGK  208 (220)
Q Consensus       162 ~~~CpIC~~~~~~p---v~l~CgH~fC~~Ci~~~l~-~~~~CP~Cr~~v~~  208 (220)
                      .-.|+||+..+.+.   +.+||.|.|+..|+.+|+. ...+||+||.++..
T Consensus       323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            46899999988643   5679999999999999998 56699999998863

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

Probab=98.02  E-value=3.9e-06  Score=75.58  Aligned_cols=55  Identities=25%  Similarity=0.732  Sum_probs=47.4

Q ss_pred             CCCccccccCCCCCCceEecccCc-cchhHHHHHHhcCCCCCCCCccccCCCceeecC
Q 027652          160 APTFSCPICMGPLSEATSTKCGHI-FCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL  216 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l~CgH~-fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iyl  216 (220)
                      +....|.||+....+.+.+||.|. .|..|.+.+......||+||+++..  +..+|.
T Consensus       288 ~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~--ll~i~~  343 (349)
T KOG4265|consen  288 ESGKECVICLSESRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEE--LLEIYV  343 (349)
T ss_pred             cCCCeeEEEecCCcceEEecchhhehhHhHHHHHHHhhcCCCccccchHh--hheecc
Confidence            446799999999999999999998 8999999887778899999999873  555554

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

Probab=97.94  E-value=8.7e-07  Score=79.60  Aligned_cols=50  Identities=38%  Similarity=0.840  Sum_probs=42.9

Q ss_pred             CCCCccccccCCCCCCceEe-cccCccchhHHHHHHhcC-CCCCCCCccccC
Q 027652          159 AAPTFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAAQ-GKCPNCRQKVGK  208 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~~-~~CP~Cr~~v~~  208 (220)
                      ..-.+.|+||++.++..+++ .|+|.||..||.+.++.. ..||.||+.+..
T Consensus        40 ~~~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S   91 (381)
T KOG0311|consen   40 FDIQVICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS   91 (381)
T ss_pred             hhhhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence            45578999999999998777 799999999999888854 589999998853

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

Probab=97.91  E-value=4.8e-06  Score=76.86  Aligned_cols=50  Identities=30%  Similarity=0.828  Sum_probs=45.6

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCccccC
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGK  208 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~  208 (220)
                      ....|.|.||+..+..|++++|||.||..||.+.+.....||.||..+..
T Consensus        81 ~~sef~c~vc~~~l~~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   81 IRSEFECCVCSRALYPPVVTPCGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             ccchhhhhhhHhhcCCCccccccccccHHHHHHHhccCCCCccccccccc
Confidence            35689999999999999999999999999999988888899999998864

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

Probab=97.89  E-value=1.4e-05  Score=69.75  Aligned_cols=50  Identities=32%  Similarity=0.731  Sum_probs=42.4

Q ss_pred             CCCCCccccccCCCCCCceEe-cccCccchhHHHHHHhc--CCCCCCCCcccc
Q 027652          158 AAAPTFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAA--QGKCPNCRQKVG  207 (220)
Q Consensus       158 ~~~~~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~--~~~CP~Cr~~v~  207 (220)
                      ....+.+||+|.+.++.|... +|||+||+.|+......  ...||.|...+.
T Consensus       235 ~~t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  235 TGTSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cccCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            356778999999999999877 59999999999887663  468999988776

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.84  E-value=1.3e-05  Score=69.16  Aligned_cols=60  Identities=20%  Similarity=0.404  Sum_probs=53.2

Q ss_pred             CCCccccccCCCCCCceE----ecccCccchhHHHHHHhcCCCCCCCCccccCCCceeecCCCC
Q 027652          160 APTFSCPICMGPLSEATS----TKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPTL  219 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~----l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iylp~~  219 (220)
                      ...+.||+|.+.+.+.+.    -+|||+||+.|+++++...+.||+|..+++.+||+.+--.+|
T Consensus       219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~LqrGGT  282 (303)
T KOG3039|consen  219 SKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIGLQRGGT  282 (303)
T ss_pred             ccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEeeecccc
Confidence            367899999999998643    399999999999999999999999999999999998876655

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

Probab=97.80  E-value=1.6e-05  Score=58.08  Aligned_cols=31  Identities=42%  Similarity=0.837  Sum_probs=27.0

Q ss_pred             cccCccchhHHHHHHhcC---CCCCCCCccccCC
Q 027652          179 KCGHIFCKDCIKGAIAAQ---GKCPNCRQKVGKR  209 (220)
Q Consensus       179 ~CgH~fC~~Ci~~~l~~~---~~CP~Cr~~v~~~  209 (220)
                      .|+|.|+..||.+|+..+   ..||+||++...+
T Consensus        51 ~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k   84 (85)
T PF12861_consen   51 KCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKFK   84 (85)
T ss_pred             cCccHHHHHHHHHHHccccCCCCCCCcCCeeeeC
Confidence            799999999999999853   5899999987643

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

Probab=97.77  E-value=7.4e-06  Score=73.11  Aligned_cols=50  Identities=36%  Similarity=0.821  Sum_probs=43.9

Q ss_pred             CCCccccccCCCCCCceEe-cccCccchhHHHHHHhcCCCCCCCCccccCC
Q 027652          160 APTFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAAQGKCPNCRQKVGKR  209 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~  209 (220)
                      .....|.+|..++.+++++ -|-|+||+.||.+++.....||.|...+...
T Consensus        13 n~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   13 NPHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             ccceehhhccceeecchhHHHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence            4567999999999998766 8999999999999999999999998877643

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

Probab=97.73  E-value=1.3e-05  Score=67.05  Aligned_cols=48  Identities=27%  Similarity=0.598  Sum_probs=42.1

Q ss_pred             CCCccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCcccc
Q 027652          160 APTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      .-.|.|.||...+..|+.+.|||.||..|..+-.+....|-+|.+...
T Consensus       194 ~IPF~C~iCKkdy~spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~  241 (259)
T COG5152         194 KIPFLCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGKATY  241 (259)
T ss_pred             CCceeehhchhhccchhhhhcchhHHHHHHHHHhccCCcceecchhhc
Confidence            346899999999999999999999999999887777789999977553

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

Probab=97.56  E-value=3.1e-05  Score=52.65  Aligned_cols=42  Identities=33%  Similarity=0.778  Sum_probs=29.7

Q ss_pred             CCCccccccCCCCCCceEe-cccCccchhHHHHHHhc--CCCCCC
Q 027652          160 APTFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAA--QGKCPN  201 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~--~~~CP~  201 (220)
                      ...+.|||.+..+.+|+.- .|||+|.+..|..++..  ...||+
T Consensus         9 ~~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen    9 TISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             B--SB-TTTSSB-SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             EeccCCCCcCChhhCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            4467999999999999875 99999999999999943  347998

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

Probab=97.53  E-value=3.2e-05  Score=69.03  Aligned_cols=58  Identities=22%  Similarity=0.524  Sum_probs=51.8

Q ss_pred             CCCccccccCCCCCCceEe-cccCccchhHHHHHHhcCCCCCCCCccccCCCceeecCC
Q 027652          160 APTFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLP  217 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iylp  217 (220)
                      .+...||+|+....+|..+ -.|-+||+.|+.+++...+.||+...+....+++++|-+
T Consensus       298 ~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~v~~l~rl~~~  356 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPASVDHLIRLFNK  356 (357)
T ss_pred             CccccChhHHhccCCCceEEecceEEeHHHHHHHHHhcCCCCccCCcchHHHHHHHhcC
Confidence            3567899999999999777 569999999999999999999999999998899998865

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

Probab=97.53  E-value=4.3e-05  Score=70.67  Aligned_cols=53  Identities=36%  Similarity=0.880  Sum_probs=47.0

Q ss_pred             CCCCccccccCCCCCCceEe-cccCccchhHHHHHHhcCCCCCCCCccccCCCc
Q 027652          159 AAPTFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGI  211 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l  211 (220)
                      ..+++.|++|...+.+|+.+ .|||.||..|+..|+.....||.|+..+...+.
T Consensus        18 ~~~~l~C~~C~~vl~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~   71 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEE   71 (391)
T ss_pred             CcccccCccccccccCCCCCCCCCCcccccccchhhccCcCCcccccccchhhc
Confidence            46788999999999999994 999999999999999998899999888765443

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

Probab=97.46  E-value=3.3e-05  Score=68.10  Aligned_cols=47  Identities=34%  Similarity=0.682  Sum_probs=42.0

Q ss_pred             CCccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCcccc
Q 027652          161 PTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      -.|.|-||...+..||.+.|||.||..|..+-++....|.+|.+.+.
T Consensus       240 ~Pf~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~  286 (313)
T KOG1813|consen  240 LPFKCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTH  286 (313)
T ss_pred             CCccccccccccccchhhcCCceeehhhhccccccCCcceecccccc
Confidence            35789999999999999999999999999888877789999987664

>PF04641 Rtf2: Rtf2 RING-finger

Probab=97.42  E-value=0.00018  Score=62.91  Aligned_cols=60  Identities=22%  Similarity=0.508  Sum_probs=48.9

Q ss_pred             CCCCCccccccCCCCCCc---e-EecccCccchhHHHHHHhcCCCCCCCCccccCCCceeecCCC
Q 027652          158 AAAPTFSCPICMGPLSEA---T-STKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPT  218 (220)
Q Consensus       158 ~~~~~~~CpIC~~~~~~p---v-~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iylp~  218 (220)
                      .....|.|||....+...   + ..+|||+|+..+++... ....||+|..++...|++.|.-++
T Consensus       109 ~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~DiI~Lnp~~  172 (260)
T PF04641_consen  109 NSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEEDIIPLNPPE  172 (260)
T ss_pred             cCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccCCEEEecCCc
Confidence            356678999999988542   2 33999999999999884 456899999999999999987654

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

Probab=97.38  E-value=0.00011  Score=66.34  Aligned_cols=51  Identities=25%  Similarity=0.526  Sum_probs=46.4

Q ss_pred             CCCCCccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCccccC
Q 027652          158 AAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGK  208 (220)
Q Consensus       158 ~~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~  208 (220)
                      +..++..||||.......+..||+|.-|+.||.+.+...+.|-.|+..+..
T Consensus       418 p~sEd~lCpICyA~pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  418 PDSEDNLCPICYAGPINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             CCcccccCcceecccchhhccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            456788999999999999999999999999999999999999999888764

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

Probab=97.34  E-value=1.9e-05  Score=69.48  Aligned_cols=42  Identities=36%  Similarity=0.823  Sum_probs=37.0

Q ss_pred             CccccccCCCCCCceEecccCc-cchhHHHHHHhcCCCCCCCCcccc
Q 027652          162 TFSCPICMGPLSEATSTKCGHI-FCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       162 ~~~CpIC~~~~~~pv~l~CgH~-fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      ...|.||++.+.+-+.|+|||. -|..|-+++    ..||+||+.+.
T Consensus       300 ~~LC~ICmDaP~DCvfLeCGHmVtCt~CGkrm----~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAPRDCVFLECGHMVTCTKCGKRM----NECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCCcceEEeecCcEEeehhhcccc----ccCchHHHHHH
Confidence            6799999999999999999995 799996644    48999999876

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

Probab=97.24  E-value=9.8e-05  Score=67.71  Aligned_cols=54  Identities=37%  Similarity=0.808  Sum_probs=44.7

Q ss_pred             CccccccCCCCCCc-----eEecccCccchhHHHHHHhcC--CCCCCCCccccCCCceeec
Q 027652          162 TFSCPICMGPLSEA-----TSTKCGHIFCKDCIKGAIAAQ--GKCPNCRQKVGKRGIFRVY  215 (220)
Q Consensus       162 ~~~CpIC~~~~~~p-----v~l~CgH~fC~~Ci~~~l~~~--~~CP~Cr~~v~~~~l~~iy  215 (220)
                      ...||||++.+..+     +.+.|||.|-..||++|+.+.  +.||.|..+..+++|.++|
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katkr~i~~e~   64 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKRQIRPEY   64 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHHHHHHHHH
Confidence            45899999988765     567999999999999999632  3799999988887777665

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

Probab=97.06  E-value=0.00015  Score=51.20  Aligned_cols=47  Identities=23%  Similarity=0.598  Sum_probs=23.7

Q ss_pred             CccccccCCCCC-C---ceEe----cccCccchhHHHHHHhcC-----------CCCCCCCccccC
Q 027652          162 TFSCPICMGPLS-E---ATST----KCGHIFCKDCIKGAIAAQ-----------GKCPNCRQKVGK  208 (220)
Q Consensus       162 ~~~CpIC~~~~~-~---pv~l----~CgH~fC~~Ci~~~l~~~-----------~~CP~Cr~~v~~  208 (220)
                      +..|+||+.... .   |..+    .|+..|+..|+.+|+...           ..||.|+.+++-
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~   67 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW   67 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence            357999998765 2   2222    699999999999998731           259999998863

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

Probab=97.05  E-value=0.00034  Score=63.58  Aligned_cols=48  Identities=31%  Similarity=0.743  Sum_probs=39.5

Q ss_pred             CCCccccccCCCCCCce-----E---ecccCccchhHHHHHHh--c-----CCCCCCCCcccc
Q 027652          160 APTFSCPICMGPLSEAT-----S---TKCGHIFCKDCIKGAIA--A-----QGKCPNCRQKVG  207 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv-----~---l~CgH~fC~~Ci~~~l~--~-----~~~CP~Cr~~v~  207 (220)
                      ..+..|.||++...+..     .   .+|.|.||..||.+|-.  +     .+.||.||....
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            55779999999888765     3   57999999999999984  3     368999998765

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

Probab=97.01  E-value=0.00045  Score=64.12  Aligned_cols=47  Identities=26%  Similarity=0.644  Sum_probs=38.1

Q ss_pred             CCCCccccccCCCCCCce----EecccCccchhHHHHHHhcCCCCCCCCcccc
Q 027652          159 AAPTFSCPICMGPLSEAT----STKCGHIFCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv----~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      ..+.-+||||++.+...+    ++.|.|.|...|+.+|.  ...||+||.-..
T Consensus       172 ~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~  222 (493)
T KOG0804|consen  172 LTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS  222 (493)
T ss_pred             cccCCCcchhHhhcCccccceeeeecccccchHHHhhcc--cCcChhhhhhcC
Confidence            445559999999887654    55899999999999884  678999987655

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

Probab=97.00  E-value=0.0003  Score=64.50  Aligned_cols=50  Identities=24%  Similarity=0.624  Sum_probs=42.1

Q ss_pred             ccccccCCCCCCceEecccCccchhHHHHHHhcC--CCCCCCCccccCCCce
Q 027652          163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQ--GKCPNCRQKVGKRGIF  212 (220)
Q Consensus       163 ~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~--~~CP~Cr~~v~~~~l~  212 (220)
                      -.|.||-+--++..+-+|||..|..|+..|....  ..||.||..++-.+-+
T Consensus       370 eLCKICaendKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~v  421 (563)
T KOG1785|consen  370 ELCKICAENDKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPV  421 (563)
T ss_pred             HHHHHhhccCCCcccccccchHHHHHHHhhcccCCCCCCCceeeEeccccce
Confidence            3799999988888888999999999999998643  5899999999754433

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

Probab=96.97  E-value=0.00043  Score=64.96  Aligned_cols=48  Identities=33%  Similarity=0.674  Sum_probs=37.9

Q ss_pred             CCCccccccCCCCCC-----------------ceEecccCccchhHHHHHHhc-CCCCCCCCcccc
Q 027652          160 APTFSCPICMGPLSE-----------------ATSTKCGHIFCKDCIKGAIAA-QGKCPNCRQKVG  207 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~-----------------pv~l~CgH~fC~~Ci~~~l~~-~~~CP~Cr~~v~  207 (220)
                      .....|+||+....-                 -+.+||.|+|+..|+++|+.. +-.||+||.++.
T Consensus       569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP  634 (636)
T KOG0828|consen  569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP  634 (636)
T ss_pred             hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence            445689999975431                 234599999999999999984 448999999876

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

Probab=96.79  E-value=0.00047  Score=60.33  Aligned_cols=54  Identities=26%  Similarity=0.668  Sum_probs=41.4

Q ss_pred             CCCCccccccCCCCCC----------ceEecccCccchhHHHHHHhc--CCCCCCCCccccCCCce
Q 027652          159 AAPTFSCPICMGPLSE----------ATSTKCGHIFCKDCIKGAIAA--QGKCPNCRQKVGKRGIF  212 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~----------pv~l~CgH~fC~~Ci~~~l~~--~~~CP~Cr~~v~~~~l~  212 (220)
                      ..++..|+||-..+..          ...+.|+|+|+..||+.|-..  ...||.|++++.-+.+.
T Consensus       221 hl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~rmf  286 (328)
T KOG1734|consen  221 HLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKRMF  286 (328)
T ss_pred             CCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhhhc
Confidence            4567789999876543          346799999999999999764  44799999988654443

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

Probab=96.74  E-value=0.00054  Score=64.87  Aligned_cols=48  Identities=27%  Similarity=0.704  Sum_probs=41.5

Q ss_pred             CCccccccCCCCCCceEecccCccchhHHHHHHhcC-----CCCCCCCccccC
Q 027652          161 PTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQ-----GKCPNCRQKVGK  208 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~-----~~CP~Cr~~v~~  208 (220)
                      ....|.+|.+...+++...|.|.||..|+++++...     -.||.|...++.
T Consensus       535 ~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Lsi  587 (791)
T KOG1002|consen  535 GEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSI  587 (791)
T ss_pred             CceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccc
Confidence            455899999999999999999999999999998742     379999887764

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

Probab=96.68  E-value=0.0016  Score=46.93  Aligned_cols=29  Identities=34%  Similarity=0.630  Sum_probs=27.2

Q ss_pred             cccCccchhHHHHHHhcCCCCCCCCcccc
Q 027652          179 KCGHIFCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       179 ~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      .|.|.|+.-||.+|+.....||+++++..
T Consensus        53 ~CnHaFH~HCI~rWL~Tk~~CPld~q~w~   81 (88)
T COG5194          53 VCNHAFHDHCIYRWLDTKGVCPLDRQTWV   81 (88)
T ss_pred             ecchHHHHHHHHHHHhhCCCCCCCCceeE
Confidence            79999999999999999999999999875

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

Probab=96.59  E-value=0.0012  Score=58.77  Aligned_cols=43  Identities=42%  Similarity=1.025  Sum_probs=37.4

Q ss_pred             CccccccCCCCCCceEe-cccCccchhHHHHHHhc-CCCCCCCCc
Q 027652          162 TFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAA-QGKCPNCRQ  204 (220)
Q Consensus       162 ~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~-~~~CP~Cr~  204 (220)
                      .+.||.|...+.+|+.+ -|+|.||..||...+.. ...||.|..
T Consensus       274 ~LkCplc~~Llrnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         274 SLKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             cccCcchhhhhhCcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            38999999999999999 57999999999987764 569999954

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

Probab=96.57  E-value=0.00037  Score=68.45  Aligned_cols=49  Identities=22%  Similarity=0.613  Sum_probs=41.0

Q ss_pred             CCCccccccCCCCCCc---eEecccCccchhHHHHHHhcCCCCCCCCccccC
Q 027652          160 APTFSCPICMGPLSEA---TSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGK  208 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~p---v~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~  208 (220)
                      .....||+|+..+.+.   ...+|+|.||..||..|-+....||+||..|..
T Consensus       121 ~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~  172 (1134)
T KOG0825|consen  121 HVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGE  172 (1134)
T ss_pred             hhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhhe
Confidence            4567899998876654   334899999999999999999999999998864

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

Probab=96.48  E-value=0.0027  Score=41.69  Aligned_cols=40  Identities=23%  Similarity=0.658  Sum_probs=31.0

Q ss_pred             cccccCC--CCCCceEeccc-----CccchhHHHHHHhcCC--CCCCCC
Q 027652          164 SCPICMG--PLSEATSTKCG-----HIFCKDCIKGAIAAQG--KCPNCR  203 (220)
Q Consensus       164 ~CpIC~~--~~~~pv~l~Cg-----H~fC~~Ci~~~l~~~~--~CP~Cr  203 (220)
                      .|.||++  ...++...||.     |.++..|+.+|+....  .||+|.
T Consensus         1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            3889997  34456677885     7799999999997554  899994

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

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=96.42  E-value=0.0018  Score=43.49  Aligned_cols=47  Identities=23%  Similarity=0.540  Sum_probs=37.8

Q ss_pred             CccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCccccCCC
Q 027652          162 TFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRG  210 (220)
Q Consensus       162 ~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~  210 (220)
                      ...|-.|...-...+.++|||..|..|+.  +..-+.||.|..++...+
T Consensus         7 ~~~~~~~~~~~~~~~~~pCgH~I~~~~f~--~~rYngCPfC~~~~~~~~   53 (55)
T PF14447_consen    7 EQPCVFCGFVGTKGTVLPCGHLICDNCFP--GERYNGCPFCGTPFEFDD   53 (55)
T ss_pred             ceeEEEccccccccccccccceeeccccC--hhhccCCCCCCCcccCCC
Confidence            34678888887888999999999999975  335568999999987654

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

Probab=96.40  E-value=0.0015  Score=59.72  Aligned_cols=49  Identities=29%  Similarity=0.723  Sum_probs=35.6

Q ss_pred             cccccCCCCCCce---Ee-cccCccchhHHHHHHhcC---CCCCCCCccccCCCce
Q 027652          164 SCPICMGPLSEAT---ST-KCGHIFCKDCIKGAIAAQ---GKCPNCRQKVGKRGIF  212 (220)
Q Consensus       164 ~CpIC~~~~~~pv---~l-~CgH~fC~~Ci~~~l~~~---~~CP~Cr~~v~~~~l~  212 (220)
                      .|.||.+......   .+ .|||+|+..|+..|+...   ..||+|+-.+....++
T Consensus         6 ~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~~~   61 (465)
T KOG0827|consen    6 ECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERHVA   61 (465)
T ss_pred             eeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccceeee
Confidence            7999966544332   22 599999999999999853   4799999666554443

