Citrus Sinensis ID: 022060

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300---
Protein Sequence
MEVLGMEEGKKPEDHMTSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRNATIFHHPTFGDFELQHLPVGASDTDLEEHILQHLTAAAAMGRAHHFGRRESHRNRSAAHGRPHFFVFSAHPGGAPPGAVAQGGGTEPAPLAGASPSVPLSSSGNDSSQHMLQFHPIQTNQNSSSASGSAVAQATRRGFSFNNRSTSSQTSSPTHDRAGPSDLQSFSESLKSRFNAVSMRYNCKGNLLSCNSNGCTIF
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEcccccccccHHHcccHHHHHccccccccccccccEHHccccccccEEcccccHHHHHHHHHHHHHcccccccccEEEcccccHHHHHHHHHHHHHcccccccccEEEcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccHHHccHHHHHHHHHHHHHHHHHHHHHHcccccccEEc
Coil and Loop (DISEMBL)
mevlgmeegkkpedhmTSAAAFVeggiqdscDDACSICleefsesdpstvtsckheFHLQCVLEWCqrssqcpmcwqpislkdaTSQELLEAVEQERsiranpprnatifhhptfgdfelqhlpvgasdtdLEEHILQHLTAAAAMGrahhfgrreshrnrsaahgrphffvfsahpggappgavaqgggtepaplagaspsvplsssgndssqhmlqfhpiqtnqnsssasgSAVAQATRrgfsfnnrstssqtsspthdragpsdlqSFSESLKSRFNAVSMRYNckgnllscnsngctif
Flexible Loop (DISEMBL)
mevlgmeegkkpedHMTSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRNATIFHHPTFGDFELQHLPVGASDTDLEEHILQHLTAAAAMGRAHHFGRRESHRNRSAAHGRPHFFVFSAHPGGAPPGAVAQGGGTEPAPLAGASPSVPLSSSGNDSSQHMLQFHPIQTNQNSSSASGSAVAQATRRGFsfnnrstssqtsspthdragpsDLQSFSESLKSRFNAVSMRYNckgnllscnsngctif
Low Complexity Region (SEG)
MEVLGMEEGKKPEDHMTSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRNATIFHHPTFGDFELQHLPVGASDTDLEEHILQHLTAAAAMGRAHHFGRRESHRNRSAAHGRPHFFVFSAHpggappgavaqgggTEPAPLAGASPSVPLSSSGNDSSQHMLQFHPIQTNQNsssasgsavaqaTRRGFSFNNRSTSSQTSSPTHDRAGPSDLQSFSESLKSRFNAVSMRYNCKGNLLSCNSNGCTIF
Disordered region (IsUnstruct)
********************AFVEGGIQDSCDDACSICLEEFSE**PSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKD***********************ATIFHHPTFGDFELQHLPVGASDTDLEEHILQHLTAAAAMG**********************FFVF***********************************************************************************************************AVSMRYNCKGNLLSCNS******
Disordered Region (DISOPRED)
*******************************DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISL******************************************************************************************************************************************************************************************************NAVSMRYNCKGNLLSCNSNGC**F
Disordered Region (DISEMBL)
**************HMTSAAAFVEGGIQDSCDDACSICLEEF***********KHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRNATIFHHPTFGDFELQHLPVGASDTDLEEHILQHLTAAAAMG****************AHGRPHFFVFSAHPGGAPPGAVAQGGGTE*********************QHMLQFHPIQ****************TRRGFSFN***********************FSESLKSRFNAVSMRYNCKGNLLSCNSNGCTIF
Disordered Region (DISPRO)
******************************CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRNATIFHHPTFGDFELQHLPVGASDTDLEEHILQHLTAAAAMGRA**F*************GRPHFFVFSA**************************************************************************************************SLKSRFNAVSMRYNCKGNLLSCNSNGCTIF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEVLGMEEGKKPEDHMTSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRNATIFHHPTFGDFELQHLPVGASDTDLEEHILQHLTAAAAMGRAHHFGRRESHRNRSAAHGRPHFFVFSAHPGGAPPGAVAQGGGTEPAPLAGASPSVPLSSSGNDSSQHMLQFHPIQTNQNSSSASGSAVAQATRRGFSFNNRSTSSQTSSPTHDRAGPSDLQSFSESLKSRFNAVSMRYNCKGNLLSCNSNGCTIF
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	303	2.2.26 [Sep-21-2011]
Q9ZT42	375	E3 ubiquitin-protein liga	yes	no	0.914	0.738	0.566	3e-81
Q4TU14	371	E3 ubiquitin-protein liga	no	no	0.405	0.331	0.5	6e-26
Q8LE94	231	E3 ubiquitin-protein liga	no	no	0.145	0.190	0.5	8e-09
Q68DV7	783	E3 ubiquitin-protein liga	yes	no	0.198	0.076	0.483	2e-07
Q5NCP0	784	E3 ubiquitin-protein liga	yes	no	0.224	0.086	0.426	6e-07
Q9VE61	147	E3 ubiquitin-protein liga	yes	no	0.201	0.414	0.363	1e-06
Q7TMV1	668	E3 ubiquitin-protein liga	no	no	0.194	0.088	0.360	2e-06
Q8BP31	155	RING finger protein 122 O	no	no	0.181	0.354	0.4	3e-06
Q9LQM2	332	RING-H2 finger protein AT	no	no	0.207	0.189	0.359	3e-06
Q5RBT7	664	E3 ubiquitin-protein liga	no	no	0.194	0.088	0.344	5e-06

>sp|Q9ZT42|RHF2A_ARATH E3 ubiquitin-protein ligase RHF2A OS=Arabidopsis thaliana GN=RHF2A PE=2 SV=1

 Score =  301 bits (772), Expect = 3e-81,   Method: Compositional matrix adjust.
 Identities = 174/307 (56%), Positives = 198/307 (64%), Gaps = 30/307 (9%)

Query: 5   GMEEGKKPEDHMTSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLE 64
           G  E    E H+TSAAAFVEGGIQD+CDDACSICLE F ESDPST+TSCKHE+HLQC+LE
Sbjct: 3   GAGETTTSEGHLTSAAAFVEGGIQDACDDACSICLESFCESDPSTLTSCKHEYHLQCILE 62

Query: 65  WCQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRNATIFHHPTFGDFELQHLP 124
           WCQRSSQCPMCWQ ISLKD TSQELLEAVEQER+ R NP RNATIF HPT GDFELQHLP
Sbjct: 63  WCQRSSQCPMCWQSISLKDPTSQELLEAVEQERNFRFNPTRNATIFRHPTLGDFELQHLP 122

Query: 125 VGASDTDLEEHILQHLTAAAAMGRAHHFGRRESHRNRSAAHGRPHFFVFSAHPGGAPPGA 184
           VG  + ++EE I+QHL AAAAMGRA H  RRE HR+RS++ G   F VFS+ P  + P  
Sbjct: 123 VGVDNAEIEERIIQHLAAAAAMGRARHGVRREGHRSRSSSQGHQQFMVFSSQPNASSPPP 182

Query: 185 VAQGGGTEPAPLAGASPS-VPLSSSGNDSSQHMLQ----FHPIQTNQNSSSASGSAVAQA 239
                 +        + S +P ++ G  S Q   Q     HP Q    S SAS S     
Sbjct: 183 HPPMPSSPSQRDESDTVSNLPHNALGEGSHQSNTQPPTSSHPRQV---SPSASDS----- 234

Query: 240 TRRGFSFNNRSTSSQTSSPTHDRAGPSDLQSFSESLKSRFNAVSMRY---------NCKG 290
                   N    +Q+S    DRAGPS+LQSFSESLKSR NAVS RY         N K 
Sbjct: 235 --------NSRPLNQSSPSEQDRAGPSELQSFSESLKSRLNAVSTRYKESISKNTRNWKD 286

Query: 291 NLLSCNS 297
            L S N+
Sbjct: 287 RLFSRNT 293

Probable E3 ubiquitin-protein ligase involved in the positive regulation of the gametogenesis progression. Required for the degradation of KRP6, a cyclin-dependent kinase inhibitor which accumulates during meiosis and blocks the progression of subsequent mitoses during gametophytes development. Functions in association with RHF1A.
Arabidopsis thaliana (taxid: 3702)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|Q4TU14|RHF1A_ARATH E3 ubiquitin-protein ligase RHF1A OS=Arabidopsis thaliana GN=RHF1A PE=1 SV=1

 Score =  118 bits (295), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 63/126 (50%), Positives = 80/126 (63%), Gaps = 3/126 (2%)

Query: 20  AAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPI 79
           A  V     ++ DDACSICLE F+  DPSTVTSCKHE+HLQC++EW QRS +CP+CWQ  
Sbjct: 31  ALVVASDDDNNTDDACSICLEPFTLQDPSTVTSCKHEYHLQCIIEWSQRSKECPICWQLF 90

Query: 80  SLKDATSQELLEAVEQERSIRA-NPPRNATIFHHPTFGDFELQHLPVGASDTDLEEHILQ 138
            L+D  SQELL AVE+ER ++  N   ++ I  H +  DF  +      S  D  E  L+
Sbjct: 91  VLRDPASQELLAAVEKERLLKTRNISSSSPISIHHSHDDFHSEEEESQFSSFD--EQFLR 148

Query: 139 HLTAAA 144
           HLT AA
Sbjct: 149 HLTEAA 154

E3 ubiquitin-protein ligase involved in the positive regulation of the gametogenesis progression. Mediates the proteasomal degradation of KRP6, a cyclin-dependent kinase inhibitor which accumulates during meiosis and blocks the progression of subsequent mitoses during gametophyte development. Functions in association with RHF2A. Possesses E3 ubiquitin ligase activity in vitro.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q8LE94|RING3_ARATH E3 ubiquitin-protein ligase At3g02290 OS=Arabidopsis thaliana GN=At3g02290 PE=2 SV=1

 Score = 61.2 bits (147), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 22/44 (50%), Positives = 29/44 (65%)

Query: 32  DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMC 75
           +D C  CLEE++  +P  VT C H FHL C+ EW +RS  CP+C
Sbjct: 178 EDVCPTCLEEYTSENPKIVTKCSHHFHLSCIYEWMERSENCPVC 221

Mediates E2-dependent protein ubiquitination.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q68DV7|RNF43_HUMAN E3 ubiquitin-protein ligase RNF43 OS=Homo sapiens GN=RNF43 PE=1 SV=1

 Score = 56.6 bits (135), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/62 (48%), Positives = 35/62 (56%), Gaps = 2/62 (3%)

Query: 30  SCDDA--CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQ 87
           SC  A  C+ICLEEFSE     V SC HEFH  CV  W  +   CP+C   I+  D+ SQ
Sbjct: 265 SCSSAPVCAICLEEFSEGQELRVISCLHEFHRNCVDPWLHQHRTCPLCMFNITEGDSFSQ 324

Query: 88  EL 89
            L
Sbjct: 325 SL 326

Probable E3 ubiquitin-protein ligase. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates.