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

Probab=96.36  E-value=0.0025  Score=58.49  Aligned_cols=57  Identities=25%  Similarity=0.479  Sum_probs=46.4

Q ss_pred             CCCccccccCCCCC---CceEecccCccchhHHHHHHhcC---CCCCCCCccccCCCceeecC
Q 027652          160 APTFSCPICMGPLS---EATSTKCGHIFCKDCIKGAIAAQ---GKCPNCRQKVGKRGIFRVYL  216 (220)
Q Consensus       160 ~~~~~CpIC~~~~~---~pv~l~CgH~fC~~Ci~~~l~~~---~~CP~Cr~~v~~~~l~~iyl  216 (220)
                      -..|.|||=.+.-.   .|+.+.|||+.|+.-+.++.+..   .+||.|-......+.+++|+
T Consensus       332 HSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~~~~~~kql~F  394 (394)
T KOG2817|consen  332 HSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQLASDTKQLYF  394 (394)
T ss_pred             cceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcccCHHhcccccC
Confidence            34689998655433   47999999999999999988754   48999999888888888885

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

Probab=96.30  E-value=0.001  Score=66.70  Aligned_cols=48  Identities=25%  Similarity=0.616  Sum_probs=37.1

Q ss_pred             CCCccccccCCCCCC-----c--eEecccCccchhHHHHHHhcC--CCCCCCCcccc
Q 027652          160 APTFSCPICMGPLSE-----A--TSTKCGHIFCKDCIKGAIAAQ--GKCPNCRQKVG  207 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~-----p--v~l~CgH~fC~~Ci~~~l~~~--~~CP~Cr~~v~  207 (220)
                      ....+|+||...+..     |  .-..|.|.|+.+|+.+|.+.+  ..||+||..++
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            344589999987652     1  223699999999999999864  48999998775

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

Probab=96.27  E-value=0.0022  Score=58.10  Aligned_cols=44  Identities=30%  Similarity=0.748  Sum_probs=34.4

Q ss_pred             CCccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCcccc
Q 027652          161 PTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      ....|.||.+...+.+.++|||+-|  |..-... -..||+||+.+.
T Consensus       304 ~p~lcVVcl~e~~~~~fvpcGh~cc--ct~cs~~-l~~CPvCR~rI~  347 (355)
T KOG1571|consen  304 QPDLCVVCLDEPKSAVFVPCGHVCC--CTLCSKH-LPQCPVCRQRIR  347 (355)
T ss_pred             CCCceEEecCCccceeeecCCcEEE--chHHHhh-CCCCchhHHHHH
Confidence            3458999999999999999999866  6544332 335999999875

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

Probab=96.24  E-value=0.0019  Score=46.28  Aligned_cols=30  Identities=40%  Similarity=0.750  Sum_probs=25.9

Q ss_pred             cccCccchhHHHHHHhc---CCCCCCCCccccC
Q 027652          179 KCGHIFCKDCIKGAIAA---QGKCPNCRQKVGK  208 (220)
Q Consensus       179 ~CgH~fC~~Ci~~~l~~---~~~CP~Cr~~v~~  208 (220)
                      .|.|.|..-||.+|+..   +..||+||+....
T Consensus        50 ~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~   82 (84)
T KOG1493|consen   50 YCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQF   82 (84)
T ss_pred             HHHHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence            79999999999999984   4589999998764

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

Probab=96.07  E-value=0.0013  Score=64.72  Aligned_cols=50  Identities=34%  Similarity=0.838  Sum_probs=42.9

Q ss_pred             ccccccCCCCCCceEecccCccchhHHHHHHhcC--CCCCCCCccccCCCcee
Q 027652          163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQ--GKCPNCRQKVGKRGIFR  213 (220)
Q Consensus       163 ~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~--~~CP~Cr~~v~~~~l~~  213 (220)
                      +.|.+|.+ ...++.+.|||.||..|+...+...  ..||.|+..+..+++..
T Consensus       455 ~~c~ic~~-~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~s  506 (674)
T KOG1001|consen  455 HWCHICCD-LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLLS  506 (674)
T ss_pred             cccccccc-cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHhh
Confidence            79999999 7888999999999999999988753  37999999887766554

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

Probab=95.79  E-value=0.0044  Score=40.61  Aligned_cols=42  Identities=33%  Similarity=0.940  Sum_probs=21.5

Q ss_pred             ccccCCCCCCc--eEe--cccCccchhHHHHHHh-cCCCCCCCCccc
Q 027652          165 CPICMGPLSEA--TST--KCGHIFCKDCIKGAIA-AQGKCPNCRQKV  206 (220)
Q Consensus       165 CpIC~~~~~~p--v~l--~CgH~fC~~Ci~~~l~-~~~~CP~Cr~~v  206 (220)
                      ||+|.+.+...  ...  +||+.+|..|+.+.+. ....||-||++.
T Consensus         1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            78888877322  233  6899999999999887 467999999864

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

Probab=95.34  E-value=0.014  Score=52.96  Aligned_cols=48  Identities=29%  Similarity=0.747  Sum_probs=40.4

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHH--HhcCCCCCCCCccc
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGA--IAAQGKCPNCRQKV  206 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~--l~~~~~CP~Cr~~v  206 (220)
                      .++...|-||.+.++-...+||+|..|..|..+.  +...+.|++||..-
T Consensus        58 DEen~~C~ICA~~~TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~  107 (493)
T COG5236          58 DEENMNCQICAGSTTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET  107 (493)
T ss_pred             ccccceeEEecCCceEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence            4566789999999999899999999999997554  55788999998754

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

Probab=95.31  E-value=0.0086  Score=55.80  Aligned_cols=36  Identities=22%  Similarity=0.678  Sum_probs=31.9

Q ss_pred             CCCccccccCCCCCCceEecccCccchhHHHHHHhc
Q 027652          160 APTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAA  195 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~  195 (220)
                      ++.+.|+||...+.+|++++|+|..|..|....+..
T Consensus         2 eeelkc~vc~~f~~epiil~c~h~lc~~ca~~~~~~   37 (699)
T KOG4367|consen    2 EEELKCPVCGSFYREPIILPCSHNLCQACARNILVQ   37 (699)
T ss_pred             cccccCceehhhccCceEeecccHHHHHHHHhhccc
Confidence            467799999999999999999999999998876653

>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=95.26  E-value=0.021  Score=46.43  Aligned_cols=50  Identities=28%  Similarity=0.615  Sum_probs=35.8

Q ss_pred             CccccccCCCCCCceEeccc------------Ccc-chhHHHHHHhc-------------------------------CC
Q 027652          162 TFSCPICMGPLSEATSTKCG------------HIF-CKDCIKGAIAA-------------------------------QG  197 (220)
Q Consensus       162 ~~~CpIC~~~~~~pv~l~Cg------------H~f-C~~Ci~~~l~~-------------------------------~~  197 (220)
                      +..||||++.+.+.|.|-|.            ..| ...|+.++.+.                               .-
T Consensus         2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L   81 (162)
T PF07800_consen    2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPEL   81 (162)
T ss_pred             CccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccccc
Confidence            45899999999999998543            221 46788777651                               11


Q ss_pred             CCCCCCccccCCCc
Q 027652          198 KCPNCRQKVGKRGI  211 (220)
Q Consensus       198 ~CP~Cr~~v~~~~l  211 (220)
                      .||+||..|.-+.+
T Consensus        82 ~CPLCRG~V~GWtv   95 (162)
T PF07800_consen   82 ACPLCRGEVKGWTV   95 (162)
T ss_pred             cCccccCceeceEE
Confidence            49999999976543

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.

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

Probab=95.25  E-value=0.01  Score=52.41  Aligned_cols=44  Identities=32%  Similarity=0.773  Sum_probs=36.0

Q ss_pred             ccccccCCCCC------CceEecccCccchhHHHHHHhcCC-CCCCCCccc
Q 027652          163 FSCPICMGPLS------EATSTKCGHIFCKDCIKGAIAAQG-KCPNCRQKV  206 (220)
Q Consensus       163 ~~CpIC~~~~~------~pv~l~CgH~fC~~Ci~~~l~~~~-~CP~Cr~~v  206 (220)
                      +.|-||-+.+.      .|..+.|||++|..|+.+.+.... .||.||...
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            36889987665      367788999999999999887654 799999984

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

Probab=95.21  E-value=0.0048  Score=53.16  Aligned_cols=49  Identities=29%  Similarity=0.703  Sum_probs=33.2

Q ss_pred             cccccCCCCC-Cc-eEecccCccchhHHHHHHhcCCCCCCCCccccCCCceee
Q 027652          164 SCPICMGPLS-EA-TSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRV  214 (220)
Q Consensus       164 ~CpIC~~~~~-~p-v~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~i  214 (220)
                      -|-.|..... .+ ..+.|+|+||..|...-.  ...||+|++.+..-.+...
T Consensus         5 hCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~--~~~C~lCkk~ir~i~l~~s   55 (233)
T KOG4739|consen    5 HCNKCFRFPSQDPFFLTACRHVFCEPCLKASS--PDVCPLCKKSIRIIQLNRS   55 (233)
T ss_pred             EeccccccCCCCceeeeechhhhhhhhcccCC--ccccccccceeeeeecccc
Confidence            5777766444 22 355999999999975332  2389999999765444433

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

Probab=95.11  E-value=0.012  Score=54.34  Aligned_cols=35  Identities=31%  Similarity=0.782  Sum_probs=28.6

Q ss_pred             CCCccccccCCCCCCc---eEecccCccchhHHHHHHh
Q 027652          160 APTFSCPICMGPLSEA---TSTKCGHIFCKDCIKGAIA  194 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~p---v~l~CgH~fC~~Ci~~~l~  194 (220)
                      ...+.|.||++...-.   +.++|+|+||+.|++.+..
T Consensus       182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~  219 (445)
T KOG1814|consen  182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFT  219 (445)
T ss_pred             hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHH
Confidence            3468999999866542   5679999999999998876

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

Probab=95.07  E-value=0.012  Score=44.49  Aligned_cols=28  Identities=25%  Similarity=0.545  Sum_probs=25.5

Q ss_pred             cccCccchhHHHHHHhcCCCCCCCCccc
Q 027652          179 KCGHIFCKDCIKGAIAAQGKCPNCRQKV  206 (220)
Q Consensus       179 ~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v  206 (220)
                      .|.|.|+.-||.+|++....||+|.+.-
T Consensus        80 ~CNHaFH~hCisrWlktr~vCPLdn~eW  107 (114)
T KOG2930|consen   80 VCNHAFHFHCISRWLKTRNVCPLDNKEW  107 (114)
T ss_pred             ecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence            6999999999999999999999997643

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.04  E-value=0.016  Score=52.49  Aligned_cols=54  Identities=28%  Similarity=0.712  Sum_probs=39.6

Q ss_pred             CccccccCCCCCCc--eE--ecccCccchhHHHHHHhc-CCCCCCCCccccCCCceeec
Q 027652          162 TFSCPICMGPLSEA--TS--TKCGHIFCKDCIKGAIAA-QGKCPNCRQKVGKRGIFRVY  215 (220)
Q Consensus       162 ~~~CpIC~~~~~~p--v~--l~CgH~fC~~Ci~~~l~~-~~~CP~Cr~~v~~~~l~~iy  215 (220)
                      +..||+|++.+...  -.  .+||...|.-|+...... ..+||.||.....+++.-+-
T Consensus        14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~~   72 (480)
T COG5175          14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYVT   72 (480)
T ss_pred             cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeEEe
Confidence            33499999977532  22  378988899998766543 56999999999887776443

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

Probab=94.26  E-value=0.028  Score=50.32  Aligned_cols=46  Identities=35%  Similarity=0.904  Sum_probs=37.7

Q ss_pred             CCCCccccccCCCCCCceEe-cccCccchhHHHHHHhcCCCCCCCCcccc
Q 027652          159 AAPTFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      ..+-+.||||.+.+..|+.- .=||.-|..|-.   +...+||.|+.++.
T Consensus        45 ~~~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   45 DLDLLDCPVCFNPLSPPIFQCDNGHLACSSCRT---KVSNKCPTCRLPIG   91 (299)
T ss_pred             chhhccCchhhccCcccceecCCCcEehhhhhh---hhcccCCccccccc
Confidence            45678999999999988543 569999999964   35679999999887

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

Probab=93.73  E-value=0.025  Score=42.00  Aligned_cols=29  Identities=34%  Similarity=0.836  Sum_probs=23.9

Q ss_pred             CccccccCCCCCCceE--ecccCccchhHHH
Q 027652          162 TFSCPICMGPLSEATS--TKCGHIFCKDCIK  190 (220)
Q Consensus       162 ~~~CpIC~~~~~~pv~--l~CgH~fC~~Ci~  190 (220)
                      ...|++|...+.+.+.  .||||+|+..|+.
T Consensus        78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence            3379999999987644  4999999999975

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 [].

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

Probab=93.62  E-value=0.045  Score=49.15  Aligned_cols=58  Identities=24%  Similarity=0.478  Sum_probs=45.6

Q ss_pred             CCCCccccccCCCCC---CceEecccCccchhHHHHHHhcC---CCCCCCCccccCCCceeecC
Q 027652          159 AAPTFSCPICMGPLS---EATSTKCGHIFCKDCIKGAIAAQ---GKCPNCRQKVGKRGIFRVYL  216 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~---~pv~l~CgH~fC~~Ci~~~l~~~---~~CP~Cr~~v~~~~l~~iyl  216 (220)
                      ....|.||+=.+.-+   .|+.+.|||+.-+.-+....+..   .+||.|...-...+++++|+
T Consensus       333 fHs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~~~~~~~~~rvrf  396 (396)
T COG5109         333 FHSLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPEMSKYENILRVRF  396 (396)
T ss_pred             ccceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCcchhhhhhhcccC
Confidence            456789998555333   47999999999999888776643   48999998888889988875

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

Probab=93.57  E-value=0.053  Score=42.89  Aligned_cols=50  Identities=24%  Similarity=0.578  Sum_probs=41.0

Q ss_pred             CCccccccCCCCCCceEec----ccCccchhHHHHHHhc---CCCCCCCCccccCCC
Q 027652          161 PTFSCPICMGPLSEATSTK----CGHIFCKDCIKGAIAA---QGKCPNCRQKVGKRG  210 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l~----CgH~fC~~Ci~~~l~~---~~~CP~Cr~~v~~~~  210 (220)
                      ..++|-||.+.-.+...+.    ||-..|..|.....+.   ...||.|+..++...
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            4568999999999988883    9999999998877764   358999999887543

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

Probab=93.53  E-value=0.033  Score=49.71  Aligned_cols=48  Identities=27%  Similarity=0.688  Sum_probs=36.9

Q ss_pred             CCccccccCCCCCCc---eEecccCccchhHHHHHHhc-----------------------CCCCCCCCccccC
Q 027652          161 PTFSCPICMGPLSEA---TSTKCGHIFCKDCIKGAIAA-----------------------QGKCPNCRQKVGK  208 (220)
Q Consensus       161 ~~~~CpIC~~~~~~p---v~l~CgH~fC~~Ci~~~l~~-----------------------~~~CP~Cr~~v~~  208 (220)
                      ....|.||+.-|.+.   +.++|-|-|+..|+.+++..                       ...||+||..+..
T Consensus       114 p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~  187 (368)
T KOG4445|consen  114 PNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI  187 (368)
T ss_pred             CCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence            344799999877753   56799999999999887751                       1259999998863

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

Probab=93.16  E-value=0.04  Score=49.34  Aligned_cols=43  Identities=28%  Similarity=0.754  Sum_probs=31.5

Q ss_pred             ccccccCCCCCC-ceEecccCccchhHHHHHHhcCCCCCCCCcccc
Q 027652          163 FSCPICMGPLSE-ATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       163 ~~CpIC~~~~~~-pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      -.|--|-..+.. ...++|.|+||..|..  ....+.||.|-.++.
T Consensus        91 HfCd~Cd~PI~IYGRmIPCkHvFCl~CAr--~~~dK~Cp~C~d~Vq  134 (389)
T KOG2932|consen   91 HFCDRCDFPIAIYGRMIPCKHVFCLECAR--SDSDKICPLCDDRVQ  134 (389)
T ss_pred             EeecccCCcceeeecccccchhhhhhhhh--cCccccCcCcccHHH
Confidence            368888665543 3567999999999964  334678999987764

>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=93.06  E-value=0.033  Score=36.34  Aligned_cols=43  Identities=23%  Similarity=0.759  Sum_probs=26.2

Q ss_pred             cccccCCCCCCceEeccc-CccchhHHHHHHhcCCCCCCCCccccC
Q 027652          164 SCPICMGPLSEATSTKCG-HIFCKDCIKGAIAAQGKCPNCRQKVGK  208 (220)
Q Consensus       164 ~CpIC~~~~~~pv~l~Cg-H~fC~~Ci~~~l~~~~~CP~Cr~~v~~  208 (220)
                      .|.-|.  +.+.-.+.|. |-.|..|+..++..+..||+|..++..
T Consensus         4 nCKsCW--f~~k~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt   47 (50)
T PF03854_consen    4 NCKSCW--FANKGLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPT   47 (50)
T ss_dssp             ---SS---S--SSEEE-SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred             cChhhh--hcCCCeeeecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence            466665  4445567886 668999999999999999999998864

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.

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

Probab=92.15  E-value=0.048  Score=50.31  Aligned_cols=45  Identities=27%  Similarity=0.740  Sum_probs=35.1

Q ss_pred             CCccccccCCCCCC-c---eEecccCccchhHHHHHHhcC--CCCCCCCcc
Q 027652          161 PTFSCPICMGPLSE-A---TSTKCGHIFCKDCIKGAIAAQ--GKCPNCRQK  205 (220)
Q Consensus       161 ~~~~CpIC~~~~~~-p---v~l~CgH~fC~~Ci~~~l~~~--~~CP~Cr~~  205 (220)
                      -.+.|-.|-+.+-. +   -.+||.|+|+.+|+..++.+.  ..||.||+-
T Consensus       364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crkl  414 (518)
T KOG1941|consen  364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKL  414 (518)
T ss_pred             HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHH
Confidence            35689999886542 2   356999999999999998754  489999943

>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=91.51  E-value=0.16  Score=45.06  Aligned_cols=38  Identities=26%  Similarity=0.718  Sum_probs=32.6

Q ss_pred             CCCCccccccCCCCCCceEecc----cCccchhHHHHHHhcC
Q 027652          159 AAPTFSCPICMGPLSEATSTKC----GHIFCKDCIKGAIAAQ  196 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~C----gH~fC~~Ci~~~l~~~  196 (220)
                      ....+.|.+|.+.+.+...+.|    .|.||+.|-.+.++.+
T Consensus       265 ~~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Q  306 (352)
T KOG3579|consen  265 PSAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQ  306 (352)
T ss_pred             CCCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhh
Confidence            3456899999999999988887    5889999999998865

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

Probab=91.11  E-value=0.055  Score=56.24  Aligned_cols=45  Identities=31%  Similarity=0.730  Sum_probs=39.8

Q ss_pred             CCCccccccCCCCC-CceEecccCccchhHHHHHHhcCCCCCCCCc
Q 027652          160 APTFSCPICMGPLS-EATSTKCGHIFCKDCIKGAIAAQGKCPNCRQ  204 (220)
Q Consensus       160 ~~~~~CpIC~~~~~-~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~  204 (220)
                      ...+.|.||.+.+. ...+..|||.+|..|...|+..+..||+|..
T Consensus      1151 ~~~~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRNQGGIAGCGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred             hcccchHHHHHHHHhcCCeeeechhHhhhHHHHHHHHhccCcchhh
Confidence            34569999999998 5677899999999999999999999999963

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

Probab=90.86  E-value=0.12  Score=51.68  Aligned_cols=42  Identities=29%  Similarity=0.808  Sum_probs=34.7

Q ss_pred             CccccccCCCCCCc-eEecccCccchhHHHHHHhcCCCCCCCCccc
Q 027652          162 TFSCPICMGPLSEA-TSTKCGHIFCKDCIKGAIAAQGKCPNCRQKV  206 (220)
Q Consensus       162 ~~~CpIC~~~~~~p-v~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v  206 (220)
                      .-.|..|...+.-| |...|||.|+..|+.   .....||.|+...
T Consensus       840 ~skCs~C~~~LdlP~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  840 VSKCSACEGTLDLPFVHFLCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeeecccCCccccceeeeecccHHHHHhhc---cCcccCCccchhh
Confidence            35899999999888 456999999999987   4566999998744

>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=90.56  E-value=0.2  Score=31.88  Aligned_cols=38  Identities=29%  Similarity=0.760  Sum_probs=23.2

Q ss_pred             ccccCCCCCCceEec---ccCccchhHHHHHHhcCC--CCCCC
Q 027652          165 CPICMGPLSEATSTK---CGHIFCKDCIKGAIAAQG--KCPNC  202 (220)
Q Consensus       165 CpIC~~~~~~pv~l~---CgH~fC~~Ci~~~l~~~~--~CP~C  202 (220)
                      |.+|.++....+.-+   |+-.++..|+.++++...  .||.|
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            667888777766554   888899999999998655  69987

; PDB: 3NW0_A 2CT0_A.