Homo sapiens (taxid: 9606)

>sp|Q5NCP0|RNF43_MOUSE E3 ubiquitin-protein ligase RNF43 OS=Mus musculus GN=Rnf43 PE=2 SV=1

 Score = 55.1 bits (131), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 35/68 (51%)

Query: 20  AAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPI 79
           A + + G   S    C+ICLEEFSE     V SC HEFH  CV  W  +   CP+C   I
Sbjct: 257 AEWPDSGSSCSSTPVCAICLEEFSEGQELRVISCLHEFHRTCVDPWLYQHRTCPLCMFNI 316

Query: 80  SLKDATSQ 87
              D+ SQ
Sbjct: 317 VEGDSFSQ 324

Probable E3 ubiquitin-protein ligase. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates.

Mus musculus (taxid: 10090)

>sp|Q9VE61|RN181_DROME E3 ubiquitin-protein ligase RNF181 homolog OS=Drosophila melanogaster GN=CG7694 PE=2 SV=1

 Score = 54.3 bits (129), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 35/66 (53%), Gaps = 5/66 (7%)

Query: 24  EGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKD 83
           EGG     D  CS+C E   E     +  CKHEFH +C+L W ++++ CP+C   +   D
Sbjct: 64  EGG-----DLECSVCKEPAEEGQKYRILPCKHEFHEECILLWLKKTNSCPLCRYELETDD 118

Query: 84  ATSQEL 89
              +EL
Sbjct: 119 PVYEEL 124

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

Drosophila melanogaster (taxid: 7227)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q7TMV1|RN139_MOUSE E3 ubiquitin-protein ligase RNF139 OS=Mus musculus GN=Rnf139 PE=1 SV=1

 Score = 53.1 bits (126), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 23  VEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLK 82
           ++G      DD C+IC  EF+ S  + +T C H FH  C+ +W      CPMC Q + ++
Sbjct: 535 IKGSHLQEIDDVCAICYHEFTTS--ARITPCNHYFHALCLRKWLYIQDTCPMCHQKVYIE 592

Query: 83  D 83
           D
Sbjct: 593 D 593

E3-ubiquitin ligase; acts as a negative regulator of the cell proliferation through mechanisms involving G2/M arrest and cell death. Required for MHC class I ubiquitination in cells expressing the cytomegalovirus protein US2 before dislocation from the endoplasmic reticulum (ER). Affects SREBP processing by hindering the SREBP/SCAP complex translocation from the ER to the Golgi, thereby reducing SREBF2 target gene expression. Required for INSIG1 ubiquitination. May be required for EIF3 complex ubiquitination. May function as a signaling receptor.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score = 52.8 bits (125), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 34/55 (61%)

Query: 35  CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQEL 89
           C++CLE+F   D   V  C+H FH +C+++W +    CPMC +PI+    TSQ +
Sbjct: 93  CAVCLEDFKGKDELGVLPCQHAFHRKCLVKWLEVRCVCPMCNKPIAGPTETSQSI 147

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

Mus musculus (taxid: 10090)

>sp|Q9LQM2|ATL81_ARATH RING-H2 finger protein ATL81 OS=Arabidopsis thaliana GN=ATL81 PE=2 SV=1

 Score = 52.8 bits (125), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 26  GIQDSCDDACSICLEEFSESDP-STVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDA 84
            ++D   D CSICL EF + D    +++C H FH  C+  W +    CP+C + + ++D 
Sbjct: 145 SVKDHGTDQCSICLTEFMDDDTIRLISTCNHSFHTICIDLWFEGHKTCPVCRRELDVEDR 204

Query: 85  TSQE 88
           TS E
Sbjct: 205 TSLE 208

Arabidopsis thaliana (taxid: 3702)

>sp|Q5RBT7|RN139_PONAB E3 ubiquitin-protein ligase RNF139 OS=Pongo abelii GN=RNF139 PE=2 SV=1

 Score = 52.0 bits (123), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 23  VEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLK 82
           ++G      +D C+IC  EF+ S  + +T C H FH  C+ +W      CPMC Q + ++
Sbjct: 535 IKGSRLQEINDVCAICYHEFTTS--ARITPCNHYFHALCLRKWLYIQDTCPMCHQKVYIE 592

Query: 83  D 83
           D
Sbjct: 593 D 593

E3-ubiquitin ligase; acts as a negative regulator of the cell proliferation through mechanisms involving G2/M arrest and cell death. Required for MHC class I ubiquitination in cells expressing the cytomegalovirus protein US2 before dislocation from the endoplasmic reticulum (ER). Affects SREBP processing by hindering the SREBP/SCAP complex translocation from the ER to the Golgi, thereby reducing SREBF2 target gene expression. Required for INSIG1 ubiquitination. May be required for EIF3 complex ubiquitination. May function as a signaling receptor.

Pongo abelii (taxid: 9601)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	303
224138254	387	predicted protein [Populus trichocarpa]	0.924	0.723	0.723	1e-115
224091469	389	predicted protein [Populus trichocarpa]	0.933	0.727	0.705	1e-111
296089345	391	unnamed protein product [Vitis vinifera]	0.933	0.723	0.694	1e-110
359481051	387	PREDICTED: E3 ubiquitin-protein ligase R	0.930	0.728	0.696	1e-109
255566215	378	protein binding protein, putative [Ricin	0.897	0.719	0.667	1e-101
356550038	398	PREDICTED: E3 ubiquitin-protein ligase R	0.937	0.713	0.656	1e-100
356543652	401	PREDICTED: E3 ubiquitin-protein ligase R	0.937	0.708	0.656	1e-100
449437506	371	PREDICTED: E3 ubiquitin-protein ligase R	0.924	0.754	0.670	1e-99
255637379	401	unknown [Glycine max]	0.937	0.708	0.653	2e-99
225436087	393	PREDICTED: E3 ubiquitin-protein ligase R	0.947	0.730	0.647	3e-99

>gi|224138254|ref|XP_002322768.1| predicted protein [Populus trichocarpa] gi|222867398|gb|EEF04529.1| predicted protein [Populus trichocarpa]

 Score =  419 bits (1078), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 207/286 (72%), Positives = 229/286 (80%), Gaps = 6/286 (2%)

Query: 6   MEEGKKPEDHMTSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEW 65
           M+E KKPE HMTSAAAFVEGGIQDSCDDACSICLEEF ESDPSTVT+CKHEFHLQC+LEW
Sbjct: 1   MDEAKKPEVHMTSAAAFVEGGIQDSCDDACSICLEEFCESDPSTVTNCKHEFHLQCILEW 60

Query: 66  CQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRNATIFHHPTFGDFELQHLPV 125
           CQRSS+CPMC Q ISLKD TSQEL EAVE+ER IRA P RNATIFHHPT GDFELQHLPV
Sbjct: 61  CQRSSECPMCLQSISLKDPTSQELFEAVERERKIRAAPSRNATIFHHPTLGDFELQHLPV 120

Query: 126 GASDTDLEEHILQHLTAAAAMGRAHHFGRRESHRNRSAAHGRPHFFVFSAHPGGAPPGAV 185
           G SD++LEE I+QHL AAAAMGR  HFGRRE  RNR+++HGRPHF VFS HPG  P G V
Sbjct: 121 GVSDSELEERIIQHLAAAAAMGRTRHFGRREGQRNRTSSHGRPHFLVFSTHPGAQPSGHV 180

Query: 186 AQ-----GGGTEPAPLAGASPSVPLSSSGNDSSQHMLQFHPIQTNQNSSSASGSAVAQAT 240
           +      GG  EPAP++ ASPS  L+S G++  Q  LQ   + T+Q SSSASGS    A 
Sbjct: 181 SSSLTQLGGENEPAPVSVASPSTQLTSVGDEPPQQALQSPSVLTDQ-SSSASGSTAMPAN 239

Query: 241 RRGFSFNNRSTSSQTSSPTHDRAGPSDLQSFSESLKSRFNAVSMRY 286
            +G SFNNRS SSQ+S P  DRAGPS+LQSFSESLKSR NAVSMRY
Sbjct: 240 NQGVSFNNRSASSQSSLPNQDRAGPSELQSFSESLKSRLNAVSMRY 285

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224091469|ref|XP_002309263.1| predicted protein [Populus trichocarpa] gi|222855239|gb|EEE92786.1| predicted protein [Populus trichocarpa]

 Score =  407 bits (1046), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 206/292 (70%), Positives = 229/292 (78%), Gaps = 9/292 (3%)

Query: 1   MEVLGMEEGKKPEDHMTSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQ 60
           MEVL ++E KKPE HMTSAAAFVEGGIQ+SCDDACSICLE+F ESDPSTVT+CKHEFHLQ
Sbjct: 1   MEVLEVDEAKKPEVHMTSAAAFVEGGIQESCDDACSICLEDFCESDPSTVTNCKHEFHLQ 60

Query: 61  CVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRNATIFHHPTFGDFEL 120
           C+LEWCQRSS+CPMC + ISLKD TSQEL EAVE+ER IRA P RNATIFHHPT GDFEL
Sbjct: 61  CILEWCQRSSECPMCLRSISLKDPTSQELFEAVERERKIRAAPSRNATIFHHPTLGDFEL 120

Query: 121 QHLPVGASDTDLEEHILQHLTAAAAMGRAHHFGRRESHRNRSAAHGRPHFFVFSAHPGGA 180
           QHLPVG SD++LEE I+QHL AAAAMGR  HFGR    RNRS+ HGRPHF VFS HPG  
Sbjct: 121 QHLPVGVSDSELEERIIQHLAAAAAMGRTGHFGRGGGQRNRSSPHGRPHFLVFSTHPGAQ 180

Query: 181 PPGAVAQ-----GGGTEPAPLAGASPSVPLSSSGNDSSQHMLQFHPIQTNQNSSSASGSA 235
           P G V+      G   EPA  + ASPS PL+S  ++ SQ  LQ  PI T+Q SSSASGS 
Sbjct: 181 PSGHVSSSLSQLGRENEPAAGSVASPSTPLTSVEDEPSQQTLQLPPILTDQ-SSSASGST 239