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

Probab=90.50  E-value=0.21  Score=42.99  Aligned_cols=44  Identities=32%  Similarity=0.743  Sum_probs=36.1

Q ss_pred             cccccCCCCC--CceEecccCccchhHHHHHHhcC--------CCCCCCCcccc
Q 027652          164 SCPICMGPLS--EATSTKCGHIFCKDCIKGAIAAQ--------GKCPNCRQKVG  207 (220)
Q Consensus       164 ~CpIC~~~~~--~pv~l~CgH~fC~~Ci~~~l~~~--------~~CP~Cr~~v~  207 (220)
                      -|.+|...+.  +.+.+.|-|.|++.|+.+|...-        -.||.|..++-
T Consensus        52 NC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiF  105 (299)
T KOG3970|consen   52 NCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIF  105 (299)
T ss_pred             CCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccC
Confidence            6999998776  45788999999999999987742        26999988764

>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=90.32  E-value=0.34  Score=31.82  Aligned_cols=42  Identities=24%  Similarity=0.661  Sum_probs=22.5

Q ss_pred             ccccccCCCCCCceEe-cccCccchhHHHHHHh---cCC--CCCCCCcc
Q 027652          163 FSCPICMGPLSEATST-KCGHIFCKDCIKGAIA---AQG--KCPNCRQK  205 (220)
Q Consensus       163 ~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~---~~~--~CP~Cr~~  205 (220)
                      +.||+....+..|+.. .|.|..|..- ..|+.   ...  .||+|.++
T Consensus         3 L~CPls~~~i~~P~Rg~~C~H~~CFDl-~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRIPVRGKNCKHLQCFDL-ESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SSEEEETT--SS--EEH-HHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEEEeCccCCcCcccceECH-HHHHHHhhccCCeECcCCcCc
Confidence            5799999999999876 8999987653 33333   222  69999763

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.

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

Probab=90.22  E-value=0.072  Score=51.90  Aligned_cols=40  Identities=30%  Similarity=0.773  Sum_probs=30.9

Q ss_pred             CCCCccccccCCCCC----CceEecccCccchhHHHHHHhcCCCCC
Q 027652          159 AAPTFSCPICMGPLS----EATSTKCGHIFCKDCIKGAIAAQGKCP  200 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~----~pv~l~CgH~fC~~Ci~~~l~~~~~CP  200 (220)
                      ..+.+.|+||...+.    .|+.+.|||+.|..|+....  ...||
T Consensus         8 w~~~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly--n~scp   51 (861)
T KOG3161|consen    8 WVLLLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY--NASCP   51 (861)
T ss_pred             hHHHhhchHHHHHHHHHhcCcccccccchHHHHHHHhHh--hccCC
Confidence            345568999977664    58899999999999998654  45676

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

Probab=90.02  E-value=0.058  Score=53.03  Aligned_cols=50  Identities=32%  Similarity=0.826  Sum_probs=40.2

Q ss_pred             CccccccCCCCCCceEecccCccchhHHHHHHhcC---CCCCCCCccccCCCc
Q 027652          162 TFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQ---GKCPNCRQKVGKRGI  211 (220)
Q Consensus       162 ~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~---~~CP~Cr~~v~~~~l  211 (220)
                      .+.|+||...+++|+.+.|-|.||..|+...+...   ..||+|+..+.+..+
T Consensus        21 ~lEc~ic~~~~~~p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~s~   73 (684)
T KOG4362|consen   21 ILECPICLEHVKEPSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKRSL   73 (684)
T ss_pred             hccCCceeEEeeccchhhhhHHHHhhhhhceeeccCccccchhhhhhhhhhhc
Confidence            45899999999999999999999999987665533   379999876665443

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

Probab=89.56  E-value=0.15  Score=54.01  Aligned_cols=53  Identities=25%  Similarity=0.565  Sum_probs=39.6

Q ss_pred             CCCCccccccCCCCC---CceEecccCccchhHHHHHHhcC----------CCCCCCCccccCCCc
Q 027652          159 AAPTFSCPICMGPLS---EATSTKCGHIFCKDCIKGAIAAQ----------GKCPNCRQKVGKRGI  211 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~---~pv~l~CgH~fC~~Ci~~~l~~~----------~~CP~Cr~~v~~~~l  211 (220)
                      .+.+..|-||+..--   ..+.+.|+|+|+..|....+...          ..||+|..++...-|
T Consensus      3483 QD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH~~L 3548 (3738)
T KOG1428|consen 3483 QDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINHIVL 3548 (3738)
T ss_pred             cccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhhHHH
Confidence            455778999987432   23678999999999998877632          269999998875433

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

Probab=89.45  E-value=0.16  Score=43.10  Aligned_cols=39  Identities=26%  Similarity=0.595  Sum_probs=31.7

Q ss_pred             ccccCCCCCCceEecccCc-cchhHHHHHHhcCCCCCCCCcccc
Q 027652          165 CPICMGPLSEATSTKCGHI-FCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       165 CpIC~~~~~~pv~l~CgH~-fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      |-.|...-...+.+||.|. +|..|-..    -..||+|+....
T Consensus       161 Cr~C~~~~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~  200 (207)
T KOG1100|consen  161 CRKCGEREATVLLLPCRHLCLCGICDES----LRICPICRSPKT  200 (207)
T ss_pred             ceecCcCCceEEeecccceEeccccccc----CccCCCCcChhh
Confidence            9999998888778899996 99999542    346999987654

>PHA03096 p28-like protein; Provisional

Probab=89.09  E-value=0.2  Score=44.65  Aligned_cols=43  Identities=23%  Similarity=0.347  Sum_probs=30.6

Q ss_pred             ccccccCCCCCCc--------eEecccCccchhHHHHHHhcC---CCCCCCCcc
Q 027652          163 FSCPICMGPLSEA--------TSTKCGHIFCKDCIKGAIAAQ---GKCPNCRQK  205 (220)
Q Consensus       163 ~~CpIC~~~~~~p--------v~l~CgH~fC~~Ci~~~l~~~---~~CP~Cr~~  205 (220)
                      -.|.||++.....        ..-.|.|.||..|+..|....   ..||.|+..
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~  232 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRL  232 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccch
Confidence            4799999866532        233799999999999998742   245555543

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.07  E-value=0.42  Score=41.81  Aligned_cols=53  Identities=17%  Similarity=0.417  Sum_probs=41.1

Q ss_pred             CCCccccccCCCCCCc----eEecccCccchhHHHHHHhcCCCCCCCCccccCCCceee
Q 027652          160 APTFSCPICMGPLSEA----TSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRV  214 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~p----v~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~i  214 (220)
                      ...|.|||-.-.+...    +...|||+|-.+-+++..  ...|++|.+.+...+++.|
T Consensus       109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeik--as~C~~C~a~y~~~dvIvl  165 (293)
T KOG3113|consen  109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIK--ASVCHVCGAAYQEDDVIVL  165 (293)
T ss_pred             cceeecccccceecceEEEEEEeccceeccHHHHHHhh--hccccccCCcccccCeEee
Confidence            4468999976666543    344899999998887764  6789999999998887754

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

Probab=88.78  E-value=1.3  Score=40.64  Aligned_cols=33  Identities=27%  Similarity=0.749  Sum_probs=25.8

Q ss_pred             ccCccchhHHHHHHhc-------------CCCCCCCCccccCCCce
Q 027652          180 CGHIFCKDCIKGAIAA-------------QGKCPNCRQKVGKRGIF  212 (220)
Q Consensus       180 CgH~fC~~Ci~~~l~~-------------~~~CP~Cr~~v~~~~l~  212 (220)
                      |....|..|+-+|+..             ...||+||+++...|+.
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilDV~  356 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILDVC  356 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeeeee
Confidence            5666799999999872             12699999999877764

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

>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=88.18  E-value=0.24  Score=39.28  Aligned_cols=37  Identities=27%  Similarity=0.636  Sum_probs=27.5

Q ss_pred             CccccccCCCCCC--c-eEeccc------CccchhHHHHHHhcCCC
Q 027652          162 TFSCPICMGPLSE--A-TSTKCG------HIFCKDCIKGAIAAQGK  198 (220)
Q Consensus       162 ~~~CpIC~~~~~~--p-v~l~Cg------H~fC~~Ci~~~l~~~~~  198 (220)
                      ..+|.||++.+.+  . +.++||      |.||..|+++|.+....
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~r   71 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRERNR   71 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhhccC
Confidence            4589999998876  3 344665      67999999999654433

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.

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=88.00  E-value=0.57  Score=38.24  Aligned_cols=48  Identities=19%  Similarity=0.398  Sum_probs=34.3

Q ss_pred             CCCccccccCCCCCCceEeccc--Cc---cchhHHHHHHhcC--CCCCCCCccccC
Q 027652          160 APTFSCPICMGPLSEATSTKCG--HI---FCKDCIKGAIAAQ--GKCPNCRQKVGK  208 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l~Cg--H~---fC~~Ci~~~l~~~--~~CP~Cr~~v~~  208 (220)
                      .....|-||++.... ..-||.  ..   .+..|+.+|+..+  ..|++|..+...
T Consensus         6 ~~~~~CRIC~~~~~~-~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i   60 (162)
T PHA02825          6 LMDKCCWICKDEYDV-VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNI   60 (162)
T ss_pred             CCCCeeEecCCCCCC-ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEE
Confidence            445589999987542 234554  32   3899999999854  479999988753

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.93  E-value=0.29  Score=42.73  Aligned_cols=36  Identities=25%  Similarity=0.403  Sum_probs=31.5

Q ss_pred             CCCccccccCCCCCCceEecccCccchhHHHHHHhc
Q 027652          160 APTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAA  195 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~  195 (220)
                      .+-..|.+|+....+|+.++=||+||..||.+++..
T Consensus        41 K~FdcCsLtLqPc~dPvit~~GylfdrEaILe~ila   76 (303)
T KOG3039|consen   41 KPFDCCSLTLQPCRDPVITPDGYLFDREAILEYILA   76 (303)
T ss_pred             CCcceeeeecccccCCccCCCCeeeeHHHHHHHHHH
Confidence            344578999999999999999999999999888753

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

Probab=87.52  E-value=0.28  Score=43.52  Aligned_cols=43  Identities=37%  Similarity=0.834  Sum_probs=35.9

Q ss_pred             CccccccCCCCC----CceEecccCccchhHHHHHHhcCCCCCCCCc
Q 027652          162 TFSCPICMGPLS----EATSTKCGHIFCKDCIKGAIAAQGKCPNCRQ  204 (220)
Q Consensus       162 ~~~CpIC~~~~~----~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~  204 (220)
                      ...||||.+.+.    .+..++|||....+|+..+....-.||+|.+
T Consensus       158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             cCCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence            445999988665    3567799999999999999887789999988

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

Probab=87.11  E-value=0.42  Score=39.84  Aligned_cols=48  Identities=27%  Similarity=0.659  Sum_probs=35.0

Q ss_pred             CCccccccCCCCCCce-------EecccCccchhHHHHHHhc-----C------CCCCCCCccccC
Q 027652          161 PTFSCPICMGPLSEAT-------STKCGHIFCKDCIKGAIAA-----Q------GKCPNCRQKVGK  208 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv-------~l~CgH~fC~~Ci~~~l~~-----~------~~CP~Cr~~v~~  208 (220)
                      ....|-||+..--+.+       ...||..|+.-|+..|++.     +      ..||.|..++..
T Consensus       164 ~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pial  229 (234)
T KOG3268|consen  164 ELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIAL  229 (234)
T ss_pred             hhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCccee
Confidence            3457888876444332       2379999999999999983     1      369999998864

>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=87.01  E-value=0.49  Score=42.07  Aligned_cols=34  Identities=26%  Similarity=0.811  Sum_probs=28.5

Q ss_pred             cccCccchhHHHHHHhc-CCCCCCCCccccCCCce
Q 027652          179 KCGHIFCKDCIKGAIAA-QGKCPNCRQKVGKRGIF  212 (220)
Q Consensus       179 ~CgH~fC~~Ci~~~l~~-~~~CP~Cr~~v~~~~l~  212 (220)
                      +|||..|..|+...+.. ...||.|...+.+.++.
T Consensus        22 ~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nfr   56 (300)
T KOG3800|consen   22 ECGHRLCESCVDRIFSLGPAQCPECMVILRKNNFR   56 (300)
T ss_pred             cccchHHHHHHHHHHhcCCCCCCcccchhhhcccc
Confidence            89999999999988774 45899999888776654

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

Probab=86.40  E-value=0.43  Score=47.95  Aligned_cols=45  Identities=27%  Similarity=0.730  Sum_probs=34.9

Q ss_pred             CCCccccccCCCCCCceEe----cccCccchhHHHHHHhcC-------CCCCCCCc
Q 027652          160 APTFSCPICMGPLSEATST----KCGHIFCKDCIKGAIAAQ-------GKCPNCRQ  204 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l----~CgH~fC~~Ci~~~l~~~-------~~CP~Cr~  204 (220)
                      ...+.|-||.+.+.....+    .|-|+|+..||++|.+..       -+||.|..
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            4578999999977654322    588999999999998742       16999983

>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=84.92  E-value=0.35  Score=42.04  Aligned_cols=52  Identities=21%  Similarity=0.609  Sum_probs=36.7

Q ss_pred             CCccccccCCCC-CCc--eEe--c-ccCccchhHHHHHHhcC-CCCC--CCCccccCCCce
Q 027652          161 PTFSCPICMGPL-SEA--TST--K-CGHIFCKDCIKGAIAAQ-GKCP--NCRQKVGKRGIF  212 (220)
Q Consensus       161 ~~~~CpIC~~~~-~~p--v~l--~-CgH~fC~~Ci~~~l~~~-~~CP--~Cr~~v~~~~l~  212 (220)
                      .+..||+|.... -+|  +.+  | |-|..|.+|+.+.+... ..||  -|.+-+.+.+++
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK~kf~   69 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRKIKFI   69 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHHhccc
Confidence            345899998743 344  222  4 99999999999988754 4899  687766654444

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

Probab=83.77  E-value=0.41  Score=44.36  Aligned_cols=50  Identities=40%  Similarity=0.885  Sum_probs=33.3

Q ss_pred             CCCccccccCCCCCCc----eEecccCccchhHHHHHHhcC------CCCCC--CCccccCC
Q 027652          160 APTFSCPICMGPLSEA----TSTKCGHIFCKDCIKGAIAAQ------GKCPN--CRQKVGKR  209 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~p----v~l~CgH~fC~~Ci~~~l~~~------~~CP~--Cr~~v~~~  209 (220)
                      .....|.||+.....+    ....|+|.||..|+++++...      ..||.  |...++..
T Consensus       144 ~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~  205 (384)
T KOG1812|consen  144 LPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLE  205 (384)
T ss_pred             cccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHH
Confidence            3456899999433322    245899999999999988733      25653  55555443

>PHA02862 5L protein; Provisional

Probab=81.38  E-value=1.3  Score=35.65  Aligned_cols=43  Identities=26%  Similarity=0.521  Sum_probs=32.0

Q ss_pred             cccccCCCCCCceEecccC-----ccchhHHHHHHhcCC--CCCCCCcccc
Q 027652          164 SCPICMGPLSEATSTKCGH-----IFCKDCIKGAIAAQG--KCPNCRQKVG  207 (220)
Q Consensus       164 ~CpIC~~~~~~pv~l~CgH-----~fC~~Ci~~~l~~~~--~CP~Cr~~v~  207 (220)
                      .|-||++.-.+. .-||.-     ..+..|+.+|+..+.  .|++|+.+..
T Consensus         4 iCWIC~~~~~e~-~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~   53 (156)
T PHA02862          4 ICWICNDVCDER-NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN   53 (156)
T ss_pred             EEEEecCcCCCC-cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence            699999876544 345542     258999999998543  7999998875

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	220
3ng2_A	71	Crystal Structure Of The Rnf4 Ring Domain Dimer Len		4e-07
4ap4_A	133	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Le		6e-07
2xeu_A	64	Ring Domain Length = 64		1e-06
2ea6_A	69	Solution Structure Of The Ring Domain Of The Human		2e-06
1jm7_A	112	Solution Structure Of The Brca1/bard1 Ring-domain H		7e-06
2ckl_B	165	Ring1b-Bmi1 E3 Catalytic Domain Structure Length =		1e-05
2h0d_B	100	Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquiti		2e-05
3rpg_C	121	Bmi1RING1B-Ubch5c Complex Structure Length = 121		4e-05
3hct_A	118	Crystal Structure Of Traf6 In Complex With Ubc13 In		5e-05
3hcs_A	170	Crystal Structure Of The N-Terminal Domain Of Traf6		6e-05
2eci_A	86	Solution Structure Of The Ring Domain Of The Human		6e-05
2jmd_A	63	Solution Structure Of The Ring Domain Of Human Traf		1e-04
3l11_A	115	Crystal Structure Of The Ring Domain Of Rnf168 Leng		6e-04

>pdb|3NG2|A Chain A, Crystal Structure Of The Rnf4 Ring Domain Dimer Length = 71

Iteration: 1
 Score = 51.2 bits (121), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 7/62 (11%)
Query: 162 TFSCPICMGPLSEAT-------STKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRV 214
           T SCPICM   SE         ST+CGH+FC  C++ ++     CP CR+K+  +    +
Sbjct: 10  TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPI 69
Query: 215 YL 216
           Y+
Sbjct: 70  YI 71

>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Length = 133

Iteration: 1
 Score = 50.4 bits (119), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 159 AAPTFSCPICMGPLSEAT-------STKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGI 211
            + T SCPICM   SE         ST+CGH+FC  C++ ++     CP CR+K+  +  
Sbjct: 4   GSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY 63
Query: 212 FRVYL 216
             +Y+
Sbjct: 64  HPIYI 68

>pdb|2XEU|A Chain A, Ring Domain Length = 64

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 7/60 (11%)
Query: 164 SCPICMGPLSEAT-------STKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL 216
           SCPICM   SE         ST+CGH+FC  C++ ++     CP CR+K+  +    +Y+
Sbjct: 5   SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI 64

>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring Finger Protein 4 Length = 69

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 31/55 (56%), Gaps = 7/55 (12%)
Query: 162 TFSCPICMGPLSEAT-------STKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKR 209
           T SCPICM   SE         ST+CGH+FC  C++ ++     CP CR+K+  +
Sbjct: 15  TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 69

>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain Heterodimer Length = 112

Iteration: 1
 Score = 47.4 bits (111), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 158 AAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQ---GKCPNCRQKVGKRGI 211
           A      CPIC+  + E  STKC HIFCK C+   +  +    +CP C+  + KR +
Sbjct: 17  AMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL 73

>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure Length = 165

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/65 (40%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 150 LQLPQDPMAAAPTFSCPICMGPLSEATSTK-CGHIFCKDCIKGAIAAQGK-CPNCRQK-V 206
           L++   P +      CPIC+  L    +TK C H FC DCI  A+ +  K CP CR+K V
Sbjct: 42  LEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLV 101
Query: 207 GKRGI 211
            KR +
Sbjct: 102 SKRSL 106

>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin Ligase Complex Length = 100

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/65 (40%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 150 LQLPQDPMAAAPTFSCPICMGPLSEATSTK-CGHIFCKDCIKGAIAAQGK-CPNCRQK-V 206
           L++   P +      CPIC+  L    +TK C H FC DCI  A+ +  K CP CR+K V
Sbjct: 22  LEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLV 81
Query: 207 GKRGI 211
            KR +
Sbjct: 82  SKRSL 86

>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure Length = 121

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 26/65 (40%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 150 LQLPQDPMAAAPTFSCPICMGPLSEATSTK-CGHIFCKDCIKGAIAAQGK-CPNCRQK-V 206
           L++   P +      CPIC+  L    +TK C H FC DCI  A+ +  K CP CR+K V
Sbjct: 41  LEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLV 100
Query: 207 GKRGI 211
            KR +
Sbjct: 101 SKRSL 105

>pdb|3HCT|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The P1 Space Group Length = 118

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG-KCP 200
           + CPIC+  L EA  T CGH FCK CI  +I   G KCP
Sbjct: 19  YECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCP 57

>pdb|3HCS|A Chain A, Crystal Structure Of The N-Terminal Domain Of Traf6 Length = 170

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG-KCP 200
           + CPIC+  L EA  T CGH FCK CI  +I   G KCP
Sbjct: 19  YECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCP 57

>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf Receptor-Associated Factor 6 Protein Length = 86

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG-KCP 200
           + CPIC+  L EA  T CGH FCK CI  +I   G KCP
Sbjct: 26  YECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCP 64

>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6 Length = 63

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG-KCP 200
           + CPIC+  L EA  T CGH FCK CI  +I   G KCP
Sbjct: 7   YECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCP 45

>pdb|3L11|A Chain A, Crystal Structure Of The Ring Domain Of Rnf168 Length = 115

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 150 LQLPQDPMAAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAI-AAQGKCPNCRQKVG 207
           + LP+D + +     C ICM  L E  +  C H  CK C +  +  A   CP CR++V 
Sbjct: 3   MALPKDAIPSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVS 61

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	220
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	8e-19
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	1e-18
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	1e-15
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	3e-15
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	4e-15
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	9e-15
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	4e-14
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	5e-14
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	8e-14
1z6u_A	150	NP95-like ring finger protein isoform B; structura	1e-13
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	1e-12
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	3e-12
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	3e-12
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	4e-12
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	8e-12
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	1e-11
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	2e-11
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	4e-11
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	4e-11
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	4e-11
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	5e-11
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	7e-11
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-08
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	8e-11
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	2e-10
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	2e-10
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	3e-10
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	3e-10
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	5e-10
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	6e-10
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	6e-10
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	2e-09
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	3e-09
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	2e-08
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	2e-08
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	4e-07
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	5e-07
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	1e-06
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	2e-06
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	3e-06
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	7e-06
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	1e-05
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	1e-05
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	3e-05
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	4e-05
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	1e-04
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	1e-04
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	1e-04
2ect_A	78	Ring finger protein 126; metal binding protein, st	1e-04
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	3e-04
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	4e-04
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	5e-04
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	5e-04
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	6e-04
2ea5_A	68	Cell growth regulator with ring finger domain prot	9e-04

>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 = 76.4 bits (188), Expect = 8e-19
 Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 7/65 (10%)

Query: 159 AAPTFSCPICMGPLSE-------ATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGI 211
            + T SCPICM   SE         ST+CGH+FC  C++ ++     CP CR+K+  +  
Sbjct: 7   PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY 66

Query: 212 FRVYL 216
             +Y+
Sbjct: 67  HPIYI 71

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

 Score = 75.6 bits (186), Expect = 1e-18
 Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 7/62 (11%)