Query: 236 VAQATRRGFSFNNRSTSSQTSSPTHDRAGPSDLQSFSESLKSRFNAVSMRYN 287
           V    R+G SFNNRSTSSQ++ P  DRAGPS+ QSFS SLKSR NAVSMRY 
Sbjct: 240 V---MRQGLSFNNRSTSSQSAPPNQDRAGPSEFQSFSVSLKSRLNAVSMRYK 288

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296089345|emb|CBI39117.3| unnamed protein product [Vitis vinifera]

 Score =  402 bits (1034), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 202/291 (69%), Positives = 232/291 (79%), Gaps = 8/291 (2%)

Query: 1   MEVLGMEEGKKPEDHMTSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQ 60
           MEV GMEE K  E+HMTSAAAFVEGG+Q++CDDACSICLE F +SDPST+TSCKHEFHLQ
Sbjct: 1   MEVEGMEEVKNSENHMTSAAAFVEGGVQEACDDACSICLEAFCDSDPSTLTSCKHEFHLQ 60

Query: 61  CVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRNATIFHHPTFGDFEL 120
           C+LEWCQRSSQCPMCWQ ISLKD TSQELLEAVE+ER+IR  PPR+A IFHHPT GDFEL
Sbjct: 61  CILEWCQRSSQCPMCWQSISLKDPTSQELLEAVERERNIRLTPPRSA-IFHHPTLGDFEL 119

Query: 121 QHLPVGASDTDLEEHILQHLTAAAAMGRAHHFGRRESHRNRSAAHGRPHFFVFSAHPG-- 178
           QHLPVG +D +LEE I+QHL AAAAMGRAHH  RRE  R+RS+AHGR HF VFS HP   
Sbjct: 120 QHLPVGTNDPELEERIIQHLAAAAAMGRAHHIARREGQRSRSSAHGRSHFLVFSTHPNAT 179

Query: 179 --GAPPGAVAQGGGTEPAPLAGASPSVPLSSSGNDSSQHMLQFHPIQTNQNSSSASGSAV 236
             G  P ++ Q G  EPA +  ASPS+PL + G++ SQ + QF  +QT+  S+SAS SAV
Sbjct: 180 ASGPVPASLVQVGENEPAAITVASPSIPLPAGGDEPSQEIPQFPSVQTDHMSASASRSAV 239

Query: 237 AQATRRGFSFNNRSTSSQTSSPTHDRAGPSDLQSFSESLKSRFNAVSMRYN 287
              T R  SFNNRS++SQ+S P  DRAGPS+LQSFSESLKSR NAVSMRY 
Sbjct: 240 ---TPRRISFNNRSSASQSSPPDQDRAGPSELQSFSESLKSRLNAVSMRYK 287

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359481051|ref|XP_002270570.2| PREDICTED: E3 ubiquitin-protein ligase RHF2A-like [Vitis vinifera]

 Score =  402 bits (1032), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 202/290 (69%), Positives = 232/290 (80%), Gaps = 8/290 (2%)

Query: 1   MEVLGMEEGKKPEDHMTSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQ 60
           MEV GMEE K  E+HMTSAAAFVEGG+Q++CDDACSICLE F +SDPST+TSCKHEFHLQ
Sbjct: 1   MEVEGMEEVKNSENHMTSAAAFVEGGVQEACDDACSICLEAFCDSDPSTLTSCKHEFHLQ 60

Query: 61  CVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRNATIFHHPTFGDFEL 120
           C+LEWCQRSSQCPMCWQ ISLKD TSQELLEAVE+ER+IR  PPR+A IFHHPT GDFEL
Sbjct: 61  CILEWCQRSSQCPMCWQSISLKDPTSQELLEAVERERNIRLTPPRSA-IFHHPTLGDFEL 119

Query: 121 QHLPVGASDTDLEEHILQHLTAAAAMGRAHHFGRRESHRNRSAAHGRPHFFVFSAHPG-- 178
           QHLPVG +D +LEE I+QHL AAAAMGRAHH  RRE  R+RS+AHGR HF VFS HP   
Sbjct: 120 QHLPVGTNDPELEERIIQHLAAAAAMGRAHHIARREGQRSRSSAHGRSHFLVFSTHPNAT 179

Query: 179 --GAPPGAVAQGGGTEPAPLAGASPSVPLSSSGNDSSQHMLQFHPIQTNQNSSSASGSAV 236
             G  P ++ Q G  EPA +  ASPS+PL + G++ SQ + QF  +QT+  S+SAS SAV
Sbjct: 180 ASGPVPASLVQVGENEPAAITVASPSIPLPAGGDEPSQEIPQFPSVQTDHMSASASRSAV 239

Query: 237 AQATRRGFSFNNRSTSSQTSSPTHDRAGPSDLQSFSESLKSRFNAVSMRY 286
              T R  SFNNRS++SQ+S P  DRAGPS+LQSFSESLKSR NAVSMRY
Sbjct: 240 ---TPRRISFNNRSSASQSSPPDQDRAGPSELQSFSESLKSRLNAVSMRY 286

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255566215|ref|XP_002524095.1| protein binding protein, putative [Ricinus communis] gi|223536663|gb|EEF38305.1| protein binding protein, putative [Ricinus communis]

 Score =  373 bits (958), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 195/292 (66%), Positives = 217/292 (74%), Gaps = 20/292 (6%)

Query: 1   MEVLGMEEGKKPED-HMTSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHL 59
           MEVLG+EE KKPE  HM SAAAFVEGGIQ+SCDDACSICLEEF ESDPSTVT+CKHE+HL
Sbjct: 1   MEVLGVEEAKKPETTHMASAAAFVEGGIQESCDDACSICLEEFCESDPSTVTNCKHEYHL 60

Query: 60  QCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRNATIFHHPTFGDFE 119
           QC+LEWCQRSS CPMC QPISLKD +SQEL EAVE+ER  RA P RNATIF HPT GDFE
Sbjct: 61  QCILEWCQRSSDCPMCLQPISLKDPSSQELFEAVERERKFRAAPSRNATIFRHPTLGDFE 120

Query: 120 LQHLPVGASDTDLEEHILQHLTAAAAMGRAHHFGRRESHRNRSAAHGRPHFFVFSAHPGG 179
           LQHLPVGASD+DLEE I+QHL AAAAMGR HHFGRRE HRNR ++HGRPHF VFS HP  
Sbjct: 121 LQHLPVGASDSDLEERIIQHLAAAAAMGRGHHFGRREGHRNRQSSHGRPHFLVFSTHPSA 180

Query: 180 APPGAVAQ-----GGGTEPAPLAGASPSVPLSSSGNDSSQHMLQFHPIQTNQNSSSASGS 234
              G V+      GG  E A     SPSVPL+  GN S         +  +Q SSSASGS
Sbjct: 181 PSSGHVSSSLAQVGGENEQASDTVTSPSVPLAYRGNVS---------VVMDQ-SSSASGS 230

Query: 235 AVAQATRRGFSFNNRSTSSQTSSPTHDRAGPSDLQSFSESLKSRFNAVSMRY 286
            V     +G    +RS+SS +     DRAGPS+ QSFS+SLKSR NA+SMRY
Sbjct: 231 TVMPINNQG----DRSSSSHSPPSNQDRAGPSEFQSFSDSLKSRLNAMSMRY 278

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356550038|ref|XP_003543397.1| PREDICTED: E3 ubiquitin-protein ligase RHF2A-like [Glycine max]

 Score =  371 bits (953), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 195/297 (65%), Positives = 219/297 (73%), Gaps = 13/297 (4%)

Query: 1   MEVLGMEEGK------KPEDHMTSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCK 54
           ME  GMEE        K E H+TSAAAFVEGGIQD+CDDACSICLE F +SDPSTVTSCK
Sbjct: 1   MEGAGMEENNIINDDNKSEAHLTSAAAFVEGGIQDACDDACSICLEAFCDSDPSTVTSCK 60

Query: 55  HEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRNATIFHHPT 114
           HEFHLQC+LEWCQRSSQCPMCWQPISLKD TSQELLEAVE+ER+ R NP RNATIFHHPT
Sbjct: 61  HEFHLQCILEWCQRSSQCPMCWQPISLKDPTSQELLEAVERERNFRFNPSRNATIFHHPT 120

Query: 115 FGDFELQHLPVGASDTDLEEHILQHLTAAAAMGRAHHFGRRESHRNRSAAHGRPHFFVFS 174
            GDFELQHLPVGASD DLEE I+QHL AAAAMGRA H  RRE  RNRS+A GR HF VFS
Sbjct: 121 LGDFELQHLPVGASDADLEERIIQHLAAAAAMGRARHVARREGQRNRSSAQGRQHFLVFS 180

Query: 175 AHPGGAPPGAVA-----QGGGTEPAPLAGASPSVPLSSSGNDSSQHMLQFHPIQTNQNSS 229
            HP  +PP A A     Q G  EP P    +   P  ++G +SSQ  L   P+Q  Q S+
Sbjct: 181 THP-NSPPMAPASSSPSQRGDDEPTPTIDVANLSPTPATGEESSQPTL-VSPVQAEQVSA 238

Query: 230 SASGSAVAQATRRGFSFNNRSTSSQTSSPTHDRAGPSDLQSFSESLKSRFNAVSMRY 286
           S SG+       +G S+NNR + +Q+S  + DRAGPS+LQSFSESLKS+ NAVS RY
Sbjct: 239 SGSGTTALATDHQGSSYNNRRSPNQSSPSSQDRAGPSELQSFSESLKSKLNAVSTRY 295

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356543652|ref|XP_003540274.1| PREDICTED: E3 ubiquitin-protein ligase RHF2A-like [Glycine max]

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 197/300 (65%), Positives = 220/300 (73%), Gaps = 16/300 (5%)

Query: 1   MEVLGMEEGK---------KPEDHMTSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVT 51
           ME  GMEE           K E H+TSAAAFVEGGIQD+CDDACSICLE F +SDPSTVT
Sbjct: 1   MEGAGMEENNIINDDDNNNKSEAHLTSAAAFVEGGIQDACDDACSICLEAFCDSDPSTVT 60

Query: 52  SCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRNATIFH 111
           SCKHEFHLQC+LEWCQRSSQCPMCWQPISLKD TSQELLEAVE+ER+ R NP RNATIFH
Sbjct: 61  SCKHEFHLQCILEWCQRSSQCPMCWQPISLKDPTSQELLEAVERERNFRFNPSRNATIFH 120

Query: 112 HPTFGDFELQHLPVGASDTDLEEHILQHLTAAAAMGRAHHFGRRESHRNRSAAHGRPHFF 171
           HPT GDFELQHLPVGASD DLEE I+QHL AAAAMGRA H  RRE  RNRS+A GRPHF 
Sbjct: 121 HPTLGDFELQHLPVGASDADLEERIIQHLAAAAAMGRARHIARREGQRNRSSAQGRPHFL 180

Query: 172 VFSAHPGGAPPGAVA-----QGGGTEPAPLAGASPSVPLSSSGNDSSQHMLQFHPIQTNQ 226
           VFS +P  +PP A A     Q G  EP P    +   P  ++G +SSQ  L   PIQ  Q
Sbjct: 181 VFSTNP-NSPPMAPASSSPSQRGDDEPIPTIAVANLSPTPATGEESSQLTL-VPPIQAEQ 238

Query: 227 NSSSASGSAVAQATRRGFSFNNRSTSSQTSSPTHDRAGPSDLQSFSESLKSRFNAVSMRY 286
            S+S SGS       +G S+NNR + +Q+S  + DRAGPS+LQSFSESLKS+ NAVS RY
Sbjct: 239 VSASGSGSTALATDHQGSSYNNRRSPNQSSPSSQDRAGPSELQSFSESLKSKLNAVSTRY 298

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449437506|ref|XP_004136533.1| PREDICTED: E3 ubiquitin-protein ligase RHF2A-like [Cucumis sativus]

 Score =  369 bits (946), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 189/282 (67%), Positives = 220/282 (78%), Gaps = 2/282 (0%)

Query: 6   MEEGKKPEDHMTSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEW 65
           MEE K  E+ +TSAAAFVEGGIQ++CDDACSICLE+F ESDPSTVT+CKHEFHLQC+LEW
Sbjct: 1   MEEEKDSENRLTSAAAFVEGGIQEACDDACSICLEDFCESDPSTVTACKHEFHLQCILEW 60

Query: 66  CQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRNATIFHHPTFGDFELQHLPV 125
           CQRSSQCPMCWQ ISLKD TSQELLEAVE+ER+IRA P RN  +FHHP  G+FELQHLP+
Sbjct: 61  CQRSSQCPMCWQSISLKDPTSQELLEAVERERNIRATPVRNTAVFHHPALGNFELQHLPL 120

Query: 126 GASDTDLEEHILQHLTAAAAMGRAHHFGRRESHRNRSAAHGRPHFFVFSAHPGGAPPGAV 185
           G ++ +LEE I+QHL AAAAMGR HH G R   R+RS++HGRPHF VFS HPGG P    
Sbjct: 121 GVNNAELEERIIQHLAAAAAMGRTHHIG-RREGRSRSSSHGRPHFLVFSTHPGGPPEHVS 179

Query: 186 AQGGGTEPAPLAGASPSVPLSSSGNDSSQHMLQFHPIQTNQNSSSASGSAVAQATRRGFS 245
           A G  TEPA +  ASPS PL+  G++ SQH+ QF  IQT+  S SASGS  + A+RRG S
Sbjct: 180 ASGVHTEPAGITVASPSSPLTPRGDEPSQHIAQFPSIQTDHVSRSASGSNFS-ASRRGAS 238

Query: 246 FNNRSTSSQTSSPTHDRAGPSDLQSFSESLKSRFNAVSMRYN 287
              R ++S + SP  DRAGPS+ QSFSESLKSR NAVS RY 
Sbjct: 239 SGIRISTSDSPSPNLDRAGPSEFQSFSESLKSRLNAVSTRYK 280

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255637379|gb|ACU19018.1| unknown [Glycine max]

 Score =  368 bits (944), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 196/300 (65%), Positives = 219/300 (73%), Gaps = 16/300 (5%)

Query: 1   MEVLGMEEGK---------KPEDHMTSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVT 51
           ME  GMEE           K E H+TSAAAFVEGGIQD+CDDACSICLE F +SDPSTVT
Sbjct: 1   MEGAGMEENNIINDDDNNNKSEAHLTSAAAFVEGGIQDACDDACSICLEAFCDSDPSTVT 60

Query: 52  SCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRNATIFH 111
           SCKHEFHLQC+LEWCQRSSQCPMCWQPISLKD TSQELLEAVE+ER+ R NP RNATIFH
Sbjct: 61  SCKHEFHLQCILEWCQRSSQCPMCWQPISLKDPTSQELLEAVERERNFRFNPSRNATIFH 120

Query: 112 HPTFGDFELQHLPVGASDTDLEEHILQHLTAAAAMGRAHHFGRRESHRNRSAAHGRPHFF 171
           HPT GDFELQHLPVGASD DLEE I+QHL AAAAMGRA H  RRE  RNRS+A GRPHF 
Sbjct: 121 HPTLGDFELQHLPVGASDADLEERIIQHLAAAAAMGRARHIARREGQRNRSSAQGRPHFL 180

Query: 172 VFSAHPGGAPPGAVA-----QGGGTEPAPLAGASPSVPLSSSGNDSSQHMLQFHPIQTNQ 226
            FS +P  +PP A A     Q G  EP P    +   P  ++G +SSQ  L   PIQ  Q
Sbjct: 181 AFSTNP-NSPPMAPASSSPSQRGDDEPIPTIAVANLSPTPATGEESSQLTL-VPPIQAEQ 238

Query: 227 NSSSASGSAVAQATRRGFSFNNRSTSSQTSSPTHDRAGPSDLQSFSESLKSRFNAVSMRY 286
            S+S SGS       +G S+NNR + +Q+S  + DRAGPS+LQSFSESLKS+ NAVS RY
Sbjct: 239 VSASGSGSTALATDHQGSSYNNRRSPNQSSPSSQDRAGPSELQSFSESLKSKLNAVSTRY 298

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225436087|ref|XP_002277399.1| PREDICTED: E3 ubiquitin-protein ligase RHF2A [Vitis vinifera] gi|296084011|emb|CBI24399.3| unnamed protein product [Vitis vinifera]

 Score =  367 bits (942), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 189/292 (64%), Positives = 216/292 (73%), Gaps = 5/292 (1%)

Query: 1   MEVLGMEEGKKPEDHMTSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQ 60
           ME  GMEE  K E H+TSAAAFVEGGIQ++CDDACSICLE F +SDPSTVTSCKHEFHLQ
Sbjct: 1   MEAPGMEESNKSECHLTSAAAFVEGGIQEACDDACSICLEAFCDSDPSTVTSCKHEFHLQ 60

Query: 61  CVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRNATIFHHPTFGDFEL 120
           C+LEWCQRSSQCPMCWQPISLKD TSQELLEAVE+ER+ R NP RNATIFHHPT GDFEL
Sbjct: 61  CILEWCQRSSQCPMCWQPISLKDPTSQELLEAVERERTFRFNPSRNATIFHHPTLGDFEL 120

Query: 121 QHLPVGASDTDLEEHILQHLTAAAAMGRAHHFGRRESHRNRSAAHGRPHFFVFSAHP--- 177
           QHLPVGA+D +LEE I+QHL AAAAMGRA H  RRE  R RS+A GRP F VFSAHP   
Sbjct: 121 QHLPVGANDAELEERIIQHLAAAAAMGRARHIARREGQRTRSSAQGRPQFLVFSAHPSTP 180

Query: 178 -GGAPPGAVAQGGGTEPAP-LAGASPSVPLSSSGNDSSQHMLQFHPIQTNQNSSSASGSA 235
             G    + AQ G  EPAP +  A PS   ++ G +SS+        Q  + ++SASGS 
Sbjct: 181 QAGPASSSPAQRGEDEPAPAITAAMPSSLPTAVGEESSRLTTSQLSSQAEEITASASGSI 240

Query: 236 VAQATRRGFSFNNRSTSSQTSSPTHDRAGPSDLQSFSESLKSRFNAVSMRYN 287
           +    + G S NNR +  Q+     D+AGPS+ QSFSE+LKSRFNAVSMRY 
Sbjct: 241 IHTTNQHGTSSNNRRSPGQSLPSGQDKAGPSEFQSFSETLKSRFNAVSMRYK 292

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	303
TAIR|locus:2129525	371	RHF1A "RING-H2 group F1A" [Ara	0.415	0.339	0.496	3.4e-32
TAIR|locus:505006415	190	RHB1A "RING-H2 finger B1A" [Ar	0.181	0.289	0.436	1.5e-11
TAIR|locus:2035843	179	AT1G14200 [Arabidopsis thalian	0.333	0.564	0.298	3.5e-10
TAIR|locus:2177881	212	AT5G41350 [Arabidopsis thalian	0.211	0.301	0.426	6.1e-10
TAIR|locus:2076542	231	AT3G02290 [Arabidopsis thalian	0.145	0.190	0.5	8e-10
TAIR|locus:2143251	232	AT5G15790 [Arabidopsis thalian	0.145	0.189	0.5	2.2e-09
ZFIN|ZDB-GENE-041114-40	149	rnf24 "ring finger protein 24"	0.198	0.402	0.360	2.8e-09
UNIPROTKB|E1BQX5	716	E1BQX5 "Uncharacterized protei	0.303	0.128	0.364	9.6e-09
MGI|MGI:1916117	155	Rnf122 "ring finger protein 12	0.181	0.354	0.4	1e-08
RGD|1561238	95	RGD1561238 "similar to ring fi	0.181	0.578	0.4	1e-08

TAIR|locus:2129525 RHF1A "RING-H2 group F1A" [Arabidopsis thaliana (taxid:3702)]

 Score = 314 (115.6 bits), Expect = 3.4e-32, Sum P(2) = 3.4e-32
 Identities = 64/129 (49%), Positives = 83/129 (64%)

Query:    17 TSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCW 76
             +S+A  V     ++ DDACSICLE F+  DPSTVTSCKHE+HLQC++EW QRS +CP+CW
Sbjct:    28 SSSALVVASDDDNNTDDACSICLEPFTLQDPSTVTSCKHEYHLQCIIEWSQRSKECPICW 87

Query:    77 QPISLKDATSQELLEAVEQERSIRA-NPPRNATIFHHPTFGDFELQHLPVGASDTDLEEH 135
             Q   L+D  SQELL AVE+ER ++  N   ++ I  H +  DF  +      S  D  E 
Sbjct:    88 QLFVLRDPASQELLAAVEKERLLKTRNISSSSPISIHHSHDDFHSEEEESQFSSFD--EQ 145