Query: 162 TFSCPICMGPLSE-------ATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRV 214
             SCPICM   SE         ST+CGH+FC  C++ ++     CP CR+K+  +    +
Sbjct: 3   MVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPI 62

Query: 215 YL 216
           Y+
Sbjct: 63  YI 64

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

 Score = 67.9 bits (166), Expect = 1e-15
 Identities = 16/47 (34%), Positives = 23/47 (48%)

Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKR 209
             C IC+       S  C H+FC  C+KGA     +C  CRQ++ + 
Sbjct: 16  PECAICLQTCVHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPED 62

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

 Score = 67.1 bits (164), Expect = 3e-15
 Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 161 PTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG-KCPNCRQKVGKRGIF 212
             + C  C   L     T+CGH FC+ C+   +++   KC  C++ + K  +F
Sbjct: 14  DKYKCEKCHLVLCSPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDKVF 66

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

 Score = 66.8 bits (163), Expect = 4e-15
 Identities = 19/50 (38%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIF 212
           F C IC         TKC H FC+ C      A  +C  C Q  G  GIF
Sbjct: 16  FRCFICRQAFQNPVVTKCRHYFCESCALEHFRATPRCYICDQPTG--GIF 63

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

 Score = 65.7 bits (160), Expect = 9e-15
 Identities = 22/58 (37%), Positives = 32/58 (55%), Gaps = 7/58 (12%)

Query: 159 AAPTFSCPICMGPLSE-------ATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKR 209
            + T SCPICM   SE         ST+CGH+FC  C++ ++     CP CR+K+  +
Sbjct: 12  PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 69

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

 Score = 65.4 bits (159), Expect = 4e-14
 Identities = 25/91 (27%), Positives = 35/91 (38%), Gaps = 11/91 (12%)

Query: 135 INVDTSNNNKNDAAPLQLPQDPMAAAPT----------FSCPICMGPLSEATSTKCGHIF 184
           I  D SN    +     L   P + +P           F C  C   +    +T C H  
Sbjct: 15  IREDKSNAKLWNEVLASLKDRPASGSPFQLFLSKVEETFQCICCQELVFRPITTVCQHNV 74

Query: 185 CKDCIKGAIAAQG-KCPNCRQKVGKRGIFRV 214
           CKDC+  +  AQ   CP CR  +G+    +V
Sbjct: 75  CKDCLDRSFRAQVFSCPACRYDLGRSYAMQV 105

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

 Score = 63.6 bits (155), Expect = 5e-14
 Identities = 20/49 (40%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 161 PTFSCPICMGPLSEATS-TKCGHIFCKDCIKGAIAAQGKCPNCRQKVGK 208
           P   C IC G L +AT+ T+C H FCK CI        +CP C   V +
Sbjct: 14  PYILCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQ 62

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

 Score = 65.4 bits (159), Expect = 8e-14
 Identities = 15/47 (31%), Positives = 22/47 (46%)

Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKR 209
             C IC     EA +  C H FC  CI   +  + +CP CR+ +  +
Sbjct: 65  LQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSK 111

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

 Score = 65.0 bits (158), Expect = 1e-13
 Identities = 24/84 (28%), Positives = 35/84 (41%), Gaps = 4/84 (4%)

Query: 135 INVDTSNNNKNDAAPLQLPQDPMAAAP---TFSCPICMGPLSEATSTKCGHIFCKDCIKG 191
           I  D  N    D     L + P        +F C  C   + +  +T+C H  CKDC++ 
Sbjct: 48  IREDCQNQKLWDEVLSHLVEGPNFLKKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQR 107

Query: 192 AIAAQGK-CPNCRQKVGKRGIFRV 214
           +  AQ   CP CR  +G+  I   
Sbjct: 108 SFKAQVFSCPACRHDLGQNYIMIP 131

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

 Score = 60.5 bits (147), Expect = 1e-12
 Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 1/54 (1%)

Query: 161 PTFSCPICMGPLSEATS-TKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFR 213
               C IC    + A    +C H +C  CI+  ++ + +CP C   V +  +  
Sbjct: 21  DLLRCGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLKN 74

>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 = 61.5 bits (149), Expect = 3e-12
 Identities = 22/55 (40%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 161 PTFSCPICMGPLSEATSTK-CGHIFCKDCIKGAIAAQGK-CPNCRQKVGKRGIFR 213
               CPIC+  L    +TK C H FC DCI  A+ +  K CP CR+K+  +   R
Sbjct: 53  SELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLR 107

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

 Score = 60.2 bits (146), Expect = 3e-12
 Identities = 22/53 (41%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG-KCPNCRQKVGKRGIFRV 214
           + CPIC+  L EA  T CGH FCK CI  +I   G KCP   + + +  +F  
Sbjct: 19  YECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPD 71

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

 Score = 59.9 bits (145), Expect = 4e-12
 Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 1/67 (1%)

Query: 148 APLQLPQDPMAAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGK-CPNCRQKV 206
             + LP+D + +     C ICM  L E  +  C H  CK C +  +      CP CR++V
Sbjct: 1   GSMALPKDAIPSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRV 60

Query: 207 GKRGIFR 213
                + 
Sbjct: 61  SSWTRYH 67

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A Length = 108

 Score = 59.1 bits (143), Expect = 8e-12
 Identities = 18/58 (31%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 161 PTFSCPICMGPLSEATS-TKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLP 217
           P   C +C G   +AT+  +C H FCK CI   +     CP C  +V K         
Sbjct: 14  PHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRS 71

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

 Score = 57.4 bits (139), Expect = 1e-11
 Identities = 20/65 (30%), Positives = 25/65 (38%), Gaps = 10/65 (15%)

Query: 157 MAAAPT-------FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGK---CPNCRQKV 206
           MA+            CPIC+  L +  +  CGH FC  CI            CP C+  V
Sbjct: 8   MASGQFVNKLQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSV 67

Query: 207 GKRGI 211
            K  I
Sbjct: 68  RKNAI 72

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

 Score = 57.8 bits (140), Expect = 2e-11
 Identities = 20/50 (40%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGK---CPNCRQKVGKR 209
             CPIC+  + E  STKC HIFCK C+   +  +     CP C+  + KR
Sbjct: 22  LECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR 71

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

 Score = 56.3 bits (136), Expect = 4e-11
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 163 FSCPICMGPLSEATSTK-CGHIFCKDCIKGAIAAQGK--CPNCRQKVGKR 209
             C IC   +++A     CG+ +C +CI+ A+    +  CP C Q     
Sbjct: 16  LLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSP 65

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

 Score = 57.2 bits (138), Expect = 4e-11
 Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 1/55 (1%)

Query: 156 PMAAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGK-CPNCRQKVGKR 209
           P     + SC IC   L++   T C H+FC+ CI   +   G  CP+CR      
Sbjct: 17  PAHFVKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPT 71

>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 = 60.5 bits (146), Expect = 4e-11
 Identities = 21/126 (16%), Positives = 39/126 (30%), Gaps = 8/126 (6%)

Query: 92  QLRHVLTDAGGLLDSLQE-VTDLAILYVKQRRNRPDEATPDNCCINVDTSNNNKNDAAPL 150
            +   +     L  +L +   +   L+   R   PD           + +  +       
Sbjct: 267 NILQTIPHNKPLFQALIDGFREGFYLFPDGRNQNPDLTG------LCEPTPQDHIKVTQE 320

Query: 151 QLPQDPMAAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGK-CPNCRQKVGKR 209
           Q        +    C IC     +     CGH+ C  C+     ++G+ CP CR ++   
Sbjct: 321 QYELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT 380

Query: 210 GIFRVY 215
               V 
Sbjct: 381 EPIVVD 386

>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 = 56.8 bits (137), Expect = 5e-11
 Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 2/56 (3%)

Query: 163 FSCPICMGPLSEATS-TKCGHIFCKDCIKGAIAAQ-GKCPNCRQKVGKRGIFRVYL 216
           F C ICM  L +A     C  + C  CI+  +  Q  +CP+CR  +  R +     
Sbjct: 23  FRCFICMEKLRDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVNCRW 78

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

 Score = 57.1 bits (137), Expect = 7e-11
 Identities = 22/58 (37%), Positives = 32/58 (55%), Gaps = 7/58 (12%)

Query: 159 AAPTFSCPICMGPLSE-------ATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKR 209
            + T SCPICM   SE         ST+CGH+FC  C++ ++     CP CR+K+  +
Sbjct: 4   GSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 61

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

 Score = 50.9 bits (121), Expect = 1e-08
 Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 7/63 (11%)

Query: 161 PTFSCPICMGPLSE-------ATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFR 213
            T SCPICM   SE         ST+CGH+FC  C++ ++     CP CR+K+  +    
Sbjct: 71  GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHP 130

Query: 214 VYL 216
           +Y+
Sbjct: 131 IYI 133

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

 Score = 55.7 bits (135), Expect = 8e-11
 Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 12/66 (18%)

Query: 156 PMAAAPT------FSCPICMGPLSEATSTKCGHIFCKDCIKG----AIAAQGK--CPNCR 203
            MA+          +CPIC+  L++  S  CGH FC+ C+      ++  +G+  CP CR
Sbjct: 7   GMASGILVNVKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCR 66

Query: 204 QKVGKR 209
                 
Sbjct: 67  ISYQPE 72

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

 Score = 53.9 bits (130), Expect = 2e-10
 Identities = 17/49 (34%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 159 AAPTFSCPICMGPLSE-ATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKV 206
           A     CPIC+   S  + +  C H FC  CI   I     CP C+  V
Sbjct: 2   ATVAERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPV 50

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

 Score = 54.3 bits (131), Expect = 2e-10
 Identities = 19/69 (27%), Positives = 25/69 (36%), Gaps = 12/69 (17%)

Query: 153 PQDPMAAAPT------FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGK------CP 200
               MA++         +CPIC+  L E  S  C H FC+ CI     +         CP
Sbjct: 4   GSSGMASSVLEMIKEEVTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCP 63

Query: 201 NCRQKVGKR 209
            CR      
Sbjct: 64  VCRVPYPFG 72

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

 Score = 53.8 bits (130), Expect = 3e-10
 Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 7/54 (12%)

Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKG-------AIAAQGKCPNCRQKVGKR 209
            +CPIC+  L+E  S  CGH  C+ CI         ++  +  CP C       
Sbjct: 13  VTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFE 66

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

 Score = 56.2 bits (135), Expect = 3e-10
 Identities = 22/53 (41%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG-KCPNCRQKVGKRGIFRV 214
           + CPIC+  L EA  T CGH FCK CI  +I   G KCP   + + +  +F  
Sbjct: 19  YECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPD 71

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

 Score = 53.6 bits (129), Expect = 5e-10
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 163 FSCPICMGPLSEATSTK-CGHIFCKDCIKGAIAAQGK--CPNCRQKVGKR 209
             C IC   +++A     CG+ +C +CI+ A+    +  CP C Q     
Sbjct: 14  LLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSP 63

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

 Score = 52.4 bits (126), Expect = 6e-10
 Identities = 9/43 (20%), Positives = 14/43 (32%), Gaps = 3/43 (6%)

Query: 164 SCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKV 206
            C  C           C H  C  C++    +  +CP C+   
Sbjct: 8   RCQQCQAEAKCPKLLPCLHTLCSGCLEA---SGMQCPICQAPW 47

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

 Score = 54.7 bits (131), Expect = 6e-10
 Identities = 10/48 (20%), Positives = 19/48 (39%), Gaps = 1/48 (2%)

Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGK-CPNCRQKVGKR 209
           + C  C   L      +CGH +C  C+   +++  + C  C  +    
Sbjct: 32  YLCSACRNVLRRPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYE 79

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

 Score = 52.0 bits (125), Expect = 2e-09
 Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 7/56 (12%)

Query: 163 FSCPICMGPLSEATST----KCGHIFCKDCIKGAIAAQG---KCPNCRQKVGKRGI 211
             CPICM   +E         CGH  C+ C++  +A+     +CP C +      +
Sbjct: 16  LECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITSL 71

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 63

 Score = 50.8 bits (122), Expect = 3e-09
 Identities = 17/56 (30%), Positives = 21/56 (37%), Gaps = 10/56 (17%)

Query: 157 MAAAPT-------FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGK---CPNC 202
           MA+            CPIC+  L +  +  CGH FC  CI            CP C
Sbjct: 8   MASGQFVNKLQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC 63

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

 Score = 50.3 bits (120), Expect = 2e-08
 Identities = 14/50 (28%), Positives = 18/50 (36%), Gaps = 3/50 (6%)

Query: 163 FSCPICMGPLSEATS-TKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGI 211
             C  C   L E      C HIFC +C+   I     CP C      + +
Sbjct: 23  LRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTG--CPVCYTPAWIQDL 70

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 58

 Score = 48.1 bits (115), Expect = 2e-08
 Identities = 16/43 (37%), Positives = 20/43 (46%), Gaps = 3/43 (6%)

Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGK---CPNC 202
            SC +C+  L E    +CGH FCK CI        +   CP C
Sbjct: 16  ASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC 58

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

 Score = 45.1 bits (107), Expect = 4e-07
 Identities = 14/44 (31%), Positives = 17/44 (38%), Gaps = 1/44 (2%)

Query: 165 CPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGK 208
           C ICM          C H FC+ CI         CP CR ++  
Sbjct: 18  CCICMDGR-ADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMTG 60

>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 = 44.6 bits (106), Expect = 5e-07
 Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 4/46 (8%)

Query: 165 CPICMGPLSEATST----KCGHIFCKDCIKGAIAAQGKCPNCRQKV 206
           CPIC+  +  +        CGH+  + C +  +    +CP C    
Sbjct: 8   CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPS 53

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

 Score = 46.9 bits (110), Expect = 1e-06
 Identities = 17/52 (32%), Positives = 22/52 (42%), Gaps = 5/52 (9%)

Query: 163 FSCPICMGPLSE-ATSTKCGHIFCKDCIKGAIAAQGK--CP--NCRQKVGKR 209
            +CPI   P      S KC H+F +D I+  +       CP   C Q V  R
Sbjct: 182 LTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMR 233

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

 Score = 43.4 bits (102), Expect = 2e-06
 Identities = 14/55 (25%), Positives = 18/55 (32%), Gaps = 6/55 (10%)

Query: 163 FSCPICMG-----PLSEATSTKCGHIFCKDCIKGAIA-AQGKCPNCRQKVGKRGI 211
             CP C       P  +     CGH  C+ C+        G CP C   + K   
Sbjct: 4   QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNF 58

>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 = 43.7 bits (102), Expect = 3e-06
 Identities = 19/78 (24%), Positives = 28/78 (35%), Gaps = 23/78 (29%)

Query: 155 DPMAAAPTFSCPICMGPLSEATS------------------TKCGHIFCKDCIKGAIAAQ 196
           + +  AP   C ICM  L+ A+                   TKC H F   C+       
Sbjct: 18  EELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNG 77

Query: 197 GK-----CPNCRQKVGKR 209
            K     CP+C+   G++
Sbjct: 78  NKDGSLQCPSCKTIYGEK 95

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

 Score = 42.0 bits (98), Expect = 7e-06
 Identities = 15/53 (28%), Positives = 20/53 (37%), Gaps = 5/53 (9%)

Query: 164 SCPICMGPLSEATST----KCGHIFCKDCIKGAIA-AQGKCPNCRQKVGKRGI 211
            CP+CM PL           CG+  C+ C         G CP CR+   +   
Sbjct: 13  ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPA 65

>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 Length = 94

 Score = 41.8 bits (98), Expect = 1e-05
 Identities = 12/56 (21%), Positives = 21/56 (37%), Gaps = 11/56 (19%)

Query: 158 AAAPTFSCPICMGPLSEA---TSTKCGHIFCKDCIKGAI--------AAQGKCPNC 202
            ++ +  C +C+G        T  +C  IFC  C+K  +             CP+ 
Sbjct: 1   GSSGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDA 56

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

 Score = 40.4 bits (95), Expect = 1e-05
 Identities = 9/45 (20%), Positives = 13/45 (28%), Gaps = 1/45 (2%)

Query: 162 TFSCPICMGPLSEA-TSTKCGHIFCKDCIKGAIAAQGKCPNCRQK 205
              C I          S K   IF K  ++  +   G  P   + 
Sbjct: 3   HMLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEP 47

>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A Length = 64

 Score = 39.8 bits (93), Expect = 3e-05
 Identities = 18/56 (32%), Positives = 21/56 (37%), Gaps = 5/56 (8%)

Query: 165 CPICMGPLSEAT--STKCGHIF-CKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLP 217
           C IC G          K GH+  C  C K        CP CRQ +  + I   Y P
Sbjct: 11  CVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPI--QMIVLTYFP 64

>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 Length = 79

 Score = 39.7 bits (93), Expect = 4e-05
 Identities = 18/57 (31%), Positives = 24/57 (42%), Gaps = 7/57 (12%)

Query: 165 CPICMGPLSEATSTKCGHIF-CKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPTLS 220
           C +C      +T   CGH   C+ C          CP CR +V    +  VYLPT +
Sbjct: 21  CMVCCEEEINSTFCPCGHTVCCESCAA----QLQSCPVCRSRV--EHVQHVYLPTHT 71

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

 Score = 38.7 bits (90), Expect = 1e-04
 Identities = 10/45 (22%), Positives = 16/45 (35%), Gaps = 4/45 (8%)

Query: 165 CPICMGPLSEATST----KCGHIFCKDCIKGAIAAQGKCPNCRQK 205
           C  C     +        +C H F   C+   +    +CP C+Q 
Sbjct: 29  CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQD 73

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3 Length = 93

 Score = 39.0 bits (90), Expect = 1e-04
 Identities = 18/66 (27%), Positives = 25/66 (37%), Gaps = 9/66 (13%)

Query: 148 APLQLPQDPMAAAPTFSCPICMGPLSEATSTKC----GHIFCKDCIKGAIAAQGK----- 198
                   PMA +    C IC   L +    +C     H FC  C + +I AQG      
Sbjct: 1   GSSGSSGSPMANSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKAQGATGEVY 60

Query: 199 CPNCRQ 204
           CP+  +
Sbjct: 61  CPSGEK 66

>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 Length = 345

 Score = 41.5 bits (95), Expect = 1e-04
 Identities = 28/138 (20%), Positives = 50/138 (36%), Gaps = 7/138 (5%)

Query: 80  NNSRRNHSQVVDQLRHVLTDAGGLLDSLQEVTDLAILYVKQRRNRPDEATPDNCCINVDT 139
           N   +    ++ Q   +   A  L+D++    + A    K      D     N  ++ + 
Sbjct: 213 NVINKQEHDIIKQKTQIPLQARELIDTILVKGNAAANIFKNSLKEIDSTLYKNLFVDKNM 272

Query: 140 SNNNKNDAAPLQLPQDPMAAAPTFSCPICMGPLSEATSTKCGH-IFCKDCIKGAIAAQGK 198
                 D + L L +         +C +CM          CGH + C++C      +  K
Sbjct: 273 KYIPTEDVSGLSLEEQLRRLQEERTCKVCMDKEVSVVFIPCGHLVVCQECAP----SLRK 328

Query: 199 CPNCRQKVGKRGIFRVYL 216
           CP CR  +  +G  R +L
Sbjct: 329 CPICRGII--KGTVRTFL 344

>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 = 38.2 bits (89), Expect = 1e-04
 Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 3/45 (6%)

Query: 165 CPICMGPLSEATSTK---CGHIFCKDCIKGAIAAQGKCPNCRQKV 206
           CP+C    +   S +   C H+F   CI   +     CP CR+ +
Sbjct: 18  CPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSL 62

>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 = 37.2 bits (86), Expect = 3e-04
 Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 3/45 (6%)

Query: 164 SCPICMGPLSEATS-TKCGHIFCKDCIKGAIAAQG--KCPNCRQK 205
            C IC   L +  S   CG      C+     +    +CP+C   
Sbjct: 17  ICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDY 61

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

 Score = 37.3 bits (87), Expect = 4e-04
 Identities = 14/45 (31%), Positives = 17/45 (37%), Gaps = 3/45 (6%)

Query: 165 CPICMGPLSEATSTK---CGHIFCKDCIKGAIAAQGKCPNCRQKV 206
           CPIC     +        C H F K C+   +   G CP CR   
Sbjct: 43  CPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMF 87

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

 Score = 37.5 bits (86), Expect = 5e-04
 Identities = 14/46 (30%), Positives = 17/46 (36%), Gaps = 2/46 (4%)

Query: 165 CPICMGPLSE-ATSTKCGHIFCKDCIKGAIAAQGK-CPNCRQKVGK 208
           C  C  P+        C H+FC DC         K CP C   V +
Sbjct: 4   CDKCGLPIKVYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQR 49

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 94

 Score = 37.2 bits (86), Expect = 5e-04
 Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 9/53 (16%)

Query: 162 TFSCPICMGPLSE-ATSTKCGHIFCKDCIKGAIAAQGK------CP--NCRQK 205
            F+CPI    + +   +  CGH + +D I   I ++ K      CP   C   
Sbjct: 7   GFTCPITKEEMKKPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT 59

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B* Length = 63

 Score = 36.0 bits (83), Expect = 6e-04
 Identities = 11/55 (20%), Positives = 25/55 (45%), Gaps = 5/55 (9%)

Query: 165 CPICMGPLSEAT--STKCGHIF-CKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL 216
           C +C     +      + GH+  C  C +    A   CP C++++  + + +V++
Sbjct: 10  CSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEI--QLVIKVFI 62

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 68

 Score = 35.9 bits (83), Expect = 9e-04
 Identities = 15/55 (27%), Positives = 21/55 (38%), Gaps = 7/55 (12%)