Query:   136 ILQHLTAAA 144
              L+HLT AA
Sbjct:   146 FLRHLTEAA 154

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0016020 "membrane" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0009561 "megagametogenesis" evidence=IGI

GO:0010498 "proteasomal protein catabolic process" evidence=IDA

GO:0016567 "protein ubiquitination" evidence=IDA

GO:0051726 "regulation of cell cycle" evidence=IGI

GO:0055046 "microgametogenesis" evidence=IGI

GO:0000165 "MAPK cascade" evidence=RCA

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

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009617 "response to bacterium" evidence=RCA

GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=RCA

GO:0009867 "jasmonic acid mediated signaling pathway" evidence=RCA

GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

GO:0031348 "negative regulation of defense response" evidence=RCA

GO:0035304 "regulation of protein dephosphorylation" evidence=RCA

TAIR|locus:505006415 RHB1A "RING-H2 finger B1A" [Arabidopsis thaliana (taxid:3702)]

 Score = 160 (61.4 bits), Expect = 1.5e-11, P = 1.5e-11
 Identities = 24/55 (43%), Positives = 35/55 (63%)

Query:    29 DSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKD 83
             D  +D C IC E++   +P   T C+HEFHL C+LEW +RS +CP+C + +   D
Sbjct:   133 DEEEDCCPICFEDYDVENPRLTTKCEHEFHLSCLLEWIERSDRCPICDKEVVFDD 187

GO:0005634 "nucleus" evidence=ISM

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

GO:0048573 "photoperiodism, flowering" evidence=RCA

TAIR|locus:2035843 AT1G14200 [Arabidopsis thaliana (taxid:3702)]

 Score = 148 (57.2 bits), Expect = 3.5e-10, P = 3.5e-10
 Identities = 31/104 (29%), Positives = 56/104 (53%)

Query:     5 GMEEGKKP--EDHMTSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCV 62
             G ++G+ P  +  + +    V G  ++    +C+ICL+E+S+ D +    CKH+FH +CV
Sbjct:    77 GGKQGRSPALKSEVENMPRVVIGEDKEKYGGSCAICLDEWSKGDVAAEMPCKHKFHSKCV 136

Query:    63 LEWCQRSSQCPMCWQPISLKDATSQELLEAVEQERSIRANPPRN 106
              EW  R + CPMC   + +++   ++ +  +    SI A   RN
Sbjct:   137 EEWLGRHATCPMCRYEMPVEEVEEEKKI-GIWIGFSINAGDRRN 179

GO:0005634 "nucleus" evidence=ISM

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

GO:0006457 "protein folding" evidence=RCA

GO:0009408 "response to heat" evidence=RCA

GO:0009644 "response to high light intensity" evidence=RCA

GO:0034976 "response to endoplasmic reticulum stress" evidence=RCA

GO:0042542 "response to hydrogen peroxide" evidence=RCA

TAIR|locus:2177881 AT5G41350 [Arabidopsis thaliana (taxid:3702)]

 Score = 152 (58.6 bits), Expect = 6.1e-10, P = 6.1e-10
 Identities = 29/68 (42%), Positives = 38/68 (55%)

Query:     8 EGKKPEDHMTSAAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQ 67
             E  +  D   S A F+   I++  D  C ICLEE+   +P  V  C H FHL C+LEW +
Sbjct:   138 ESTEEIDPKLSKAVFIP--IEEEED--CPICLEEYDIENPKLVAKCDHHFHLACILEWME 193

Query:    68 RSSQCPMC 75
             RS  CP+C
Sbjct:   194 RSETCPVC 201

GO:0005634 "nucleus" evidence=ISM

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

GO:0005739 "mitochondrion" evidence=IDA

GO:0006914 "autophagy" evidence=RCA

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=RCA

TAIR|locus:2076542 AT3G02290 [Arabidopsis thaliana (taxid:3702)]

 Score = 156 (60.0 bits), Expect = 8.0e-10, P = 8.0e-10
 Identities = 22/44 (50%), Positives = 29/44 (65%)

Query:    32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMC 75
             +D C  CLEE++  +P  VT C H FHL C+ EW +RS  CP+C
Sbjct:   178 EDVCPTCLEEYTSENPKIVTKCSHHFHLSCIYEWMERSENCPVC 221

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2143251 AT5G15790 [Arabidopsis thaliana (taxid:3702)]

 Score = 153 (58.9 bits), Expect = 2.2e-09, P = 2.2e-09
 Identities = 22/44 (50%), Positives = 28/44 (63%)

Query:    32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMC 75
             +D C  CLEE+   +P  VT C H FHL C+ EW +RS  CP+C
Sbjct:   179 EDVCPTCLEEYISENPKIVTKCSHHFHLSCIYEWMERSENCPVC 222

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

ZFIN|ZDB-GENE-041114-40 rnf24 "ring finger protein 24" [Danio rerio (taxid:7955)]

 Score = 140 (54.3 bits), Expect = 2.8e-09, P = 2.8e-09
 Identities = 22/61 (36%), Positives = 37/61 (60%)

Query:    33 DACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEA 92
             + C++CLEEF + D   +  CKH FH +C+++W +    CP+C  P+ L+ A  Q + E 
Sbjct:    76 EICAVCLEEFKQKDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPV-LQLAQQQSMSEP 134

Query:    93 V 93
             +
Sbjct:   135 I 135

GO:0008270 "zinc ion binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|E1BQX5 E1BQX5 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 159 (61.0 bits), Expect = 9.6e-09, P = 9.6e-09
 Identities = 35/96 (36%), Positives = 47/96 (48%)

Query:    30 SCDDA--CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQ 87
             SC  A  C+ICLEEF+E     + SC HEFH +CV  W Q+   CP+C   I  +D+  Q
Sbjct:   257 SCSSAPVCAICLEEFTEGQELRIISCSHEFHRECVDPWLQQHHTCPLCMFNILARDSVDQ 316

Query:    88 ELLEAVEQERSIRANPPRNATIFH-HPTFGDFELQH 122
               + A  +       P R   +F  HP    + L H
Sbjct:   317 ATV-AGSRLAPRDMEPGRRLHLFRQHPGHSLYHLPH 351

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005109 "frizzled binding" evidence=IEA

GO:0005887 "integral to plasma membrane" evidence=IEA

GO:0038018 "Wnt receptor catabolic process" evidence=IEA

GO:0042787 "protein ubiquitination involved in ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0072089 "stem cell proliferation" evidence=IEA

MGI|MGI:1916117 Rnf122 "ring finger protein 122" [Mus musculus (taxid:10090)]

 Score = 135 (52.6 bits), Expect = 1.0e-08, P = 1.0e-08
 Identities = 22/55 (40%), Positives = 34/55 (61%)

Query:    35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQEL 89
             C++CLE+F   D   V  C+H FH +C+++W +    CPMC +PI+    TSQ +
Sbjct:    93 CAVCLEDFKGKDELGVLPCQHAFHRKCLVKWLEVRCVCPMCNKPIAGPTETSQSI 147

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

RGD|1561238 RGD1561238 "similar to ring finger protein 122 homolog" [Rattus norvegicus (taxid:10116)]

 Score = 135 (52.6 bits), Expect = 1.0e-08, P = 1.0e-08
 Identities = 22/55 (40%), Positives = 34/55 (61%)

Query:    35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQEL 89
             C++CLE+F   D   V  C+H FH +C+++W +    CPMC +PI+    TSQ +
Sbjct:    33 CAVCLEDFKGKDELGVLPCQHAFHRKCLVKWLEVRCVCPMCNKPIAGPTETSQSI 87

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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9ZT42	RHF2A_ARATH	6, ., 3, ., 2, ., -	0.5667	0.9141	0.7386	yes	no

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: eugene3.00160596 hypothetical protein (388 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	303
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	2e-12
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	1e-10
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	1e-09
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	2e-08
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	2e-07
smart00184	40	smart00184, RING, Ring finger	3e-07
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	7e-07
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	1e-06
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	1e-06
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	7e-05
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	5e-04
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	6e-04
pfam11793	70	pfam11793, FANCL_C, FANCL C-terminal domain	0.003

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

 Score = 60.1 bits (146), Expect = 2e-12
 Identities = 17/41 (41%), Positives = 25/41 (60%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMC 75
          C ICL+EF   +   V  C H FH +C+ +W + S+ CP+C
Sbjct: 3  CPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLC 43

Length = 46

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

 Score = 55.9 bits (135), Expect = 1e-10
 Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 3/46 (6%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPI 79
          C ICLEEF   +P  +  C H F   C+ +W +   + CP+C  PI
Sbjct: 2  CPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 53.6 bits (129), Expect = 1e-09
 Identities = 19/57 (33%), Positives = 24/57 (42%), Gaps = 10/57 (17%)

Query: 29 DSCDDACSICLEEFSE--------SDPSTV--TSCKHEFHLQCVLEWCQRSSQCPMC 75
          D  DD C+IC   F           D   V    C H FHL C+  W +  + CP+C
Sbjct: 16 DIEDDVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLC 72

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

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

 Score = 49.4 bits (118), Expect = 2e-08
 Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 2/44 (4%)

Query: 32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMC 75
          +  C ICL+     DP  +T C H F  +C+L + ++ S+CP+C
Sbjct: 2  ELECPICLDLLR--DPVVLTPCGHVFCRECILRYLKKKSKCPIC 43

Length = 45

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

 Score = 51.5 bits (123), Expect = 2e-07
 Identities = 18/46 (39%), Positives = 27/46 (58%), Gaps = 1/46 (2%)

Query: 35  CSICLEEFSESDPSTVTSCKHEFHLQCVLEWC-QRSSQCPMCWQPI 79
           C+IC+  F ++D   V  C H FH+ CV +W    S++CP+C   I
Sbjct: 326 CAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAI 371

Length = 374

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

 Score = 45.6 bits (108), Expect = 3e-07
 Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 3/42 (7%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWC-QRSSQCPMC 75
          C ICLEE+ +     +  C H F   C+ +W    ++ CP+C
Sbjct: 1  CPICLEEYLK--DPVILPCGHTFCRSCIRKWLESGNNTCPIC 40

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

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

 Score = 45.9 bits (109), Expect = 7e-07
 Identities = 20/65 (30%), Positives = 26/65 (40%), Gaps = 13/65 (20%)

Query: 32 DDACSICLEEFSESDPS----------TVTSCKHEFHLQCVLEWCQRSS---QCPMCWQP 78
          DD C IC   F  + P               CKH FH+ C+L+W    +    CPMC Q 
Sbjct: 21 DDVCGICRVSFDGTCPQCKFPGDDCPLVWGKCKHNFHMHCILKWLATETSKGLCPMCRQT 80