Query: 165 CPICMGPLSEATSTKCGH-IFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPT 218
           C +C           C H   C  C+K       +CP CRQ V  +  F +  P+
Sbjct: 18  CVVCQNGTVNWVLLPCRHTCLCDGCVK----YFQQCPMCRQFV--QESFALSGPS 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	220
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.52
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.5
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.46
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.44
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.44
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.43
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.41
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.41
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.41
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.4
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.39
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.39
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.38
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.38
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.37
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.36
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.35
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.35
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.35
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.35
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.31
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.3
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.29
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.29
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.29
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.28
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.27
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.26
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.26
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.25
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.24
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.24
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.24
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.23
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.22
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.21
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.21
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.21
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.2
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.2
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.2
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.18
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.17
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.17
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.16
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.15
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.13
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.12
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	99.12
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.11
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.11
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.1
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	99.08
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.07
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.07
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.07
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.06
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.02
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.01
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.97
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.93
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	98.88
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.85
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.71
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	98.63
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.63
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	98.53
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	98.27
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	97.86
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	97.74
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	97.72
3nw0_A	238	Non-structural maintenance of chromosomes element	96.4
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	95.87
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	95.61
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	95.13
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	93.31
3i2d_A	371	E3 SUMO-protein ligase SIZ1; signal transduction,	87.49
4fo9_A	360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	85.79
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	80.25

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

Probab=99.52  E-value=3.5e-15  Score=103.28  Aligned_cols=58  Identities=40%  Similarity=1.025  Sum_probs=53.7

Q ss_pred             CCCCccccccCCCCCCc-------eEecccCccchhHHHHHHhcCCCCCCCCccccCCCceeecC
Q 027652          159 AAPTFSCPICMGPLSEA-------TSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL  216 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~p-------v~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iyl  216 (220)
                      ..+.+.|+||++.+.++       +.++|||+||..|+.+|+.....||+||+.+..++++++||
T Consensus         7 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~l   71 (71)
T 3ng2_A            7 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI   71 (71)
T ss_dssp             CTTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCCCSCCCCCC
T ss_pred             CCCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccChhheeeccC
Confidence            45677999999999887       88899999999999999999999999999999999999997

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

Probab=99.50  E-value=8.1e-15  Score=99.22  Aligned_cols=56  Identities=39%  Similarity=1.046  Sum_probs=52.0

Q ss_pred             CCccccccCCCCCCc-------eEecccCccchhHHHHHHhcCCCCCCCCccccCCCceeecC
Q 027652          161 PTFSCPICMGPLSEA-------TSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL  216 (220)
Q Consensus       161 ~~~~CpIC~~~~~~p-------v~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iyl  216 (220)
                      +.+.|+||++.+.++       +.++|||.||..|+.+|+.....||+||+.+..++++++||
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~l   64 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI   64 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTTTCEEECCC
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCccceeeeeC
Confidence            456899999999876       78899999999999999999889999999999999999997

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

Probab=99.46  E-value=6.8e-14  Score=98.78  Aligned_cols=57  Identities=19%  Similarity=0.469  Sum_probs=51.1

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhc-CCCCCCCCccccCCCceeec
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAA-QGKCPNCRQKVGKRGIFRVY  215 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~-~~~CP~Cr~~v~~~~l~~iy  215 (220)
                      ..+.+.|+||++.+.+|+.++|||+||..||.+|+.. ...||+|++.+...++.+.+
T Consensus         5 ~~~~~~C~IC~~~~~~Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~l~~n~   62 (78)
T 1t1h_A            5 FPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNY   62 (78)
T ss_dssp             CSSSSSCTTTSCCCSSEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEECT
T ss_pred             CcccCCCCCccccccCCEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChhhCccCH
Confidence            4567899999999999999999999999999999986 67899999999887777654

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

Probab=99.44  E-value=3.5e-14  Score=98.83  Aligned_cols=57  Identities=28%  Similarity=0.574  Sum_probs=50.5

Q ss_pred             CCCCCccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCccccCCCceee
Q 027652          158 AAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRV  214 (220)
Q Consensus       158 ~~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~i  214 (220)
                      ...+.+.|+||++.+.+++.++|||+||..||.+|+.....||+||+.+...++.+.
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~p   67 (71)
T 2d8t_A           11 PSLTVPECAICLQTCVHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDFLDSG   67 (71)
T ss_dssp             SSSSCCBCSSSSSBCSSEEEETTTEEEEHHHHHHCTTCSSBCSSSCCBCCHHHHSCS
T ss_pred             cCCCCCCCccCCcccCCCEEccCCCHHHHHHHHHHHHCCCcCcCcCchhCHhhccCC
Confidence            356678999999999999999999999999999999888899999999987665543

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

Probab=99.44  E-value=1.5e-13  Score=95.81  Aligned_cols=56  Identities=34%  Similarity=0.704  Sum_probs=50.7

Q ss_pred             CCCCccccccCCCCCCceEe-cccCccchhHHHHHHhcCCCCCCCCccccCCCceee
Q 027652          159 AAPTFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRV  214 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~i  214 (220)
                      ..+.+.|+||++.+.+|+.+ +|||+||..||.+|+.....||+||+.+...++...
T Consensus        12 ~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   68 (72)
T 2djb_A           12 LTPYILCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLSG   68 (72)
T ss_dssp             CCGGGSCTTTSSCCSSCEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSCSCCC
T ss_pred             cCCCCCCCCCChHHHCcCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCccccccc
Confidence            46678999999999999987 999999999999999988899999999998777654

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

Probab=99.43  E-value=3.2e-13  Score=96.00  Aligned_cols=59  Identities=31%  Similarity=0.676  Sum_probs=52.6

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhc------CCCCCCCCccccCCCceeecCC
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAA------QGKCPNCRQKVGKRGIFRVYLP  217 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~------~~~CP~Cr~~v~~~~l~~iylp  217 (220)
                      ..+.+.|+||++.+.+|+.++|||+||..|+..|+..      ...||+||..+...++.+.+.-
T Consensus        16 ~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~n~~l   80 (85)
T 2ecw_A           16 IKEEVTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLKPNLHV   80 (85)
T ss_dssp             CCTTTSCTTTCSCCSSCEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTCCEECSCC
T ss_pred             CccCCCCcCCChhhCcceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHhCCcCHHH
Confidence            4567899999999999999999999999999999987      5689999999998888877653

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

Probab=99.41  E-value=1.9e-13  Score=93.59  Aligned_cols=53  Identities=26%  Similarity=0.746  Sum_probs=47.5

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHh-cCCCCCCCCccccCCCc
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIA-AQGKCPNCRQKVGKRGI  211 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~-~~~~CP~Cr~~v~~~~l  211 (220)
                      ..+.+.|+||++.+.+|+.++|||+||..|+.+|+. ....||+||+.+..+++
T Consensus        12 ~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~i   65 (66)
T 2ecy_A           12 VEDKYKCEKCHLVLCSPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDKV   65 (66)
T ss_dssp             CCCCEECTTTCCEESSCCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTTC
T ss_pred             CCcCCCCCCCChHhcCeeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChhhc
Confidence            456789999999999999999999999999999995 45689999999988765

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

Probab=99.41  E-value=4.1e-13  Score=95.42  Aligned_cols=58  Identities=29%  Similarity=0.700  Sum_probs=51.7

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhc------CCCCCCCCccccCCCceeecC
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAA------QGKCPNCRQKVGKRGIFRVYL  216 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~------~~~CP~Cr~~v~~~~l~~iyl  216 (220)
                      ..+.+.|+||++.+.+|+.++|||+||..|+..|+..      ...||+||..+...++.+.+.
T Consensus        16 ~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~n~~   79 (85)
T 2ecv_A           16 VKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRPNRH   79 (85)
T ss_dssp             CCCCCCCTTTCSCCSSCBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSSCCCSCC
T ss_pred             ccCCCCCCCCCcccCCceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHhcCccHH
Confidence            4567899999999999999999999999999999987      678999999999887776654

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

Probab=99.41  E-value=3.4e-13  Score=93.77  Aligned_cols=53  Identities=36%  Similarity=0.770  Sum_probs=47.2

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHh---cCCCCCCCCccccCCCc
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIA---AQGKCPNCRQKVGKRGI  211 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~---~~~~CP~Cr~~v~~~~l  211 (220)
                      ..+.+.|+||++.+.+|+.++|||+||..|+.+|+.   ....||+||+.+..+++
T Consensus        17 ~~~~~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~   72 (73)
T 2ysl_A           17 LQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNAI   72 (73)
T ss_dssp             CCCCCBCTTTCSBCSSEEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCCC
T ss_pred             CccCCEeccCCcccCCeEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcccC
Confidence            566789999999999999999999999999999996   34589999999987665

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

Probab=99.40  E-value=2.4e-13  Score=95.43  Aligned_cols=51  Identities=27%  Similarity=0.740  Sum_probs=45.4

Q ss_pred             CCCCCccccccCCCCCCceEec-ccCccchhHHHHHHhcC--CCCCCCCccccC
Q 027652          158 AAAPTFSCPICMGPLSEATSTK-CGHIFCKDCIKGAIAAQ--GKCPNCRQKVGK  208 (220)
Q Consensus       158 ~~~~~~~CpIC~~~~~~pv~l~-CgH~fC~~Ci~~~l~~~--~~CP~Cr~~v~~  208 (220)
                      ...+.+.|+||++.+.+|+.++ |||+||..||..|+...  ..||+||+.+..
T Consensus        11 ~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A           11 PIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS   64 (74)
T ss_dssp             CSCGGGSCSSSCCCCTTCEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCC
T ss_pred             cCCCCCCCcCCChHHhCCeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCC
Confidence            3567789999999999999999 99999999999999865  589999998654

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

Probab=99.39  E-value=3.3e-13  Score=96.91  Aligned_cols=55  Identities=29%  Similarity=0.779  Sum_probs=48.1

Q ss_pred             CCCCCccccccCCCCCC----ceEecccCccchhHHHHHHhcC---CCCCCCCccccCCCce
Q 027652          158 AAAPTFSCPICMGPLSE----ATSTKCGHIFCKDCIKGAIAAQ---GKCPNCRQKVGKRGIF  212 (220)
Q Consensus       158 ~~~~~~~CpIC~~~~~~----pv~l~CgH~fC~~Ci~~~l~~~---~~CP~Cr~~v~~~~l~  212 (220)
                      ...+.+.|+||++.+.+    ++.++|||+||..|+.+|+...   ..||+||+.+...++.
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~i~   72 (88)
T 2ct2_A           11 ALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITSLT   72 (88)
T ss_dssp             CCCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCSSTT
T ss_pred             hccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccchhHH
Confidence            35667899999999998    9999999999999999999875   6899999999876543

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

Probab=99.39  E-value=3.3e-13  Score=97.69  Aligned_cols=56  Identities=16%  Similarity=0.174  Sum_probs=51.3

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCccccCCCceee
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRV  214 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~i  214 (220)
                      ..+.+.||||++.+.+||+++|||+||..||.+|+.....||.|+.++...+|++.
T Consensus        11 ~p~~~~CpI~~~~m~dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~l~pn   66 (85)
T 2kr4_A           11 APDEFRDPLMDTLMTDPVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTESMLEPV   66 (85)
T ss_dssp             CCTTTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCGGGCEEC
T ss_pred             CchheECcccCchhcCCeECCCCCEECHHHHHHHHhcCCCCCCCcCCCChHhcchH
Confidence            45688999999999999999999999999999999988899999999998777764

>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=99.38  E-value=1.3e-13  Score=102.44  Aligned_cols=57  Identities=32%  Similarity=0.737  Sum_probs=51.3

Q ss_pred             CCCccccccCCCCCCceE-ecccCccchhHHHHHHhcC-CCCCCCCccccCCCceeecC
Q 027652          160 APTFSCPICMGPLSEATS-TKCGHIFCKDCIKGAIAAQ-GKCPNCRQKVGKRGIFRVYL  216 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~-l~CgH~fC~~Ci~~~l~~~-~~CP~Cr~~v~~~~l~~iyl  216 (220)
                      .+.+.|+||++.+.+|+. ++|||+||..||.+|+... ..||+||..+...++++.++
T Consensus        20 ~~~~~C~IC~~~~~~p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~l~~~~~   78 (100)
T 3lrq_A           20 AEVFRCFICMEKLRDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVNCRW   78 (100)
T ss_dssp             HHHTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEECTT
T ss_pred             CCCCCCccCCccccCccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHHHhHhhHH
Confidence            456799999999999999 9999999999999999987 69999999999888877654

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

Probab=99.38  E-value=2.6e-13  Score=92.68  Aligned_cols=57  Identities=23%  Similarity=0.621  Sum_probs=49.3

Q ss_pred             CCccccccCC-CCCCc----eEecccCccchhHHHHHHhc-CCCCCCCCccccCCCceeecCC
Q 027652          161 PTFSCPICMG-PLSEA----TSTKCGHIFCKDCIKGAIAA-QGKCPNCRQKVGKRGIFRVYLP  217 (220)
Q Consensus       161 ~~~~CpIC~~-~~~~p----v~l~CgH~fC~~Ci~~~l~~-~~~CP~Cr~~v~~~~l~~iylp  217 (220)
                      +++.|+||++ .+.++    +.++|||+||..|+.+|+.. ...||+||+.+..+++++.++.
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~~   64 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQLFE   64 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCCEEECCC
T ss_pred             CCCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccccceeeccc
Confidence            3568999999 78877    46799999999999999664 4579999999999999998875

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

Probab=99.37  E-value=1.2e-13  Score=97.46  Aligned_cols=58  Identities=28%  Similarity=0.630  Sum_probs=50.9

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhc-------CCCCCCCCccccCCCceeecC
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAA-------QGKCPNCRQKVGKRGIFRVYL  216 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~-------~~~CP~Cr~~v~~~~l~~iyl  216 (220)
                      ..+.+.|+||++.+.+|+.++|||+||..|+.+|+..       ...||+||..+...++.+.+.
T Consensus         9 ~~~~~~C~IC~~~~~~p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~n~~   73 (79)
T 2egp_A            9 VQEEVTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEHLQANQH   73 (79)
T ss_dssp             CCCCCEETTTTEECSSCCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSGGGTCSS
T ss_pred             cccCCCCcCCCcccCCeeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhhCCcCHH
Confidence            4567899999999999999999999999999999876       458999999998877776654

>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=99.36  E-value=7.4e-13  Score=98.46  Aligned_cols=57  Identities=14%  Similarity=0.074  Sum_probs=51.9

Q ss_pred             CCCCccccccCCCCCCceEeccc-CccchhHHHHHHhcCCCCCCCCccccCCCceeec
Q 027652          159 AAPTFSCPICMGPLSEATSTKCG-HIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVY  215 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~Cg-H~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iy  215 (220)
                      ..+.+.||||++++.+||+++|| |+||..||.+|+.....||+|+.++...+|++.+
T Consensus        19 ~p~~~~CpI~~~~m~dPV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~L~pn~   76 (98)
T 1wgm_A           19 ACDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRPNT   76 (98)
T ss_dssp             CCTTTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEECH
T ss_pred             CcHhcCCcCccccccCCeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCChhhceEcH
Confidence            45689999999999999999999 9999999999998888999999999988877653

>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=99.35  E-value=7.2e-13  Score=98.84  Aligned_cols=57  Identities=18%  Similarity=0.167  Sum_probs=51.9

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCccccCCCceeec
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVY  215 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iy  215 (220)
                      ..+.+.||||++.+.+||+++|||+||..||.+|+.....||.|+.++...+|++.+
T Consensus        26 ~p~~~~CpI~~~~m~dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~L~pn~   82 (100)
T 2kre_A           26 APDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTESMLEPVP   82 (100)
T ss_dssp             CSTTTBCTTTCSBCSSEEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCTTSSEECH
T ss_pred             CcHhhCCcCccCcccCCeECCCCCEEchHHHHHHHHcCCCCCCCCCCCChhhceECH
Confidence            456889999999999999999999999999999998888999999999988877653

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

Probab=99.35  E-value=5.9e-13  Score=96.78  Aligned_cols=55  Identities=25%  Similarity=0.724  Sum_probs=47.0

Q ss_pred             CCCCccccccCCCCCCceEec-ccCccchhHHHHHHhcC--CCCCCCCccc-cCCCcee
Q 027652          159 AAPTFSCPICMGPLSEATSTK-CGHIFCKDCIKGAIAAQ--GKCPNCRQKV-GKRGIFR  213 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~-CgH~fC~~Ci~~~l~~~--~~CP~Cr~~v-~~~~l~~  213 (220)
                      ..+.+.|+||++.+.+|++++ |||+||..||..|+...  ..||+||..+ ...++..
T Consensus        10 ~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~~~~~   68 (92)
T 3ztg_A           10 IPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDALIA   68 (92)
T ss_dssp             CCTTTEETTTTEECSSCEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSCCTTSCEE
T ss_pred             CCcCCCCCCCChhhcCceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCCCccccCc
Confidence            567889999999999999999 99999999999998754  4899999997 4445544

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

Probab=99.35  E-value=1.2e-12  Score=93.08  Aligned_cols=49  Identities=33%  Similarity=0.718  Sum_probs=45.5

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCcccc
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      ....+.|+||++.+.+|+.++|||+||..||.+|+.....||+||+.+.
T Consensus        12 ~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           12 EEIPFRCFICRQAFQNPVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCCSBCSSSCSBCCSEEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCCcCCCchhcCeeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            4567899999999999999999999999999999998889999999986

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

Probab=99.35  E-value=6.1e-13  Score=91.13  Aligned_cols=50  Identities=44%  Similarity=1.097  Sum_probs=45.2

Q ss_pred             CCCCccccccCCCCCCc-------eEecccCccchhHHHHHHhcCCCCCCCCccccC
Q 027652          159 AAPTFSCPICMGPLSEA-------TSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGK  208 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~p-------v~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~  208 (220)
                      ..+.+.|+||++.+.++       +.++|||+||..||.+|+.....||+||+.+..
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           12 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             TTCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            45678999999999887       888999999999999999998899999998864

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

Probab=99.31  E-value=2.6e-12  Score=90.55  Aligned_cols=56  Identities=21%  Similarity=0.600  Sum_probs=47.9

Q ss_pred             CCCCccccccCCCCCCc---eEecccCccchhHHHHHHhcCCCCCCCCccccCCCceee
Q 027652          159 AAPTFSCPICMGPLSEA---TSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRV  214 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~p---v~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~i  214 (220)
                      ......|+||++.+..+   +.++|||.||..||.+|+.....||+||+.+...++...
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   70 (78)
T 2ect_A           12 VGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATN   70 (78)
T ss_dssp             SSSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCCCSCSCCC
T ss_pred             CCCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccCCcccCCC
Confidence            45677999999988765   456999999999999999988899999999988776653

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

Probab=99.30  E-value=9.4e-13  Score=100.83  Aligned_cols=59  Identities=39%  Similarity=1.005  Sum_probs=54.5

Q ss_pred             CCCccccccCCCCCCc-------eEecccCccchhHHHHHHhcCCCCCCCCccccCCCceeecCCC
Q 027652          160 APTFSCPICMGPLSEA-------TSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPT  218 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~p-------v~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iylp~  218 (220)
                      .+.+.|+||++.+.++       +.++|||+||..||.+|++....||+||+.+..+++.++|+.+
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l~~l~i~~   70 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYIGS   70 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCEEECBCSS
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCccccccccccCC
Confidence            4567999999999988       8999999999999999999888999999999999999998864

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

Probab=99.29  E-value=9.2e-13  Score=91.02  Aligned_cols=56  Identities=25%  Similarity=0.501  Sum_probs=48.4

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCccccCCCceeec
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVY  215 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iy  215 (220)
                      ..+.+.|+||++.+.+ +.++|||.||..|+.+|+.....||+||+.+...+...++
T Consensus        12 ~~~~~~C~IC~~~~~~-~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~   67 (70)
T 2ecn_A           12 LTDEEECCICMDGRAD-LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANESSGP   67 (70)
T ss_dssp             CCCCCCCSSSCCSCCS-EEETTTEEECHHHHHHSSCCCSSCHHHHHCTTCCCCCCCC
T ss_pred             CCCCCCCeeCCcCccC-cccCCCCcccHHHHHHHHHCcCcCCCcCCcccCCCccccC
Confidence            4556799999999999 8999999999999999998888999999999866554443

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

Probab=99.29  E-value=9.9e-13  Score=102.95  Aligned_cols=47  Identities=32%  Similarity=0.770  Sum_probs=43.9

Q ss_pred             CccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCccccC
Q 027652          162 TFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGK  208 (220)
Q Consensus       162 ~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~  208 (220)
                      .+.|+||++.+.+|++++|||+||..||..|+.....||+||+.+..
T Consensus        53 ~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           53 ELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKS   99 (138)
T ss_dssp             HSBCTTTCSBCSSEEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCC
T ss_pred             cCCCcccCcccCCceECCCCCCccHHHHHHHHHcCCcCCCCCCcCCC
Confidence            45799999999999999999999999999999988899999999864

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

Probab=99.29  E-value=1.4e-12  Score=96.23  Aligned_cols=54  Identities=24%  Similarity=0.605  Sum_probs=48.6

Q ss_pred             CCccccccCCCCCCceEe-cccCccchhHHHHHHhcCCCCCCCCccccCCCceee
Q 027652          161 PTFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRV  214 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~i  214 (220)
                      +.+.|+||++.+.+|+.+ +|||+||..|+.+|+.....||+||..+...++.+.
T Consensus        21 ~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~l~~n   75 (99)
T 2y43_A           21 DLLRCGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLKNN   75 (99)
T ss_dssp             HHTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCEEC
T ss_pred             CCCCcccCChhhCCcCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCChhhCCcC
Confidence            467999999999999988 899999999999999988899999999987666654

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

Probab=99.28  E-value=5.4e-12  Score=85.43  Aligned_cols=44  Identities=36%  Similarity=0.828  Sum_probs=39.9

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhc---CCCCCCC
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAA---QGKCPNC  202 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~---~~~CP~C  202 (220)
                      ..+.+.|+||++.+.+|+.++|||+||..||.+|+..   ...||+|
T Consensus        17 ~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           17 LQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCBCTTTCSBCSSCEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             CccCCCCCcCCchhCCeEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            5677899999999999999999999999999999983   4589998