Query: 79 ISLKD 83
              +
Sbjct: 81 FVFAE 85

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

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

 Score = 49.6 bits (118), Expect = 1e-06
 Identities = 25/114 (21%), Positives = 38/114 (33%), Gaps = 13/114 (11%)

Query: 30  SCDDACSICLEEFSESDPSTVT----------SCKHEFHLQCVLEWCQRSSQCPMCWQPI 79
           + D  C+IC++E    D   +            C H  HL C+  W +R   CP+C +P+
Sbjct: 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPV 344

Query: 80  --SLKDATSQELLEAVEQERSIRANPPRNATIFHHPTFGDFELQHLPVGASDTD 131
                  T         Q  +   NP    T    P   +         AS  +
Sbjct: 345 IFDQSSPTPASPNVRNTQIATQVPNPDNTPTTTAVPGITN-SSNQGDPQASTFN 397

Length = 491

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

 Score = 44.0 bits (104), Expect = 1e-06
 Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 3/42 (7%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQ-RSSQCPMC 75
          C ICLEE    DP T+  C H F  +C+L W +  +  CP+C
Sbjct: 1  CPICLEEPK--DPVTILPCGHLFCSKCILSWLESGNVTCPLC 40

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

>gnl|CDD|227521 COG5194, APC11, Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]

 Score = 40.6 bits (95), Expect = 7e-05
 Identities = 15/56 (26%), Positives = 18/56 (32%), Gaps = 2/56 (3%)

Query: 32 DDACSICLEEFSESDPSTVT--SCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDAT 85
             C  C    +  D   V    C H FH  C+  W      CP+  Q   L D  
Sbjct: 31 MGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLADGG 86

Length = 88

>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional

 Score = 40.5 bits (95), Expect = 5e-04
 Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 5/52 (9%)

Query: 29  DSCDDACSICLEEFSESDPSTV-----TSCKHEFHLQCVLEWCQRSSQCPMC 75
            S D  C+IC+E+  + +   +     ++C H F ++C+  W +  + CP+C
Sbjct: 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVC 222

Length = 238

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

 Score = 41.2 bits (96), Expect = 6e-04
 Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 6/47 (12%)

Query: 35   CSIC---LEEFSESDPS-TVTSCKHEFHLQCVLEWCQRS--SQCPMC 75
            C+IC   L+    S PS    +CK++FH +C+ +W   S  S CP+C
Sbjct: 1472 CAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLC 1518

Length = 1525

>gnl|CDD|204746 pfam11793, FANCL_C, FANCL C-terminal domain

 Score = 35.1 bits (81), Expect = 0.003
 Identities = 18/66 (27%), Positives = 24/66 (36%), Gaps = 16/66 (24%)

Query: 35 CSICLEEFSESDPSTVTSCKHE-----FHLQCVLEW--CQRSS---------QCPMCWQP 78
          C IC     +       SC +      FH+ C+ EW    R S          CP C   
Sbjct: 5  CGICYAYRLDGGEIPDISCDNPKCGLPFHIACLYEWLRTLRDSRQSFNVSFGTCPYCKAK 64

Query: 79 ISLKDA 84
          IS+K +
Sbjct: 65 ISVKFS 70

This domain is found at the C-terminus of the Fancl protein in humans which is the putative E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2. Length = 70

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	303
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.36
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.12
PHA02929	238	N1R/p28-like protein; Provisional	99.08
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.04
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.04
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.04
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.01
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.99
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	98.94
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.92
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.92
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.87
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.87
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.86
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.86
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	98.82
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.8
PHA02926	242	zinc finger-like protein; Provisional	98.77
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.77
PF14634	44	zf-RING_5: zinc-RING finger domain	98.72
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.67
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.59
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.5
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.5
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.49
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.48
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.46
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.35
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.33
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.3
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.26
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.24
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.23
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.2
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	97.97
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.92
KOG2660	331	consensus Locus-specific chromosome binding protei	97.82
COG5219	1525	Uncharacterized conserved protein, contains RING Z	97.78
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	97.76
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.75
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.74
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	97.68
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.64
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.57
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.45
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.39
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	97.38
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.38
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.36
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.33
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.24
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.23
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.22
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.2
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.15
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.14
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.08
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.01
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	96.79
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.79
COG5152	259	Uncharacterized conserved protein, contains RING a	96.66
KOG1002	791	consensus Nucleotide excision repair protein RAD16	96.31
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.22
COG5222	427	Uncharacterized conserved protein, contains RING Z	96.12
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.06
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.97
COG5236	493	Uncharacterized conserved protein, contains RING Z	95.96
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	95.54
KOG3039	303	consensus Uncharacterized conserved protein [Funct	95.52
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	95.43
KOG4739	233	consensus Uncharacterized protein involved in syna	95.33
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.3
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	95.29
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	95.13
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	95.08
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	95.08
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	94.79
PHA03096	284	p28-like protein; Provisional	94.48
PF04641	260	Rtf2: Rtf2 RING-finger	94.15
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	93.37
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	93.35
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	93.25
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	93.24
KOG1940	276	consensus Zn-finger protein [General function pred	92.93
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	92.9
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	92.9
PHA02825	162	LAP/PHD finger-like protein; Provisional	92.75
KOG1001	674	consensus Helicase-like transcription factor HLTF/	92.67
KOG0298	1394	consensus DEAD box-containing helicase-like transc	92.45
PHA02862	156	5L protein; Provisional	92.42
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	92.14
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	92.14
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	90.56
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	90.48
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	90.26
KOG3002	299	consensus Zn finger protein [General function pred	89.24
KOG4367	699	consensus Predicted Zn-finger protein [Function un	89.12
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	87.9
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	86.26
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	85.63
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	85.39
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	85.2
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	85.11
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	85.06
KOG3053	293	consensus Uncharacterized conserved protein [Funct	83.94
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	83.41
KOG3899	381	consensus Uncharacterized conserved protein [Funct	83.34
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	83.01
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	82.72
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	80.91
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	80.4

>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=99.36  E-value=3e-13  Score=92.31  Aligned_cols=44  Identities=43%  Similarity=1.099  Sum_probs=39.3

Q ss_pred             cccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCc
Q 022060           33 DACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCW   76 (303)
Q Consensus        33 ~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR   76 (303)
                      ++|+||++.|...+.++.++|+|.||..||.+|++.+..||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence            46999999998777888889999999999999999999999997

...

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

Probab=99.12  E-value=2.9e-11  Score=115.67  Aligned_cols=48  Identities=35%  Similarity=1.019  Sum_probs=43.8

Q ss_pred             cccccccccccCCCCeeeccCCccccHHhHHHHHhcC-CCCCCCcccCc
Q 022060           33 DACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS-SQCPMCWQPIS   80 (303)
Q Consensus        33 ~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~-~~CP~CR~~l~   80 (303)
                      ++|.||+|+|..++.+++|+|+|.||..||+.|+... ..||+||..+.
T Consensus       230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~  278 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIR  278 (348)
T ss_pred             ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCC
Confidence            5899999999999999999999999999999999765 56999999764

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.08  E-value=9e-11  Score=107.54  Aligned_cols=53  Identities=28%  Similarity=0.830  Sum_probs=43.1

Q ss_pred             CCCCccccccccccccCCCC-----eeeccCCccccHHhHHHHHhcCCCCCCCcccCc
Q 022060           28 QDSCDDACSICLEEFSESDP-----STVTSCKHEFHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~~~~-----~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      +.+.+.+|+||++.+.+...     ..+++|+|.||..||..|+..+.+||+||..+.
T Consensus       170 ~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~  227 (238)
T PHA02929        170 NRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI  227 (238)
T ss_pred             cCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence            34557899999999743221     245689999999999999999999999999875

>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.04  E-value=1.7e-10  Score=87.42  Aligned_cols=45  Identities=36%  Similarity=1.006  Sum_probs=36.1

Q ss_pred             ccccccccccccC----------CCCeeeccCCccccHHhHHHHHhcCCCCCCCc
Q 022060           32 DDACSICLEEFSE----------SDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCW   76 (303)
Q Consensus        32 d~~C~ICle~f~~----------~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR   76 (303)
                      ++.|.||++.|.+          .-++.+..|+|.||..||..|++.+.+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            4459999999931          23345678999999999999999999999997

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 ....

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.04  E-value=1.3e-10  Score=102.96  Aligned_cols=54  Identities=33%  Similarity=0.784  Sum_probs=42.5

Q ss_pred             CCCCccccccccccccCCCCeeeccCCccccHHhHHHHHhc----------------CCCCCCCcccCcCCCc
Q 022060           28 QDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR----------------SSQCPMCWQPISLKDA   84 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~----------------~~~CP~CR~~l~~~d~   84 (303)
                      +...+.+|+||++.+  .++ +++.|+|.||+.||..|+..                ...||+||..+....+
T Consensus        14 ~~~~~~~CpICld~~--~dP-VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~L   83 (193)
T PLN03208         14 DSGGDFDCNICLDQV--RDP-VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATL   83 (193)
T ss_pred             cCCCccCCccCCCcC--CCc-EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcE
Confidence            344578899999998  444 55799999999999999842                2479999999975543

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

Probab=99.04  E-value=1.1e-10  Score=108.27  Aligned_cols=52  Identities=33%  Similarity=0.901  Sum_probs=44.2

Q ss_pred             CCccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCc
Q 022060           30 SCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDA   84 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~   84 (303)
                      +.+..|.|||+..   ..+..++|||.|||.||.+|+..+..||+||..+...++
T Consensus       237 ~a~~kC~LCLe~~---~~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskv  288 (293)
T KOG0317|consen  237 EATRKCSLCLENR---SNPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKV  288 (293)
T ss_pred             CCCCceEEEecCC---CCCCcCcCcchHHHHHHHHHHccccCCCcccccCCCcce
Confidence            3467799999996   345778999999999999999999999999999876543

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

Probab=99.01  E-value=1.5e-10  Score=104.32  Aligned_cols=54  Identities=35%  Similarity=0.751  Sum_probs=43.3

Q ss_pred             CCCccccccccccccCCCCeeeccCCccccHHhHHHHHhc---CCCCCCCcccCcCCCcc
Q 022060           29 DSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR---SSQCPMCWQPISLKDAT   85 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~---~~~CP~CR~~l~~~d~~   85 (303)
                      +...-+|.||||.-  .+ ++++.|||.|||.||++|++.   ++.||+||..+..+...
T Consensus        44 ~~~~FdCNICLd~a--kd-PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vv  100 (230)
T KOG0823|consen   44 DGGFFDCNICLDLA--KD-PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVV  100 (230)
T ss_pred             CCCceeeeeecccc--CC-CEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEE
Confidence            44466899999996  34 566789999999999999975   45799999988766544