>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=99.27  E-value=2e-12  Score=99.25  Aligned_cols=48  Identities=38%  Similarity=0.841  Sum_probs=43.6

Q ss_pred             CCccccccCCCCCCceEecccCccchhHHHHHHhcCC-CCCCCCccccC
Q 027652          161 PTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG-KCPNCRQKVGK  208 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~-~CP~Cr~~v~~  208 (220)
                      +.+.|+||++.+.+|++++|||+||..||..|+.... .||+||..+..
T Consensus        51 ~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           51 ETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHTBCTTTSSBCSSEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             cCCCCCcCChHHcCcEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            4568999999999999999999999999999998544 89999999976

>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=99.26  E-value=3.3e-12  Score=95.67  Aligned_cols=55  Identities=36%  Similarity=0.861  Sum_probs=48.3

Q ss_pred             CCccccccCCCCCCceEecccCccchhHHHHHHhcCC---CCCCCCccccCCCceeec
Q 027652          161 PTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG---KCPNCRQKVGKRGIFRVY  215 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~---~CP~Cr~~v~~~~l~~iy  215 (220)
                      +.+.|+||++.+.+|+.++|||+||..|+..|+....   .||+||..+...++...+
T Consensus        20 ~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~~~~~   77 (112)
T 1jm7_A           20 KILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQEST   77 (112)
T ss_dssp             HHTSCSSSCCCCSSCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBCCC
T ss_pred             CCCCCcccChhhcCeEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhhcCccH
Confidence            3458999999999999999999999999999998653   899999999987776654

>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=99.26  E-value=2.6e-12  Score=96.26  Aligned_cols=50  Identities=36%  Similarity=0.786  Sum_probs=46.1

Q ss_pred             CCCccccccCCCCCCceEe-cccCccchhHHHHHHhcCCCCCCCCccccCC
Q 027652          160 APTFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAAQGKCPNCRQKVGKR  209 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~  209 (220)
                      .+.+.|+||++.+.+|+.+ +|||+||..||..|+.....||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           13 NPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GGGTBCTTTSSBCSSEEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             CCcCCCccCChHHhCcCEeCCCCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            4567999999999999998 9999999999999999888999999998864

>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=99.25  E-value=3.6e-12  Score=87.35  Aligned_cols=57  Identities=32%  Similarity=0.621  Sum_probs=50.8

Q ss_pred             CCCCccccccCCCCCCceEe--cccCc-cchhHHHHHHhcCCCCCCCCccccCCCceeecCC
Q 027652          159 AAPTFSCPICMGPLSEATST--KCGHI-FCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLP  217 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l--~CgH~-fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iylp  217 (220)
                      ..++..|+||++.+.+++.+  +|||. ||..|+.+|......||+||+++.  .++++|+|
T Consensus         5 ~~~~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~--~~i~i~~~   64 (64)
T 2vje_A            5 LNAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQ--MIVLTYFP   64 (64)
T ss_dssp             CGGGSCCTTTSSSCSCEEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCC--EEEEEECC
T ss_pred             CCCcCCCCcCCCCCCCEEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchh--ceEeeecC
Confidence            34566899999999999987  99999 899999999988889999999986  68999985

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

Probab=99.24  E-value=2e-12  Score=98.93  Aligned_cols=57  Identities=40%  Similarity=1.041  Sum_probs=52.7

Q ss_pred             CCCccccccCCCCCCc-------eEecccCccchhHHHHHHhcCCCCCCCCccccCCCceeecC
Q 027652          160 APTFSCPICMGPLSEA-------TSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL  216 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~p-------v~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iyl  216 (220)
                      .+...|+||++.+.++       +.++|||+||..|+.+|+.....||+||..+..++++++||
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~  133 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI  133 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGGGEEEECC
T ss_pred             CCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChhcceeeeC
Confidence            4566899999998876       88899999999999999999999999999999999999997

>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=99.24  E-value=6e-12  Score=82.67  Aligned_cols=48  Identities=25%  Similarity=0.710  Sum_probs=42.2

Q ss_pred             CCCccccccCCCCCC----ceEecccCccchhHHHHHHhcCCCCCCCCcccc
Q 027652          160 APTFSCPICMGPLSE----ATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~----pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      .....|+||++.+.+    ++.++|||.||..|+.+|+.....||+||+.+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            3 SGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             SCCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            345689999999865    678899999999999999998899999998874

>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=99.24  E-value=3.4e-12  Score=97.22  Aligned_cols=56  Identities=39%  Similarity=0.836  Sum_probs=49.5

Q ss_pred             CCCCCccccccCCCCCCceEecccCccchhHHHHHHhcCC-CCCCCCccccCCCcee
Q 027652          158 AAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG-KCPNCRQKVGKRGIFR  213 (220)
Q Consensus       158 ~~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~-~CP~Cr~~v~~~~l~~  213 (220)
                      ...+.+.|+||++.+.+|+.++|||+||..||.+|+.... .||+||..+...++++
T Consensus        14 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~   70 (118)
T 3hct_A           14 PLESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFP   70 (118)
T ss_dssp             CCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGCEE
T ss_pred             CCCCCCCCCcCChhhcCeEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHHhccc
Confidence            3567789999999999999999999999999999998765 9999999998766654

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

Probab=99.23  E-value=8.1e-12  Score=85.62  Aligned_cols=47  Identities=34%  Similarity=0.694  Sum_probs=42.8

Q ss_pred             CCccccccCCCCCCc-eEecccCccchhHHHHHHhcCCCCCCCCcccc
Q 027652          161 PTFSCPICMGPLSEA-TSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       161 ~~~~CpIC~~~~~~p-v~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      ....|+||++.+.++ +.++|||.||..|+.+|+.....||+||+.+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~   51 (68)
T 1chc_A            4 VAERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCCSSCCSCCCSCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCCeeCCccccCCcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhH
Confidence            455899999999986 77899999999999999998899999999886

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

Probab=99.22  E-value=6.5e-12  Score=82.59  Aligned_cols=48  Identities=29%  Similarity=0.725  Sum_probs=42.3

Q ss_pred             CCCccccccCCCCCC---ceEec-ccCccchhHHHHHHhcCCCCCCCCcccc
Q 027652          160 APTFSCPICMGPLSE---ATSTK-CGHIFCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~---pv~l~-CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      ++...|+||++.+.+   ++.++ |||.||..|+.+|++....||+||+.+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            456689999999887   67776 9999999999999998889999998774

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

Probab=99.21  E-value=9.6e-12  Score=87.14  Aligned_cols=49  Identities=27%  Similarity=0.645  Sum_probs=43.6

Q ss_pred             CCCccccccCCCCCCc---eEecccCccchhHHHHHHhcCCCCCCCCccccC
Q 027652          160 APTFSCPICMGPLSEA---TSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGK  208 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~p---v~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~  208 (220)
                      .+...|+||++.+..+   +.++|||.||..||.+|++....||+||+.+..
T Consensus        21 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~   72 (75)
T 1x4j_A           21 SEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGP   72 (75)
T ss_dssp             SSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCCcCcCcCCcCCC
Confidence            4567899999988876   678999999999999999999999999998864

>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=99.21  E-value=1.7e-11  Score=84.38  Aligned_cols=50  Identities=26%  Similarity=0.658  Sum_probs=43.1

Q ss_pred             CCCCccccccCCCCC---CceEecccCccchhHHHHHHhcCCCCCCCCccccC
Q 027652          159 AAPTFSCPICMGPLS---EATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGK  208 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~---~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~  208 (220)
                      ......|+||++.+.   .++.++|||.||..||.+|+.....||+||+.+..
T Consensus        11 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   63 (69)
T 2kiz_A           11 EDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEA   63 (69)
T ss_dssp             TTCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCS
T ss_pred             CCCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccC
Confidence            445678999999875   35778999999999999999988899999998864

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

Probab=99.21  E-value=7e-12  Score=92.14  Aligned_cols=56  Identities=27%  Similarity=0.685  Sum_probs=48.1

Q ss_pred             CCCCccccccCCCCCCceEec-ccCccchhHHHHHHhcC------CCCCC--CCcc-ccCCCceee
Q 027652          159 AAPTFSCPICMGPLSEATSTK-CGHIFCKDCIKGAIAAQ------GKCPN--CRQK-VGKRGIFRV  214 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~-CgH~fC~~Ci~~~l~~~------~~CP~--Cr~~-v~~~~l~~i  214 (220)
                      ..+.+.||||++.|.+||+++ |||+||..||.+|+...      ..||+  |+.. +...+|++.
T Consensus         4 ~~~~~~CPI~~~~~~dPV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~~~L~pn   69 (94)
T 2yu4_A            4 GSSGFTCPITKEEMKKPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSDLIQD   69 (94)
T ss_dssp             CSSCCBCTTTCSBCSSEEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCGGGEEEC
T ss_pred             CCcEeECcCcCchhcCCEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCHhhCcCC
Confidence            456789999999999999996 99999999999999853      48999  8877 777777654

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

Probab=99.20  E-value=1.3e-11  Score=81.81  Aligned_cols=44  Identities=36%  Similarity=0.785  Sum_probs=38.9

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHh---cCCCCCCC
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIA---AQGKCPNC  202 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~---~~~~CP~C  202 (220)
                      ..+.+.|+||++.+.+|+.++|||+||..||.+|+.   ....||+|
T Consensus        12 ~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           12 LQVEASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             SCCCCBCSSSCCBCSSCCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cccCCCCccCCcccCccEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            456789999999999999999999999999999954   45689988

>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=99.20  E-value=8.6e-12  Score=106.60  Aligned_cols=56  Identities=14%  Similarity=0.169  Sum_probs=49.5

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhcCC-CCCCCCccccCCCceee
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG-KCPNCRQKVGKRGIFRV  214 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~-~CP~Cr~~v~~~~l~~i  214 (220)
                      ..+.+.||||++.+.+||+++|||+||..||.+|+.... .||+|+.++...++++.
T Consensus       205 ~~~~~~c~i~~~~~~dPv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~l~~n  261 (281)
T 2c2l_A          205 IPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPN  261 (281)
T ss_dssp             CCSTTBCTTTCSBCSSEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEEC
T ss_pred             CCcccCCcCcCCHhcCCeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCchhcCccc
Confidence            446789999999999999999999999999999998644 59999999988777654

>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=99.20  E-value=7.8e-12  Score=99.57  Aligned_cols=49  Identities=35%  Similarity=0.845  Sum_probs=44.6

Q ss_pred             CCccccccCCCCCCceEecccCccchhHHHHHHhcCC-CCCCCCccccCC
Q 027652          161 PTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG-KCPNCRQKVGKR  209 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~-~CP~Cr~~v~~~  209 (220)
                      +.+.|+||++.+.+|++++|||+||..||..|+.... .||+||..+...
T Consensus        77 ~~~~C~IC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCSSEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhhcCCEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            4568999999999999999999999999999998654 899999999865

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

Probab=99.18  E-value=1.8e-11  Score=85.28  Aligned_cols=50  Identities=20%  Similarity=0.521  Sum_probs=43.2

Q ss_pred             CCCCccccccCCCCCCceE---ecccCccchhHHHHHHhcCCCCCCCCccccC
Q 027652          159 AAPTFSCPICMGPLSEATS---TKCGHIFCKDCIKGAIAAQGKCPNCRQKVGK  208 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~---l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~  208 (220)
                      ......|+||++.+..+..   ++|||.||..||.+|++....||+||+.+..
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2ep4_A           12 LNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQ   64 (74)
T ss_dssp             CCCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCSBCTTTCCBCSS
T ss_pred             CCCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCCcCCCcCccccc
Confidence            4556799999999876643   4999999999999999988899999999864

>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=99.17  E-value=3e-12  Score=96.87  Aligned_cols=50  Identities=32%  Similarity=0.778  Sum_probs=44.7

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhc-CCCCCCCCccccC
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAA-QGKCPNCRQKVGK  208 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~-~~~CP~Cr~~v~~  208 (220)
                      ..+.+.|+||++.+.+|+.++|||+||..||.+|+.. ...||+||..+..
T Consensus        12 ~~~~~~C~iC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           12 SLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             CHHHHBCTTTCSBCSSCEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCCCccCCcccCceeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            4567899999999999999999999999999999875 5589999998863

>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=99.17  E-value=1.2e-11  Score=93.73  Aligned_cols=54  Identities=30%  Similarity=0.691  Sum_probs=47.9

Q ss_pred             CCCccccccCCCCCCceEecccCccchhHHHHHHhc-CCCCCCCCccccCCCcee
Q 027652          160 APTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAA-QGKCPNCRQKVGKRGIFR  213 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~-~~~CP~Cr~~v~~~~l~~  213 (220)
                      .+.+.|+||++.+.+|+.++|||+||..||.+|+.. ...||+||..+...++..
T Consensus        21 ~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~   75 (116)
T 1rmd_A           21 VKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLES   75 (116)
T ss_dssp             HHHTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCBC
T ss_pred             cCCCCCCCCCcHhcCcEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhhccc
Confidence            346799999999999999999999999999999987 668999999998766543

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

Probab=99.16  E-value=1.5e-11  Score=89.68  Aligned_cols=49  Identities=33%  Similarity=0.717  Sum_probs=43.4

Q ss_pred             CCCccccccCCCCCC---ceEecccCccchhHHHHHHhcCCCCCCCCccccC
Q 027652          160 APTFSCPICMGPLSE---ATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGK  208 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~---pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~  208 (220)
                      .+...|+||++.+..   ++.++|||.||..||.+|+.....||+||+.+..
T Consensus        38 ~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           38 GQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFPP   89 (91)
T ss_dssp             SSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTCBCTTTCCBSSC
T ss_pred             CCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCCcCcCcCccCCC
Confidence            456789999998876   6778999999999999999988899999998864

>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=99.15  E-value=7.4e-12  Score=95.21  Aligned_cols=53  Identities=26%  Similarity=0.624  Sum_probs=46.5

Q ss_pred             CCCccccccCCCCCCceEe-cccCccchhHHHHHHhcCCCCCCCCccccCCCceee
Q 027652          160 APTFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRV  214 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~i  214 (220)
                      .+.+.|+||++.+.+|+.+ +|||+||..||..|+.  ..||+||..+...++...
T Consensus        20 ~~~~~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~~~~n   73 (117)
T 1jm7_B           20 EKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLKIN   73 (117)
T ss_dssp             HHTTSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCCCC
T ss_pred             hhCCCCCCCChHhhCccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCcccccccc
Confidence            3567999999999999999 9999999999999986  789999999977666543

>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=99.13  E-value=2.5e-11  Score=97.37  Aligned_cols=50  Identities=38%  Similarity=0.903  Sum_probs=44.8

Q ss_pred             CCCCccccccCCCCCCceEe-cccCccchhHHHHHHhc-CCCCCCCCccccC
Q 027652          159 AAPTFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAA-QGKCPNCRQKVGK  208 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~-~~~CP~Cr~~v~~  208 (220)
                      ..+.+.|+||++.+.+|+.+ +|||+||..||.+|+.. ...||+||..+..
T Consensus        51 ~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           51 LHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             CHHHHBCTTTSSBCSSEEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCCCcccChHhhCcCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            34567999999999999988 99999999999999986 6689999999864

>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=99.12  E-value=2.4e-11  Score=82.99  Aligned_cols=55  Identities=20%  Similarity=0.594  Sum_probs=48.4

Q ss_pred             CCCccccccCCCCCCceEe--cccCc-cchhHHHHHHhcCCCCCCCCccccCCCceeecC
Q 027652          160 APTFSCPICMGPLSEATST--KCGHI-FCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL  216 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l--~CgH~-fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iyl  216 (220)
                      .....|+||++.+.+++.+  +|||. ||..|+.++......||+||+++.  .++++|+
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~--~~i~i~~   62 (63)
T 2vje_B            5 NLLKPCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQ--LVIKVFI   62 (63)
T ss_dssp             GGGSBCTTTSSSBSCEEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCC--EEEEEEE
T ss_pred             CcCCCCcccCCcCCCeEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhh--ceEEEec
Confidence            3455899999999999888  99998 999999999888889999999986  6888885

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

Probab=99.12  E-value=3.2e-11  Score=98.86  Aligned_cols=57  Identities=14%  Similarity=0.153  Sum_probs=50.4

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhcCC-CCCCCCccccCCCceeec
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG-KCPNCRQKVGKRGIFRVY  215 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~-~CP~Cr~~v~~~~l~~iy  215 (220)
                      ..+.+.||||++++.+||+++|||+||..||..|+.... .||+|+.++...++++.+
T Consensus       103 ip~~f~CPI~~elm~DPV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~L~pN~  160 (179)
T 2f42_A          103 IPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPNL  160 (179)
T ss_dssp             CCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEECH
T ss_pred             CcHhhcccCccccCCCCeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChhhCcchH
Confidence            356789999999999999999999999999999998643 699999999987877653

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

Probab=99.11  E-value=1.4e-11  Score=86.66  Aligned_cols=50  Identities=28%  Similarity=0.644  Sum_probs=44.2

Q ss_pred             CCccccccCCCCCCceEecccCc-cchhHHHHHHhcCCCCCCCCccccCCCceeecC
Q 027652          161 PTFSCPICMGPLSEATSTKCGHI-FCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL  216 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l~CgH~-fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iyl  216 (220)
                      +.+.|+||++.+.+++.++|||. ||..|+..|    ..||+||+.+.  ..+++|+
T Consensus        23 ~~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~--~~~~i~~   73 (74)
T 4ic3_A           23 EEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVIT--FKQKILM   73 (74)
T ss_dssp             HHTBCTTTSSSBCCEEEETTCCBCCCHHHHTTC----SBCTTTCCBCS--EEEECBC
T ss_pred             cCCCCCCCCCCCCCEEEcCCCChhHHHHhhhcC----ccCCCcCcCcc--CcEEEee
Confidence            45689999999999999999999 999998876    78999999987  4677776

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

Probab=99.11  E-value=1.7e-11  Score=81.56  Aligned_cols=46  Identities=20%  Similarity=0.521  Sum_probs=40.6

Q ss_pred             CCCccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCccccC
Q 027652          160 APTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGK  208 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~  208 (220)
                      .+.+.|+||++.+.+|+.++|||+||..|+..   ....||+||+.+..
T Consensus         4 ~~~~~C~IC~~~~~~p~~l~CgH~fC~~Ci~~---~~~~CP~Cr~~~~~   49 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEA---SGMQCPICQAPWPL   49 (56)
T ss_dssp             CCCSSCSSSCSSCBCCSCSTTSCCSBTTTCSS---SSSSCSSCCSSSSC
T ss_pred             ccCCCceEeCCccCCeEEcCCCCcccHHHHcc---CCCCCCcCCcEeec
Confidence            46678999999999999999999999999876   35689999998864

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

Probab=99.10  E-value=8.9e-11  Score=83.66  Aligned_cols=56  Identities=27%  Similarity=0.651  Sum_probs=44.2

Q ss_pred             CCCCccccccCCCCC--CceEec--ccCccchhHHHHHHhc-CCCCCCCCccccCCCceee
Q 027652          159 AAPTFSCPICMGPLS--EATSTK--CGHIFCKDCIKGAIAA-QGKCPNCRQKVGKRGIFRV  214 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~--~pv~l~--CgH~fC~~Ci~~~l~~-~~~CP~Cr~~v~~~~l~~i  214 (220)
                      ..+.+.||||++.+.  +++.++  |||.||..|+.++... ...||.||+.+....+...
T Consensus         8 ~~~~~~CpICle~~~~~d~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~~~~   68 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAVYK   68 (78)
T ss_dssp             CCCCCBCTTTCCBCCTTTTTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSSCCC
T ss_pred             cccCCcCCccCccCccccccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCchhhc
Confidence            456789999999774  345555  9999999999988753 4589999999987766543

>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=99.08  E-value=5.8e-11  Score=80.81  Aligned_cols=56  Identities=16%  Similarity=0.215  Sum_probs=51.8

Q ss_pred             CccccccCCCCCCceEe-cccCccchhHHHHHHhcCCCCCCCCccccCCCceeecCC
Q 027652          162 TFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLP  217 (220)
Q Consensus       162 ~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iylp  217 (220)
                      .+.||||++.+.+|+.+ +|||+|++.||.+|+.....||++++++..++|+++...
T Consensus         3 ~~~CpIs~~~m~dPV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~Lip~~~~   59 (61)
T 2bay_A            3 HMLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEIVPS   59 (61)
T ss_dssp             -CCCTTTCSCCSSEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCEECCCC
T ss_pred             eEEecCCCCCCCCCEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhhcEECccC
Confidence            47899999999999999 999999999999999988889999999999999998754

>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=99.07  E-value=6.2e-11  Score=89.23  Aligned_cols=47  Identities=34%  Similarity=0.706  Sum_probs=39.4

Q ss_pred             CccccccCCCCCCce------------------EecccCccchhHHHHHHh-----cCCCCCCCCccccC
Q 027652          162 TFSCPICMGPLSEAT------------------STKCGHIFCKDCIKGAIA-----AQGKCPNCRQKVGK  208 (220)
Q Consensus       162 ~~~CpIC~~~~~~pv------------------~l~CgH~fC~~Ci~~~l~-----~~~~CP~Cr~~v~~  208 (220)
                      +..|+||++.+..+.                  .++|||.||..||.+|+.     ....||+||..+..
T Consensus        25 ~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~   94 (114)
T 1v87_A           25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGE   94 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSS
T ss_pred             CCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCC
Confidence            358999999986653                  679999999999999994     45689999998864

>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=99.07  E-value=5.8e-11  Score=95.63  Aligned_cols=55  Identities=40%  Similarity=0.850  Sum_probs=48.9