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

Probab=98.99  E-value=2.5e-10  Score=75.96  Aligned_cols=39  Identities=41%  Similarity=1.144  Sum_probs=33.9

Q ss_pred             cccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCC
Q 022060           35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMC   75 (303)
Q Consensus        35 C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~C   75 (303)
                      |+||++.+  .+++++++|||.||..||.+|++....||+|
T Consensus         1 C~iC~~~~--~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDEL--RDPVVVTPCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB---SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcc--cCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence            89999999  5666789999999999999999998899998

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

Probab=98.94  E-value=4.5e-09  Score=100.39  Aligned_cols=57  Identities=30%  Similarity=0.846  Sum_probs=44.5

Q ss_pred             hhcCCCCCCccccccccccc-cCC---------CCeeeccCCccccHHhHHHHHhcCCCCCCCcccCc
Q 022060           23 VEGGIQDSCDDACSICLEEF-SES---------DPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        23 ~~~~~~~~~d~~C~ICle~f-~~~---------~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      .+.++ ...|..|.||+|++ ..+         ..++.++|||.||.+|+.-|++++++||+||.++.
T Consensus       279 t~eql-~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~i  345 (491)
T COG5243         279 TEEQL-TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVI  345 (491)
T ss_pred             hhhhh-cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccc
Confidence            33333 44588999999994 322         12356799999999999999999999999999853

>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A

Probab=98.92  E-value=8.4e-10  Score=77.26  Aligned_cols=47  Identities=34%  Similarity=0.798  Sum_probs=39.3

Q ss_pred             CccccccccccccCCCCeeeccCCcc-ccHHhHHHHHhcCCCCCCCcccCc
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHE-FHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~-Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      ++..|.||++.+   ..+.+++|+|. ||..|+..|++....||+||+++.
T Consensus         1 ~~~~C~iC~~~~---~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    1 EDEECPICFENP---RDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             -HSB-TTTSSSB---SSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             CcCCCccCCccC---CceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            367899999997   33677799999 999999999999999999999875

...

>smart00504 Ubox Modified RING finger domain

Probab=98.92  E-value=1.7e-09  Score=78.54  Aligned_cols=58  Identities=21%  Similarity=0.430  Sum_probs=47.5

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCcchHHHHHH
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEA   92 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~~~~~l~e~   92 (303)
                      +..|+||++.+  .+| .+++|||.||..||.+|++.+..||+|+..+...++..+..+..
T Consensus         1 ~~~Cpi~~~~~--~~P-v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~~~l~~   58 (63)
T smart00504        1 EFLCPISLEVM--KDP-VILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPNLALKS   58 (63)
T ss_pred             CcCCcCCCCcC--CCC-EECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeCHHHHH
Confidence            35799999999  555 45699999999999999988889999999997777666544443

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

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

Probab=98.87  E-value=7.6e-10  Score=96.22  Aligned_cols=53  Identities=34%  Similarity=0.709  Sum_probs=43.6

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCc
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDA   84 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~   84 (303)
                      .--.|+|||+.+....+ .-++|||.||..||...++....||+|++.|..+.+
T Consensus       130 ~~~~CPiCl~~~sek~~-vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~~  182 (187)
T KOG0320|consen  130 GTYKCPICLDSVSEKVP-VSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQF  182 (187)
T ss_pred             cccCCCceecchhhccc-cccccchhHHHHHHHHHHHhCCCCCCcccccchhhh
Confidence            34569999999943222 447999999999999999999999999998876654

>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=98.87  E-value=1.8e-09  Score=71.87  Aligned_cols=44  Identities=41%  Similarity=1.090  Sum_probs=38.2

Q ss_pred             ccccccccccCCCCeeeccCCccccHHhHHHHHhc-CCCCCCCcccC
Q 022060           34 ACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPI   79 (303)
Q Consensus        34 ~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l   79 (303)
                      +|+||++.+  .++..+++|+|.||..|+..|+.. ...||.|+..+
T Consensus         1 ~C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEF--REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhh--hCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            499999998  566777779999999999999987 77899998764

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

Probab=98.86  E-value=1.4e-09  Score=73.79  Aligned_cols=38  Identities=37%  Similarity=0.947  Sum_probs=28.7

Q ss_pred             cccccccccCCCCeeeccCCccccHHhHHHHHhcC----CCCCCC
Q 022060           35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS----SQCPMC   75 (303)
Q Consensus        35 C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~----~~CP~C   75 (303)
                      |+||++.|  .+|++ ++|||.||..||..|++..    ..||.|
T Consensus         1 CpiC~~~~--~~Pv~-l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLF--KDPVS-LPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB---SSEEE--SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhh--CCccc-cCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999  56655 5999999999999999653    369987

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

Probab=98.86  E-value=2e-09  Score=83.51  Aligned_cols=52  Identities=42%  Similarity=1.013  Sum_probs=41.3

Q ss_pred             Ccccccccccccc----------CCCCeeeccCCccccHHhHHHHHhc---CCCCCCCcccCcCC
Q 022060           31 CDDACSICLEEFS----------ESDPSTVTSCKHEFHLQCVLEWCQR---SSQCPMCWQPISLK   82 (303)
Q Consensus        31 ~d~~C~ICle~f~----------~~~~~~vl~C~H~Fc~~CI~~Wl~~---~~~CP~CR~~l~~~   82 (303)
                      .|+.|.||...|.          +.-++..-.|+|.||..||++|+..   +..||+||+++..+
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k   84 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKFK   84 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeeeC
Confidence            3788999999885          1224555689999999999999975   46899999988644

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

Probab=98.82  E-value=1.9e-09  Score=100.50  Aligned_cols=49  Identities=37%  Similarity=0.911  Sum_probs=44.1

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHh-cCCCCCCCcccCc
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQ-RSSQCPMCWQPIS   80 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~-~~~~CP~CR~~l~   80 (303)
                      ..+|.||++.|...+.+++++|.|.||..|+.+|+. .+..||+||..+.
T Consensus       323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP  372 (374)
T COG5540         323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP  372 (374)
T ss_pred             CceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence            467999999997777889999999999999999998 5789999999875

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.80  E-value=4.9e-09  Score=102.54  Aligned_cols=60  Identities=27%  Similarity=0.560  Sum_probs=48.8

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCcchHHHHHHH
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAV   93 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~~~~~l~e~~   93 (303)
                      ....|+||++.|  ..++ +++|+|.||..||..|+.....||+|+..+....+..+..+..+
T Consensus        25 ~~l~C~IC~d~~--~~Pv-itpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~N~~L~~i   84 (397)
T TIGR00599        25 TSLRCHICKDFF--DVPV-LTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRSNWLVSEI   84 (397)
T ss_pred             cccCCCcCchhh--hCcc-CCCCCCchhHHHHHHHHhCCCCCCCCCCccccccCccchHHHHH
Confidence            378999999999  5554 67999999999999999888899999999876666555544443

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

>PHA02926 zinc finger-like protein; Provisional

Probab=98.77  E-value=3.4e-09  Score=95.34  Aligned_cols=54  Identities=26%  Similarity=0.644  Sum_probs=41.7

Q ss_pred             CCCCCccccccccccccCC------CCeeeccCCccccHHhHHHHHhcC------CCCCCCcccCc
Q 022060           27 IQDSCDDACSICLEEFSES------DPSTVTSCKHEFHLQCVLEWCQRS------SQCPMCWQPIS   80 (303)
Q Consensus        27 ~~~~~d~~C~ICle~f~~~------~~~~vl~C~H~Fc~~CI~~Wl~~~------~~CP~CR~~l~   80 (303)
                      .+.+.+.+|+||+|.+...      ....+.+|+|.||..||..|...+      ..||+||..+.
T Consensus       165 ~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        165 YRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             HhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            3556689999999986322      123567999999999999999753      45999999875

>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=98.77  E-value=4.8e-09  Score=70.09  Aligned_cols=39  Identities=44%  Similarity=1.162  Sum_probs=34.1

Q ss_pred             cccccccccCCCCeeeccCCccccHHhHHHHHh--cCCCCCCC
Q 022060           35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQ--RSSQCPMC   75 (303)
Q Consensus        35 C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~--~~~~CP~C   75 (303)
                      |+||++.+  .++..+++|+|.||..||..|++  ....||+|
T Consensus         1 C~iC~~~~--~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPF--EDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBC--SSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccc--cCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            89999998  56666889999999999999998  45679988

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 ....

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.72  E-value=1.1e-08  Score=69.95  Aligned_cols=44  Identities=36%  Similarity=0.870  Sum_probs=38.7

Q ss_pred             ccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcc
Q 022060           34 ACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQ   77 (303)
Q Consensus        34 ~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~   77 (303)
                      .|+||++.|.+..+..+++|+|.||..|+..+......||+|++
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            49999999965667889999999999999999866778999985

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

Probab=98.67  E-value=9.6e-09  Score=97.16  Aligned_cols=61  Identities=28%  Similarity=0.670  Sum_probs=51.7

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCcchHHHHHHHHH
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQ   95 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~~~~~l~e~~~~   95 (303)
                      -+.|.||.|+|  ..+ .+++|+|.||..||..+|..+..||.|+.++.+.++..+.+++.+.+
T Consensus        23 lLRC~IC~eyf--~ip-~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n~il~Eiv~   83 (442)
T KOG0287|consen   23 LLRCGICFEYF--NIP-MITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNNRILDEIVK   83 (442)
T ss_pred             HHHHhHHHHHh--cCc-eeccccchHHHHHHHHHhccCCCCCceecccchhhhhhhhHHHHHHH
Confidence            56799999999  444 55689999999999999999999999999999888887766655443

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

Probab=98.59  E-value=7.7e-08  Score=91.58  Aligned_cols=49  Identities=27%  Similarity=0.691  Sum_probs=42.4

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhc-CCCCCCCcccCcCC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPISLK   82 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l~~~   82 (303)
                      ++.|+|||+.+  ...++...|.|.||.+||..-+.. .+.||.||+.+..+
T Consensus        43 ~v~c~icl~ll--k~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Sk   92 (381)
T KOG0311|consen   43 QVICPICLSLL--KKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSK   92 (381)
T ss_pred             hhccHHHHHHH--HhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcccc
Confidence            77899999999  666788899999999999888865 67999999988544

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

Probab=98.50  E-value=1.7e-07  Score=70.78  Aligned_cols=63  Identities=22%  Similarity=0.381  Sum_probs=46.9

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhc-CCCCCCCcccCcCCCcchHHHHHHHHHH
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPISLKDATSQELLEAVEQE   96 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l~~~d~~~~~l~e~~~~e   96 (303)
                      ++..|+||.+.|  .+|+. ++|||.|+..||..|+.. ...||+|+..+...++.++..+.....+
T Consensus         3 ~~f~CpIt~~lM--~dPVi-~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn~~Lk~~I~~   66 (73)
T PF04564_consen    3 DEFLCPITGELM--RDPVI-LPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPNRALKSAIEE   66 (73)
T ss_dssp             GGGB-TTTSSB---SSEEE-ETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-HHHHHHHHH
T ss_pred             cccCCcCcCcHh--hCcee-CCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceECHHHHHHHHH
Confidence            367899999999  56554 589999999999999988 7899999999998888887666554443

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 ....