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhcCC-CCCCCCccccCCCcee
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG-KCPNCRQKVGKRGIFR  213 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~-~CP~Cr~~v~~~~l~~  213 (220)
                      ..+.+.|+||++.+.+|+.++|||+||..||.+|+.... .||+||..+...++++
T Consensus        15 ~~~~~~C~IC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~   70 (170)
T 3hcs_A           15 LESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFP   70 (170)
T ss_dssp             CCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGCEE
T ss_pred             CCCCCCCCCCChhhcCcEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchhhhhh
Confidence            567889999999999999999999999999999998644 9999999998766554

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

Probab=99.07  E-value=2.6e-11  Score=95.59  Aligned_cols=49  Identities=20%  Similarity=0.630  Sum_probs=44.4

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhcCC-CCCCCCcccc
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG-KCPNCRQKVG  207 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~-~CP~Cr~~v~  207 (220)
                      ..+.+.|+||++.+.+|+.++|||+||..||.+|+.... .||+||.++.
T Consensus        28 l~~~~~C~IC~~~~~~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~   77 (141)
T 3knv_A           28 LEAKYLCSACRNVLRRPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGI   77 (141)
T ss_dssp             CCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHGGGSCEECHHHHHTTC
T ss_pred             CCcCcCCCCCChhhcCcEECCCCCccCHHHHHHHHhcCCCCCCCCCCccc
Confidence            467889999999999999999999999999999998665 8999999764

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

Probab=99.06  E-value=1.5e-10  Score=82.70  Aligned_cols=52  Identities=23%  Similarity=0.508  Sum_probs=43.0

Q ss_pred             CCCccccccCCCCCC--------------ceEe-cccCccchhHHHHHHhcCCCCCCCCccccCCCc
Q 027652          160 APTFSCPICMGPLSE--------------ATST-KCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGI  211 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~--------------pv~l-~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l  211 (220)
                      .++..|+||++.+.+              ++.+ +|||.||..||.+|+.....||+||+.+...++
T Consensus        13 ~~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~~   79 (81)
T 2ecl_A           13 VECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRI   79 (81)
T ss_dssp             CCCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEEEE
T ss_pred             CCCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchhhc
Confidence            345679999998866              4455 599999999999999998999999999875543

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

Probab=99.02  E-value=9.2e-11  Score=82.43  Aligned_cols=50  Identities=28%  Similarity=0.680  Sum_probs=42.9

Q ss_pred             CCccccccCCCCCCceEecccCc-cchhHHHHHHhcCCCCCCCCccccCCCceeecC
Q 027652          161 PTFSCPICMGPLSEATSTKCGHI-FCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL  216 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l~CgH~-fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iyl  216 (220)
                      +...|+||++.+.+++.++|||. ||..|+.+    ...||+||+++..  .+++|+
T Consensus        24 ~~~~C~IC~~~~~~~~~~pCgH~~~C~~C~~~----~~~CP~Cr~~i~~--~~~i~~   74 (75)
T 2ecg_A           24 EEKLCKICMDRNIAIVFVPCGHLVTCKQCAEA----VDKCPMCYTVITF--KQKIFM   74 (75)
T ss_dssp             HHHSCSSSCSSCCCBCCSSSCCCCBCHHHHHH----CSBCTTTCCBCCC--CCBCCC
T ss_pred             CCCCCCcCCCCCCCEEEecCCCHHHHHHHhhC----CCCCccCCceecC--cEEEec
Confidence            35689999999999999999999 99999853    4789999999874  567775

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

Probab=99.01  E-value=5.5e-10  Score=77.39  Aligned_cols=54  Identities=28%  Similarity=0.592  Sum_probs=46.7

Q ss_pred             CCCCccccccCCCCCCceEecccCc-cchhHHHHHHhcCCCCCCCCccccCCCceeecCCC
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHI-FCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPT  218 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~-fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iylp~  218 (220)
                      ..+...|+||++...+++.++|||. ||..|+..    ...||+||+.+.  ..+++|.|.
T Consensus        12 ~~~~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~----~~~CP~CR~~i~--~~~~i~~~~   66 (68)
T 2ea5_A           12 EENSKDCVVCQNGTVNWVLLPCRHTCLCDGCVKY----FQQCPMCRQFVQ--ESFALSGPS   66 (68)
T ss_dssp             CCCSSCCSSSSSSCCCCEETTTTBCCSCTTHHHH----CSSCTTTCCCCC--CEECCCSSC
T ss_pred             CCCCCCCCCcCcCCCCEEEECCCChhhhHHHHhc----CCCCCCCCcchh--ceEEeecCC
Confidence            3456789999999999999999999 99999873    478999999887  478888875

>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=98.97  E-value=1.8e-10  Score=82.17  Aligned_cols=52  Identities=35%  Similarity=0.797  Sum_probs=45.4

Q ss_pred             CccccccCCCCCCceEecccCc-cchhHHHHHHhcCCCCCCCCccccCCCceeecCCCC
Q 027652          162 TFSCPICMGPLSEATSTKCGHI-FCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYLPTL  219 (220)
Q Consensus       162 ~~~CpIC~~~~~~pv~l~CgH~-fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iylp~~  219 (220)
                      ...|+||++.+.+++.++|||. ||..|+..+    ..||+||..+..  .+++|+|..
T Consensus        18 ~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~--~~~i~~p~~   70 (79)
T 2yho_A           18 AMLCMVCCEEEINSTFCPCGHTVCCESCAAQL----QSCPVCRSRVEH--VQHVYLPTH   70 (79)
T ss_dssp             HTBCTTTSSSBCCEEEETTCBCCBCHHHHTTC----SBCTTTCCBCCE--EEECBCTTC
T ss_pred             CCEeEEeCcccCcEEEECCCCHHHHHHHHHhc----CcCCCCCchhhC--eEEEEeCcc
Confidence            4589999999999999999999 999998754    499999999884  688898853

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

Probab=98.93  E-value=3.6e-10  Score=102.56  Aligned_cols=50  Identities=24%  Similarity=0.592  Sum_probs=45.0

Q ss_pred             CccccccCCCCCCceEecccCccchhHHHHHHh-cCCCCCCCCccccCCCc
Q 027652          162 TFSCPICMGPLSEATSTKCGHIFCKDCIKGAIA-AQGKCPNCRQKVGKRGI  211 (220)
Q Consensus       162 ~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~-~~~~CP~Cr~~v~~~~l  211 (220)
                      ...|+||++.+.+++.++|||.||..|+..|+. ....||+||..+....+
T Consensus       332 ~~~C~ICle~~~~pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~~~  382 (389)
T 2y1n_A          332 FQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP  382 (389)
T ss_dssp             SSBCTTTSSSBCCEEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEEEE
T ss_pred             CCCCCccCcCCCCeEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCcee
Confidence            369999999999999999999999999999998 57799999999986443

>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=98.88  E-value=9e-10  Score=82.88  Aligned_cols=47  Identities=21%  Similarity=0.431  Sum_probs=40.3

Q ss_pred             CccccccCCCCCCc------------------eEecccCccchhHHHHHHhcCCCCCCCCccccC
Q 027652          162 TFSCPICMGPLSEA------------------TSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGK  208 (220)
Q Consensus       162 ~~~CpIC~~~~~~p------------------v~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~  208 (220)
                      ...|+||++.+.++                  +.++|||.||..||.+|+.....||+||+.+..
T Consensus        37 ~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~~  101 (106)
T 3dpl_R           37 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEF  101 (106)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCCE
T ss_pred             CCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcCCcCcCCCCccee
Confidence            44799999988754                  446999999999999999998999999998753

>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=98.85  E-value=9e-10  Score=94.96  Aligned_cols=56  Identities=30%  Similarity=0.644  Sum_probs=48.7

Q ss_pred             CCCCccccccCCCCCCceEe-cccCccchhHHHHHHhcC--CCCCC--CCccccCCCceee
Q 027652          159 AAPTFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAAQ--GKCPN--CRQKVGKRGIFRV  214 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~~--~~CP~--Cr~~v~~~~l~~i  214 (220)
                      ....+.||||+..+.+||+. .|||+||+.||..|+...  ..||+  |++.+...+|...
T Consensus       178 ~~~el~CPIcl~~f~DPVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL~pN  238 (267)
T 3htk_C          178 GKIELTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFVRD  238 (267)
T ss_dssp             SBCCSBCTTTSSBCSSEEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGEEEC
T ss_pred             CceeeECcCccCcccCCeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhCCcC
Confidence            45678999999999999985 999999999999998754  37999  9999988877653

>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=98.71  E-value=2.7e-09  Score=95.64  Aligned_cols=50  Identities=32%  Similarity=0.833  Sum_probs=43.6

Q ss_pred             CCccccccCCCCCCceEecccCc-cchhHHHHHHhcCCCCCCCCccccCCCceeecC
Q 027652          161 PTFSCPICMGPLSEATSTKCGHI-FCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL  216 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l~CgH~-fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iyl  216 (220)
                      +...|+||++.+.+++.++|||. ||..|+..|    ..||+||.++.  ..+++|+
T Consensus       294 ~~~~C~IC~~~~~~~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~--~~~~i~~  344 (345)
T 3t6p_A          294 EERTCKVCMDKEVSVVFIPCGHLVVCQECAPSL----RKCPICRGIIK--GTVRTFL  344 (345)
T ss_dssp             TTCBCTTTSSSBCCEEEETTCCEEECTTTGGGC----SBCTTTCCBCC--EEEECC-
T ss_pred             CCCCCCccCCcCCceEEcCCCChhHhHHHHhcC----CcCCCCCCCcc--CeEEeec
Confidence            46799999999999999999999 999998865    78999999987  4567775

>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=98.63  E-value=4.5e-09  Score=80.48  Aligned_cols=47  Identities=21%  Similarity=0.441  Sum_probs=0.0

Q ss_pred             ccccccCCCCCCc------------------eEecccCccchhHHHHHHhcCCCCCCCCccccCC
Q 027652          163 FSCPICMGPLSEA------------------TSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKR  209 (220)
Q Consensus       163 ~~CpIC~~~~~~p------------------v~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~  209 (220)
                      ..|+||++.+.++                  +.++|+|.||..||.+|+.....||+||+.+...
T Consensus        49 d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~~~  113 (117)
T 4a0k_B           49 DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQ  113 (117)
T ss_dssp             -----------------------------------------------------------------
T ss_pred             CcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeeeee
Confidence            4799999988653                  2248999999999999999988999999987543

>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=98.63  E-value=4.5e-09  Score=76.65  Aligned_cols=54  Identities=26%  Similarity=0.664  Sum_probs=42.3

Q ss_pred             CCCccccccCCCCCCceEe---cccCccchhHHHHHHhc--------CCCCCC--CCcc--ccCCCcee
Q 027652          160 APTFSCPICMGPLSEATST---KCGHIFCKDCIKGAIAA--------QGKCPN--CRQK--VGKRGIFR  213 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l---~CgH~fC~~Ci~~~l~~--------~~~CP~--Cr~~--v~~~~l~~  213 (220)
                      .+.+.|+||++.+..+..+   +|||.||..|+..++..        ...||.  |+..  +....+..
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~~~i~~   71 (94)
T 1wim_A            3 SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQENEIEC   71 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECHHHHHH
T ss_pred             CCCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCHHHHHH
Confidence            3467899999998887554   69999999999999873        137999  9998  66554443

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

Probab=98.53  E-value=8.5e-08  Score=68.45  Aligned_cols=50  Identities=20%  Similarity=0.392  Sum_probs=41.1

Q ss_pred             CCCccccccCCCCC--CceEeccc-----CccchhHHHHHHhcC--CCCCCCCccccCC
Q 027652          160 APTFSCPICMGPLS--EATSTKCG-----HIFCKDCIKGAIAAQ--GKCPNCRQKVGKR  209 (220)
Q Consensus       160 ~~~~~CpIC~~~~~--~pv~l~Cg-----H~fC~~Ci~~~l~~~--~~CP~Cr~~v~~~  209 (220)
                      .+...|.||++.+.  ++..++|.     |.|+..||.+|+...  ..||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~~~~l~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~   71 (80)
T 2d8s_A           13 SSQDICRICHCEGDDESPLITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIME   71 (80)
T ss_dssp             TTSCCCSSSCCCCCSSSCEECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCC
T ss_pred             CCCCCCeEcCccccCCCeeEeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecC
Confidence            34558999998764  56778996     999999999999865  4899999998743

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

Probab=98.27  E-value=1.4e-06  Score=61.24  Aligned_cols=48  Identities=23%  Similarity=0.531  Sum_probs=40.3

Q ss_pred             CCCccccccCCCCCCceEe-cccCccchhHHHHHHhcC--CCCCCCCcccc
Q 027652          160 APTFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAAQ--GKCPNCRQKVG  207 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~~--~~CP~Cr~~v~  207 (220)
                      +....|+||+..+.....- .|+|.|+..||.+|++..  ..||+|+..+.
T Consensus        13 ~~i~~C~IC~~~i~~g~~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~   63 (74)
T 2ct0_A           13 DAVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWP   63 (74)
T ss_dssp             SSSCBCSSSCCBCSSSEECSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCC
T ss_pred             CCCCcCcchhhHcccCCccCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCC
Confidence            3456899999988755444 899999999999999876  78999998876

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

Probab=97.86  E-value=8.3e-06  Score=60.27  Aligned_cols=45  Identities=29%  Similarity=0.654  Sum_probs=37.4

Q ss_pred             cccccCCCCCCc-eEecccCccchhHHHHHHhc-CCCCCCCCccccC
Q 027652          164 SCPICMGPLSEA-TSTKCGHIFCKDCIKGAIAA-QGKCPNCRQKVGK  208 (220)
Q Consensus       164 ~CpIC~~~~~~p-v~l~CgH~fC~~Ci~~~l~~-~~~CP~Cr~~v~~  208 (220)
                      .|++|.-++..- ..+||+|+||+.|+..|.+. .+.||.|+.++..
T Consensus         3 fC~~C~~Pi~iygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~r   49 (101)
T 3vk6_A            3 FCDKCGLPIKVYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQR   49 (101)
T ss_dssp             BCTTTCSBCSEEEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCSE
T ss_pred             ecCccCCCeEEEeeeccccccHHHHHHHHHHhccCCCCcCcCCeeee
Confidence            689998877754 45699999999999998754 6789999999873

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

Probab=97.74  E-value=8.1e-06  Score=72.90  Aligned_cols=49  Identities=22%  Similarity=0.553  Sum_probs=38.8

Q ss_pred             CCCccccccCCCCCC----ce----EecccCccchhHHHHHHhcC-----------CCCCCCCccccC
Q 027652          160 APTFSCPICMGPLSE----AT----STKCGHIFCKDCIKGAIAAQ-----------GKCPNCRQKVGK  208 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~----pv----~l~CgH~fC~~Ci~~~l~~~-----------~~CP~Cr~~v~~  208 (220)
                      +....|+||+..+.+    |.    ...|||.|+..|+.+|++..           ..||.|+.+++.
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~  373 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLST  373 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCc
Confidence            456789999998776    21    23799999999999999742           369999998864

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

Probab=97.72  E-value=2.6e-05  Score=52.40  Aligned_cols=49  Identities=18%  Similarity=0.391  Sum_probs=38.7

Q ss_pred             CCCccccccCCCCCCceEeccc--C---ccchhHHHHHHhc--CCCCCCCCccccC
Q 027652          160 APTFSCPICMGPLSEATSTKCG--H---IFCKDCIKGAIAA--QGKCPNCRQKVGK  208 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l~Cg--H---~fC~~Ci~~~l~~--~~~CP~Cr~~v~~  208 (220)
                      ++...|.||++...++..+||.  +   .|+..|+.+|+..  ...||+|+..+..
T Consensus         4 ~~~~~CrIC~~~~~~~l~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCEeEEeecCCCCceecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            3445899999876666667854  4   7999999999975  4689999998764

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

Probab=96.40  E-value=0.0025  Score=53.95  Aligned_cols=47  Identities=23%  Similarity=0.561  Sum_probs=38.6

Q ss_pred             CccccccCCCCCCceEe-cccCccchhHHHHHHhcCC--CCCCCCccccC
Q 027652          162 TFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAAQG--KCPNCRQKVGK  208 (220)
Q Consensus       162 ~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~~~--~CP~Cr~~v~~  208 (220)
                      ...|.+|.+.......- .|+|.|+..|+.+|++...  .||.|+.....
T Consensus       180 i~~C~iC~~iv~~g~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~  229 (238)
T 3nw0_A          180 VKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPH  229 (238)
T ss_dssp             CCBCTTTCSBCSSCEECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCS
T ss_pred             CCcCcchhhHHhCCcccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCC
Confidence            34899999988866555 4999999999999987544  89999887654

>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=95.87  E-value=0.0053  Score=61.21  Aligned_cols=55  Identities=11%  Similarity=0.104  Sum_probs=50.1

Q ss_pred             CCCccccccCCCCCCceEeccc-CccchhHHHHHHhcCCCCCCCCccccCCCceee
Q 027652          160 APTFSCPICMGPLSEATSTKCG-HIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRV  214 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l~Cg-H~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~i  214 (220)
                      .+.|.|||-.+.+.+||+++.| ++|=..+|.+|+.....||..|.++...++++.
T Consensus       889 P~~F~cPIs~~lM~DPVilpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~liPN  944 (968)
T 3m62_A          889 PDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTPN  944 (968)
T ss_dssp             CGGGBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCEEC
T ss_pred             cHHhCCcchhhHHhCCeEcCCCCEEECHHHHHHHHhcCCCCCCCCCCCCccccccc
Confidence            4688999999999999999998 589999999999988899999999998887764

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

Probab=95.61  E-value=0.0048  Score=44.66  Aligned_cols=32  Identities=22%  Similarity=0.691  Sum_probs=26.7

Q ss_pred             CCccccccCCC-CCCceE--ecccCccchhHHHHH
Q 027652          161 PTFSCPICMGP-LSEATS--TKCGHIFCKDCIKGA  192 (220)
Q Consensus       161 ~~~~CpIC~~~-~~~pv~--l~CgH~fC~~Ci~~~  192 (220)
                      ++..|+||.+. +.+++.  +.|+|.||..|+..+
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            34689999975 677777  799999999999873

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=93.31  E-value=0.055  Score=38.29  Aligned_cols=37  Identities=30%  Similarity=0.724  Sum_probs=31.0

Q ss_pred             CCCCccccccCCCCCCceEecc----cCccchhHHHHHHhc
Q 027652          159 AAPTFSCPICMGPLSEATSTKC----GHIFCKDCIKGAIAA  195 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~C----gH~fC~~Ci~~~l~~  195 (220)
                      ....+.|.+|.+.+.+...+.|    +|.||..|-...++.
T Consensus        12 ~~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~   52 (93)
T 2cs3_A           12 NSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   52 (93)
T ss_dssp             SCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CCCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHh
Confidence            3456799999999999877766    588999999998884

>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication, ring E3, PIAS, ubiquitin, UBC9, metal-binding, nucleus; 2.60A {Saccharomyces cerevisiae}

Probab=87.49  E-value=0.45  Score=42.60  Aligned_cols=52  Identities=19%  Similarity=0.506  Sum_probs=38.1

Q ss_pred             CCccccccCCCCCCceEe-cccCccchhH--HHHHHhcC--CCCCCCCccccCCCce
Q 027652          161 PTFSCPICMGPLSEATST-KCGHIFCKDC--IKGAIAAQ--GKCPNCRQKVGKRGIF  212 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l-~CgH~fC~~C--i~~~l~~~--~~CP~Cr~~v~~~~l~  212 (220)
                      -.+.||+-...+..|+.- .|.|..|+.-  +..+....  -.||+|.+.+...+|+
T Consensus       248 vSL~CPlS~~ri~~PvRg~~C~HlQCFDl~sfL~~~~~~~~W~CPIC~k~~~~~dL~  304 (371)
T 3i2d_A          248 MSLQCPISYTRMKYPSKSINCKHLQCFDALWFLHSQLQIPTWQCPVCQIDIALENLA  304 (371)
T ss_dssp             EESBCTTTSSBCSSEEEETTCCSSCCEEHHHHHHHHHHSCCCBCTTTCCBCCGGGEE
T ss_pred             EeecCCCccccccccCcCCcCCCcceECHHHHHHHhhcCCceeCCCCCcccCHHHee
Confidence            357999999999999876 8999977664  33332222  3799999988766654

>4fo9_A E3 SUMO-protein ligase PIAS2; E3 ligase, pinit domain, SP-ring domain, structural GE consortium, SGC; 2.39A {Homo sapiens} PDB: 2asq_B

Probab=85.79  E-value=0.63  Score=41.54  Aligned_cols=52  Identities=21%  Similarity=0.456  Sum_probs=37.8

Q ss_pred             CCccccccCCCCCCceEe-cccCccchhHH--HHHHhcC--CCCCCCCccccCCCce
Q 027652          161 PTFSCPICMGPLSEATST-KCGHIFCKDCI--KGAIAAQ--GKCPNCRQKVGKRGIF  212 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci--~~~l~~~--~~CP~Cr~~v~~~~l~  212 (220)
                      -.+.||+-...+..|+.- .|.|.-|+.-.  ..+....  -.||+|.+.+...+|.
T Consensus       214 vSL~CPlS~~ri~~P~Rg~~C~HlqCFDl~sfL~~~~~~~~W~CPiC~k~~~~~dL~  270 (360)
T 4fo9_A          214 VSLMCPLGKMRLTIPCRAVTCTHLQCFDAALYLQMNEKKPTWICPVCDKKAAYESLI  270 (360)
T ss_dssp             EESBCTTTCSBCSSEEEETTCCCCCCEEHHHHHHHHHHSCCCBCTTTCSBCCGGGEE
T ss_pred             EeeeCCCccceeccCCcCCCCCCCccCCHHHHHHHHhhCCCeECCCCCcccCHHHeE
Confidence            456899999999999876 89999776542  2222222  3799999998866654

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=80.25  E-value=1  Score=33.34  Aligned_cols=50  Identities=18%  Similarity=0.371  Sum_probs=37.9

Q ss_pred             CccccccCCCCCC---ceEecccCccchhHHHHHHhcCCCCCCCCccccCCCc
Q 027652          162 TFSCPICMGPLSE---ATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGI  211 (220)
Q Consensus       162 ~~~CpIC~~~~~~---pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l  211 (220)
                      =|.|..|...+.+   .....=|..||..|..+.+....+|..|..+|....+
T Consensus        32 CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~~~~   84 (122)
T 1m3v_A           32 CLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSGGDV   84 (122)
T ss_dssp             HHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCCEES
T ss_pred             CCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCchhe
Confidence            3789999988863   3445677889999998876544589999998886443

---

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	220
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	1e-11
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	6e-11
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	1e-10
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	4e-10
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	4e-10
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	2e-08
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	4e-06
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	1e-05
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	4e-05
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	5e-05
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	7e-05
d1t1ha_	78	g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cre	9e-05
d2c2la2	80	g.44.1.2 (A:225-304) STIP1 homology and U box-cont	2e-04
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	7e-04
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	0.002
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	0.003

>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 = 56.8 bits (137), Expect = 1e-11
 Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 4/62 (6%)

Query: 149 PLQLPQDPMAAAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG-KCPNCRQKVG 207
            +  P   + +    SC IC   L++   T C H+FC+ CI   +   G  CP+CR    
Sbjct: 13  AVDFPAHFVKS---ISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCF 69

Query: 208 KR 209
             
Sbjct: 70  PT 71

>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 = 55.5 bits (133), Expect = 6e-11
 Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 3/57 (5%)

Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG---KCPNCRQKVGKRGIFRVYL 216
             CPIC+  + E  STKC HIFCK C+   +  +    +CP C+  + KR +     
Sbjct: 22  LECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTR 78

>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 = 53.4 bits (128), Expect = 1e-10
 Identities = 17/49 (34%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 159 AAPTFSCPICMGPLSE-ATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKV 206
           A     CPIC+   S  + +  C H FC  CI   I     CP C+  V
Sbjct: 2   ATVAERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPV 50

>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 = 52.3 bits (125), Expect = 4e-10
 Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 165 CPICMGPLSEATSTKCGHIFCKDCIKGAIAAQG-KCPNCRQKV 206
           C IC     +     CGH+ C  C+     ++G  CP CR ++
Sbjct: 26  CKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEI 68

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.4 bits (123), Expect = 4e-10
 Identities = 9/42 (21%), Positives = 14/42 (33%), Gaps = 3/42 (7%)

Query: 165 CPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKV 206
           C  C           C H  C  C++    +  +CP C+   
Sbjct: 9   CQQCQAEAKCPKLLPCLHTLCSGCLEA---SGMQCPICQAPW 47

>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 = 47.2 bits (112), Expect = 2e-08
 Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 4/46 (8%)

Query: 165 CPICMGPLSE----ATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKV 206
           C +C+  L +        +CGH F  +C+   + +   CP CR  V
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>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 = 41.3 bits (96), Expect = 4e-06
 Identities = 14/54 (25%), Positives = 17/54 (31%), Gaps = 6/54 (11%)

Query: 164 SCPICMGPLSEATS-----TKCGHIFCKDCIKGAIAA-QGKCPNCRQKVGKRGI 211
            CP C        S       CGH  C+ C+        G CP C   + K   
Sbjct: 5   GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNF 58

>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 = 40.1 bits (93), Expect = 1e-05
 Identities = 16/75 (21%), Positives = 26/75 (34%), Gaps = 14/75 (18%)

Query: 131 DNCCINVDTSNNNKNDAAPLQLPQDPMAAAPTFSCPICMGPLSEATSTKCGHIFCKDCIK 190
           DNC I  +   +   +       Q   A+A +  C +  G         C H F   CI 
Sbjct: 22  DNCAICRNHIMDLCIEC------QANQASATSEECTVAWGV--------CNHAFHFHCIS 67

Query: 191 GAIAAQGKCPNCRQK 205
             +  +  CP   ++
Sbjct: 68  RWLKTRQVCPLDNRE 82

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 37.8 bits (87), Expect = 4e-05
 Identities = 8/52 (15%), Positives = 15/52 (28%), Gaps = 1/52 (1%)

Query: 165 CPICMGPLSEATSTK-CGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVY 215
           C I          +     IF K  ++  +   G  P   + +    I  + 
Sbjct: 3   CAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEIV 54

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.0 bits (90), Expect = 5e-05
 Identities = 14/55 (25%), Positives = 18/55 (32%), Gaps = 3/55 (5%)

Query: 163 FSCPICMGPLSEA-TSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVYL 216
             C  C   L E      C HIFC +C+   I     CP C      + +     
Sbjct: 23  LRCSRCTNILREPVCLGGCEHIFCSNCVSDCI--GTGCPVCYTPAWIQDLKINRQ 75

>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 = 7e-05
 Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 5/50 (10%)

Query: 164 SCPICMGPLSEA----TSTKCGHIFCKDCIKGAI-AAQGKCPNCRQKVGK 208
            CP+CM PL           CG+  C+ C         G CP CR+   +
Sbjct: 2   ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE 51

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 78

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]

 Score = 37.8 bits (87), Expect = 9e-05
 Identities = 9/42 (21%), Positives = 16/42 (38%)

Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQ 204
           F CPI +  + +      G  + +  I+  + A  K     Q
Sbjct: 9   FRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQ 50

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 80

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]

 Score = 36.8 bits (84), Expect = 2e-04
 Identities = 6/40 (15%), Positives = 11/40 (27%)

Query: 163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNC 202
               I    + E   T  G  + +  I+  +   G     
Sbjct: 8   LCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPV 47

>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 = 35.8 bits (81), Expect = 7e-04
 Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 5/37 (13%)

Query: 178 TKCGHIFCKDCIK-----GAIAAQGKCPNCRQKVGKR 209
           TKC H F   C+      G      +CP+C+   G++
Sbjct: 59  TKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK 95

>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 = 33.9 bits (77), Expect = 0.002
 Identities = 12/58 (20%), Positives = 21/58 (36%), Gaps = 11/58 (18%)

Query: 159 AAPTFSCPICMGPLSEA---TSTKCGHIFCKDCIKGAIAAQG--------KCPNCRQK 205
           ++ +  C +C+G        T  +C  IFC  C+K  +             CP+    
Sbjct: 2   SSGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACP 59

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

 Score = 32.9 bits (74), Expect = 0.003
 Identities = 9/52 (17%), Positives = 12/52 (23%), Gaps = 7/52 (13%)

Query: 165 CPICMGPLSEA-----TSTKCGHIFCKDCIKGAIAAQG--KCPNCRQKVGKR 209
           C IC   L          T       + C+   +       C  C      R
Sbjct: 9   CWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNTR 60

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	220
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.47
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.39
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.39
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.36
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.36
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.34
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.3
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.26
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.2
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.19
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.19
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.19
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.06
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	98.92
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	98.92
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.63
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.05
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	93.89

>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=99.47  E-value=8.4e-15  Score=96.67  Aligned_cols=53  Identities=17%  Similarity=0.241  Sum_probs=49.4

Q ss_pred             ccccccCCCCCCceEe-cccCccchhHHHHHHhcCCCCCCCCccccCCCceeec
Q 027652          163 FSCPICMGPLSEATST-KCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRVY  215 (220)
Q Consensus       163 ~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~iy  215 (220)
                      +.|+||++.+.+|+.+ .|||+||+.||.+|++.+..||+||+++..++|+++.
T Consensus         1 l~C~Ic~~~~~~Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dLipik   54 (56)
T d2baya1           1 MLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEIV   54 (56)
T ss_dssp             CCCTTTCSCCSSEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCEECC
T ss_pred             CCCccCCchHHhcCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhceeCC
Confidence            3699999999999988 5999999999999999999999999999999998874

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.39  E-value=6.6e-14  Score=100.20  Aligned_cols=53  Identities=30%  Similarity=0.703  Sum_probs=46.8

Q ss_pred             CCccccccCCCCCCceEecccCccchhHHHHHHhc-CCCCCCCCccccCCCcee
Q 027652          161 PTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAA-QGKCPNCRQKVGKRGIFR  213 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~-~~~CP~Cr~~v~~~~l~~  213 (220)
                      +.+.|+||++.+.+|++++|||+||..||.+|++. ..+||+||.++...++..
T Consensus        22 ~~l~C~IC~~~~~~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l~~   75 (86)
T d1rmda2          22 KSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLES   75 (86)
T ss_dssp             HHTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCBC
T ss_pred             cCcCCccCCcchhcceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChhhccC
Confidence            45789999999999999999999999999999975 458999999998777653

>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=99.39  E-value=1e-13  Score=101.91  Aligned_cols=55  Identities=36%  Similarity=0.870  Sum_probs=48.0

Q ss_pred             CCccccccCCCCCCceEecccCccchhHHHHHHhcC---CCCCCCCccccCCCceeec
Q 027652          161 PTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQ---GKCPNCRQKVGKRGIFRVY  215 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~---~~CP~Cr~~v~~~~l~~iy  215 (220)
                      +.+.||||++.+.+|++++|||+||..||.+|+...   ..||+||..+...++...+
T Consensus        20 ~~l~CpIC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l~~n~   77 (103)
T d1jm7a_          20 KILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQEST   77 (103)
T ss_dssp             HHTSCSSSCCCCSSCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBCCC
T ss_pred             cCcCCCccCchhCCeEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhCCcCH
Confidence            346899999999999999999999999999999754   3799999999887776554

>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=99.36  E-value=2.7e-13  Score=94.72  Aligned_cols=57  Identities=19%  Similarity=0.456  Sum_probs=50.4

Q ss_pred             CCCCccccccCCCCCCceEecccCccchhHHHHHHhcC-CCCCCCCccccCCCceeec
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQ-GKCPNCRQKVGKRGIFRVY  215 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~-~~CP~Cr~~v~~~~l~~iy  215 (220)
                      ..++|.||||++.+.+|++++|||+||+.||.+|+... ..||.|+.++...++.+.+
T Consensus         5 iP~~l~CpIc~~~m~dPV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~l~pN~   62 (78)
T d1t1ha_           5 FPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNY   62 (78)
T ss_dssp             CSSSSSCTTTSCCCSSEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEECT
T ss_pred             CCccCCCcCcCchhhCceEccCCCcchHHHHHHHHHHCCCCCCcccccCCcccccchH
Confidence            34779999999999999999999999999999999764 5799999999988877654

>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=99.36  E-value=1.6e-13  Score=96.43  Aligned_cols=55  Identities=13%  Similarity=0.128  Sum_probs=48.9

Q ss_pred             CCCccccccCCCCCCceEecccCccchhHHHHHHhcC-CCCCCCCccccCCCceee
Q 027652          160 APTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQ-GKCPNCRQKVGKRGIFRV  214 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~-~~CP~Cr~~v~~~~l~~i  214 (220)
                      .+.+.||||++.+.+|++++|||+||..||.+|+... ..||.|+.++...++++.
T Consensus         5 P~~l~CpIc~~l~~dPv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~l~pN   60 (80)
T d2c2la2           5 PDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPN   60 (80)
T ss_dssp             CSTTBCTTTCSBCSSEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEEC
T ss_pred             CccccCcCcCchhhhhcccCCcCeecHHHHHHHHhcCCccCCCccccccccccccH
Confidence            4678999999999999999999999999999999754 479999999987777654

>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=99.34  E-value=2.8e-13  Score=95.23  Aligned_cols=50  Identities=24%  Similarity=0.620  Sum_probs=44.1

Q ss_pred             ccccccCCCCCCceEecccCccchhHHHHHHhc-CCCCCCCCccccCCCce
Q 027652          163 FSCPICMGPLSEATSTKCGHIFCKDCIKGAIAA-QGKCPNCRQKVGKRGIF  212 (220)
Q Consensus       163 ~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~-~~~CP~Cr~~v~~~~l~  212 (220)
                      ..|+||++.+.+++.++|||.||..||.+|+.. ...||+||..+...+.+
T Consensus        24 ~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~i   74 (79)
T d1fbva4          24 QLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPI   74 (79)
T ss_dssp             TBCTTTSSSBCCEECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCCS
T ss_pred             CCCccCCCcCCCeEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCcee
Confidence            369999999999999999999999999999974 56899999999865543

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.30  E-value=5e-13  Score=90.49  Aligned_cols=57  Identities=23%  Similarity=0.592  Sum_probs=45.6

Q ss_pred             CCccccccCCCCCC-----ceEecccCccchhHHHHHHhc-CCCCCCCCccccCCCceeecCC
Q 027652          161 PTFSCPICMGPLSE-----ATSTKCGHIFCKDCIKGAIAA-QGKCPNCRQKVGKRGIFRVYLP  217 (220)
Q Consensus       161 ~~~~CpIC~~~~~~-----pv~l~CgH~fC~~Ci~~~l~~-~~~CP~Cr~~v~~~~l~~iylp  217 (220)
                      ++..||||++.+..     .+.++|||.||..||.+|+.. ...||+||+++..+++...++.
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~~~~~~fd   64 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQLFE   64 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCCEEECCC
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCcccccccccCCC
Confidence            45689999986432     245699999999999999864 4579999999998888776653

>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=99.26  E-value=1.2e-12  Score=89.30  Aligned_cols=44  Identities=36%  Similarity=0.776  Sum_probs=40.3

Q ss_pred             cccccCCCCCCceE-ecccCccchhHHHHHHhcCCCCCCCCcccc
Q 027652          164 SCPICMGPLSEATS-TKCGHIFCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       164 ~CpIC~~~~~~pv~-l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      .|+||++.+.+++. ++|||+||..|+.+|++.+..||+||.++.
T Consensus         7 ~C~IC~~~~~~~~~~~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~   51 (68)
T d1chca_           7 RCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCSSCCSCCCSCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCccCCcCccCCcEEeCCCCcCcHHHHHHHHHhCCcCCCCCcchH
Confidence            69999999987755 699999999999999999999999999875

>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=99.20  E-value=1e-11  Score=90.50  Aligned_cols=56  Identities=14%  Similarity=0.102  Sum_probs=50.0

Q ss_pred             CCCCccccccCCCCCCceEecccC-ccchhHHHHHHhcCCCCCCCCccccCCCceee
Q 027652          159 AAPTFSCPICMGPLSEATSTKCGH-IFCKDCIKGAIAAQGKCPNCRQKVGKRGIFRV  214 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~pv~l~CgH-~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~i  214 (220)
                      ..+.|.||||..+|.+||+++||| +||+.||.+|+.....||+|++++...+|+..
T Consensus        19 ~P~~f~CPI~~~lm~dPV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L~pN   75 (98)
T d1wgma_          19 ACDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRPN   75 (98)
T ss_dssp             CCTTTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEEC
T ss_pred             CcHHhCCcCchhHHHHHHhcccccchhhHHHHHHHHHhcCCcccccccccchhhcch
Confidence            345799999999999999998875 79999999999988899999999998887754

>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=99.19  E-value=1.5e-12  Score=85.68  Aligned_cols=46  Identities=20%  Similarity=0.530  Sum_probs=40.3

Q ss_pred             CCccccccCCCCCCceEecccCccchhHHHHHHhcCCCCCCCCccccCC
Q 027652          161 PTFSCPICMGPLSEATSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGKR  209 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~  209 (220)
                      +.+.|+||++.+.+|+.++|||+||..|+.+|   ...||+||+++...
T Consensus         5 ~~l~C~IC~~~~~~p~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T d1bora_           5 QFLRCQQCQAEAKCPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CCSSCSSSCSSCBCCSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             CCCCCcccCcccCCCEEecCCCHHhHHHHHcC---CCcCcCCCCcccCC
Confidence            45699999999999999999999999998643   56899999999754

>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=99.19  E-value=1.9e-12  Score=94.00  Aligned_cols=51  Identities=27%  Similarity=0.652  Sum_probs=44.1

Q ss_pred             CCccccccCCCCCCceEe-cccCccchhHHHHHHhcCCCCCCCCccccCCCcee
Q 027652          161 PTFSCPICMGPLSEATST-KCGHIFCKDCIKGAIAAQGKCPNCRQKVGKRGIFR  213 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l-~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~~~l~~  213 (220)
                      +.+.|+||++.+.+|+.+ +|||+||..||.+|+  ...||.||.++...++..
T Consensus        21 ~~l~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~--~~~CP~Cr~~~~~~~l~~   72 (97)
T d1jm7b_          21 KLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCI--GTGCPVCYTPAWIQDLKI   72 (97)
T ss_dssp             HTTSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGT--TTBCSSSCCBCSCSSCCC
T ss_pred             hcCCCccCCchhhcCceeCCCCCchhHHHHHHHH--hccccccCCcCchhhCcc
Confidence            456899999999999976 899999999999997  346999999988777654

>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=99.19  E-value=4.4e-12  Score=83.09  Aligned_cols=49  Identities=27%  Similarity=0.715  Sum_probs=41.0

Q ss_pred             CCCCccccccCCCCCCc---eEe-cccCccchhHHHHHHhcCCCCCCCCcccc
Q 027652          159 AAPTFSCPICMGPLSEA---TST-KCGHIFCKDCIKGAIAAQGKCPNCRQKVG  207 (220)
Q Consensus       159 ~~~~~~CpIC~~~~~~p---v~l-~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~  207 (220)
                      .++...|+||++.+...   ..+ .|||.||..|+.+|++.+..||+||+++.
T Consensus         2 ~ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           2 MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            35566899999988753   344 69999999999999999999999998764

>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=99.06  E-value=2.7e-11  Score=78.27  Aligned_cols=46  Identities=33%  Similarity=0.837  Sum_probs=37.8

Q ss_pred             ccccccCCCCCCc----eEecccCccchhHHHHHHhcC-CCCCCCCccccC
Q 027652          163 FSCPICMGPLSEA----TSTKCGHIFCKDCIKGAIAAQ-GKCPNCRQKVGK  208 (220)
Q Consensus       163 ~~CpIC~~~~~~p----v~l~CgH~fC~~Ci~~~l~~~-~~CP~Cr~~v~~  208 (220)
                      +.||||++.+...    ..++|||.||..|+.+|+... .+||+||+++..
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            3799999987542    345899999999999999854 479999998864

>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=98.92  E-value=2.6e-10  Score=81.12  Aligned_cols=33  Identities=21%  Similarity=0.369  Sum_probs=30.0

Q ss_pred             eEecccCccchhHHHHHHhcCCCCCCCCccccC
Q 027652          176 TSTKCGHIFCKDCIKGAIAAQGKCPNCRQKVGK  208 (220)
Q Consensus       176 v~l~CgH~fC~~Ci~~~l~~~~~CP~Cr~~v~~  208 (220)
                      +.++|||.||..||.+|++.+..||+||+++..
T Consensus        53 ~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   85 (88)
T d3dplr1          53 AWGVCNHAFHFHCISRWLKTRQVCPLDNREWEF   85 (88)
T ss_dssp             EEETTSCEEEHHHHHHHHTTCSBCSSSCSBCCE
T ss_pred             EEccccCcccHHHHHHHHHHCCcCCCCCCcccc
Confidence            456899999999999999999999999998874

>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=98.92  E-value=3e-10  Score=84.07  Aligned_cols=48  Identities=33%  Similarity=0.685  Sum_probs=38.0

Q ss_pred             CccccccCCCCCCc------------------eEecccCccchhHHHHHHhcC-----CCCCCCCccccCC
Q 027652          162 TFSCPICMGPLSEA------------------TSTKCGHIFCKDCIKGAIAAQ-----GKCPNCRQKVGKR  209 (220)
Q Consensus       162 ~~~CpIC~~~~~~p------------------v~l~CgH~fC~~Ci~~~l~~~-----~~CP~Cr~~v~~~  209 (220)
                      +..|+||++.+..+                  ..++|||.||..||..|+...     ..||+||..+..+
T Consensus        25 ~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             cccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            34799999876532                  356899999999999999853     3799999988654

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=98.63  E-value=9.6e-09  Score=67.60  Aligned_cols=49  Identities=16%  Similarity=0.329  Sum_probs=39.5

Q ss_pred             CCCccccccCCCCCCceEecc-----cCccchhHHHHHHhc--CCCCCCCCccccC
Q 027652          160 APTFSCPICMGPLSEATSTKC-----GHIFCKDCIKGAIAA--QGKCPNCRQKVGK  208 (220)
Q Consensus       160 ~~~~~CpIC~~~~~~pv~l~C-----gH~fC~~Ci~~~l~~--~~~CP~Cr~~v~~  208 (220)
                      ++...|+||++.+.++...+|     +|.||..||.+|+..  ...||+||+++..
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            455689999998877766654     599999999999864  4589999998864

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.05  E-value=8.1e-07  Score=62.81  Aligned_cols=43  Identities=28%  Similarity=0.712  Sum_probs=32.5

Q ss_pred             CccccccCCCCCC---ceEecccCccchhHHHHHHhcC--------CCCCCCCc
Q 027652          162 TFSCPICMGPLSE---ATSTKCGHIFCKDCIKGAIAAQ--------GKCPNCRQ  204 (220)
Q Consensus       162 ~~~CpIC~~~~~~---pv~l~CgH~fC~~Ci~~~l~~~--------~~CP~Cr~  204 (220)
                      ...|+||++.+..   +..++|||.||..|++.|+...        -+||.|..
T Consensus         5 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           5 SSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            4589999998753   3345899999999999998721        16998643

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.89  E-value=0.039  Score=36.41  Aligned_cols=35  Identities=31%  Similarity=0.758  Sum_probs=29.8

Q ss_pred             CCccccccCCCCCCceEecc----cCccchhHHHHHHhc
Q 027652          161 PTFSCPICMGPLSEATSTKC----GHIFCKDCIKGAIAA  195 (220)
Q Consensus       161 ~~~~CpIC~~~~~~pv~l~C----gH~fC~~Ci~~~l~~  195 (220)
                      ..+.|.+|.+.+.+...+.|    +|.||..|-+..++.
T Consensus         7 ~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~   45 (80)
T d2cs3a1           7 GPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   45 (80)
T ss_dssp             CSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHh
Confidence            34789999999999877766    588999999998884