>smart00184 RING Ring finger

Probab=98.50  E-value=1.2e-07  Score=60.80  Aligned_cols=38  Identities=39%  Similarity=1.095  Sum_probs=32.4

Q ss_pred             cccccccccCCCCeeeccCCccccHHhHHHHHh-cCCCCCCC
Q 022060           35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQ-RSSQCPMC   75 (303)
Q Consensus        35 C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~-~~~~CP~C   75 (303)
                      |+||++..   ..+.+++|+|.||..|+..|+. ....||+|
T Consensus         1 C~iC~~~~---~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEEL---KDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCC---CCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            78999984   4466679999999999999998 56679987

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)

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

Probab=98.49  E-value=4.4e-08  Score=99.89  Aligned_cols=51  Identities=33%  Similarity=0.785  Sum_probs=42.7

Q ss_pred             CccccccccccccCCCC--eeeccCCccccHHhHHHHHhcCCCCCCCcccCcC
Q 022060           31 CDDACSICLEEFSESDP--STVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISL   81 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~--~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~   81 (303)
                      .++.|.||+|.+.....  ++.++|+|.||..|+..|++++.+||+||..+..
T Consensus       290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~~  342 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLYD  342 (543)
T ss_pred             cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhhc
Confidence            37889999999943322  5667999999999999999999999999995543

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

Probab=98.48  E-value=6e-08  Score=96.17  Aligned_cols=52  Identities=40%  Similarity=0.769  Sum_probs=42.2

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcC-----CCCCCCcccCcCCCcch
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS-----SQCPMCWQPISLKDATS   86 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~-----~~CP~CR~~l~~~d~~~   86 (303)
                      +..|||||+..  .- +..+.|||+||+.||..++...     ..||+||..|..+++.+
T Consensus       186 ~~~CPICL~~~--~~-p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~p  242 (513)
T KOG2164|consen  186 DMQCPICLEPP--SV-PVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLP  242 (513)
T ss_pred             CCcCCcccCCC--Cc-ccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceee
Confidence            77899999997  33 3445799999999999988653     46999999998877654

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

Probab=98.46  E-value=7.4e-08  Score=88.59  Aligned_cols=50  Identities=36%  Similarity=0.824  Sum_probs=41.7

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHH-HHhcCCC-CCCCcccCcCCCc
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLE-WCQRSSQ-CPMCWQPISLKDA   84 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~-Wl~~~~~-CP~CR~~l~~~d~   84 (303)
                      |-.|.||++..  .. +..++|+|.||+.||.. |-.++.. ||+||+.+..++.
T Consensus       215 d~kC~lC~e~~--~~-ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v  266 (271)
T COG5574         215 DYKCFLCLEEP--EV-PSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV  266 (271)
T ss_pred             ccceeeeeccc--CC-cccccccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence            66799999997  44 45569999999999999 9877765 9999999877653

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

Probab=98.35  E-value=3.2e-07  Score=62.62  Aligned_cols=34  Identities=41%  Similarity=0.898  Sum_probs=21.6

Q ss_pred             ccccccccc-CCCCeeeccCCccccHHhHHHHHhcC
Q 022060           35 CSICLEEFS-ESDPSTVTSCKHEFHLQCVLEWCQRS   69 (303)
Q Consensus        35 C~ICle~f~-~~~~~~vl~C~H~Fc~~CI~~Wl~~~   69 (303)
                      |+||++ |. +..++.+|+|||.||..||.+|+...
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~   35 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKS   35 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcC
Confidence            899999 63 34567778999999999999999743

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

Probab=98.33  E-value=2.1e-07  Score=68.40  Aligned_cols=57  Identities=28%  Similarity=0.695  Sum_probs=29.5

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCcchHHHHHH
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEA   92 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~~~~~l~e~   92 (303)
                      -..|++|.+.|  .+|+.+..|.|.||..||...+.  ..||+|+.+...+|...+..+..
T Consensus         7 lLrCs~C~~~l--~~pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD~~~NrqLd~   63 (65)
T PF14835_consen    7 LLRCSICFDIL--KEPVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQDIQINRQLDS   63 (65)
T ss_dssp             TTS-SSS-S----SS-B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS----HHHHH
T ss_pred             hcCCcHHHHHh--cCCceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHHHHhhhhhhc
Confidence            46799999999  78888889999999999977554  35999999999898877766554

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

Probab=98.30  E-value=3.8e-07  Score=69.55  Aligned_cols=36  Identities=31%  Similarity=0.700  Sum_probs=31.4

Q ss_pred             eeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCC
Q 022060           48 STVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKD   83 (303)
Q Consensus        48 ~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d   83 (303)
                      +..-.|.|.||.+||.+||..+..||++|+++...+
T Consensus        49 v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~~   84 (88)
T COG5194          49 VVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLAD   84 (88)
T ss_pred             EEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEec
Confidence            445679999999999999999999999999986544

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

Probab=98.26  E-value=3.4e-07  Score=82.60  Aligned_cols=45  Identities=31%  Similarity=0.778  Sum_probs=39.1

Q ss_pred             CCccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcc
Q 022060           30 SCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQ   77 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~   77 (303)
                      .++..|+||++.|  .++ ++++|+|.||..||..|+.....||.||.
T Consensus        11 ~~~~~C~iC~~~~--~~p-~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   11 QEELTCPICLEYF--REP-VLLPCGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             cccccChhhHHHh--hcC-ccccccchHhHHHHHHhcCCCcCCcccCC
Confidence            3488999999999  555 77899999999999999885568999995

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

Probab=98.24  E-value=2.7e-07  Score=69.81  Aligned_cols=51  Identities=39%  Similarity=0.931  Sum_probs=39.0

Q ss_pred             cccccccccccc----------CCCCeeeccCCccccHHhHHHHHhc---CCCCCCCcccCcCC
Q 022060           32 DDACSICLEEFS----------ESDPSTVTSCKHEFHLQCVLEWCQR---SSQCPMCWQPISLK   82 (303)
Q Consensus        32 d~~C~ICle~f~----------~~~~~~vl~C~H~Fc~~CI~~Wl~~---~~~CP~CR~~l~~~   82 (303)
                      +++|.||.-.|.          ++-|...-.|.|.||..||++|+..   +..||+||+.+..+
T Consensus        20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~~   83 (84)
T KOG1493|consen   20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQFK   83 (84)
T ss_pred             CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEec
Confidence            448999988884          2234445579999999999999964   45799999987643

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.23  E-value=9.1e-07  Score=83.80  Aligned_cols=54  Identities=24%  Similarity=0.477  Sum_probs=39.4

Q ss_pred             ccccccccccccCCCC--eeeccCCccccHHhHHHHH-hcCCCCCCCcccCcCCCcc
Q 022060           32 DDACSICLEEFSESDP--STVTSCKHEFHLQCVLEWC-QRSSQCPMCWQPISLKDAT   85 (303)
Q Consensus        32 d~~C~ICle~f~~~~~--~~vl~C~H~Fc~~CI~~Wl-~~~~~CP~CR~~l~~~d~~   85 (303)
                      +..||||.........  ..+..|||.||..|+..++ .....||.|+..+....+.
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr   59 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFR   59 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhcc
Confidence            5679999995322222  2333799999999999966 4456899999988776644

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).

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

Probab=98.20  E-value=7.8e-07  Score=82.91  Aligned_cols=51  Identities=24%  Similarity=0.421  Sum_probs=43.0

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCcc
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDAT   85 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~~   85 (303)
                      -+.|-||-+.|  .. +..++|+|.||..||..+|..+..||+||....+....
T Consensus        25 ~lrC~IC~~~i--~i-p~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~esrlr   75 (391)
T COG5432          25 MLRCRICDCRI--SI-PCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCESRLR   75 (391)
T ss_pred             HHHhhhhhhee--ec-ceecccccchhHHHHHHHhcCCCCCccccccHHhhhcc
Confidence            66799999998  44 35579999999999999999999999999987654433

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

Probab=97.97  E-value=1.5e-06  Score=80.33  Aligned_cols=53  Identities=32%  Similarity=0.802  Sum_probs=41.3

Q ss_pred             CCccccccccccccCCC-------CeeeccCCccccHHhHHHHHh--cCCCCCCCcccCcCC
Q 022060           30 SCDDACSICLEEFSESD-------PSTVTSCKHEFHLQCVLEWCQ--RSSQCPMCWQPISLK   82 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~-------~~~vl~C~H~Fc~~CI~~Wl~--~~~~CP~CR~~l~~~   82 (303)
                      -+|..|.||-..+....       ....+.|+|.||..||..|+.  ++++||+|++.+..+
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~  283 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLK  283 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHh
Confidence            34778999998874322       345579999999999999984  467899999887543

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

Probab=97.92  E-value=1.8e-06  Score=64.92  Aligned_cols=50  Identities=40%  Similarity=0.893  Sum_probs=24.3

Q ss_pred             ccccccccccccCCC--Ceee---ccCCccccHHhHHHHHhc---C--------CCCCCCcccCcC
Q 022060           32 DDACSICLEEFSESD--PSTV---TSCKHEFHLQCVLEWCQR---S--------SQCPMCWQPISL   81 (303)
Q Consensus        32 d~~C~ICle~f~~~~--~~~v---l~C~H~Fc~~CI~~Wl~~---~--------~~CP~CR~~l~~   81 (303)
                      +.+|.||+..+.+..  +..+   ..|+..||..||.+|+..   .        ..||.|+++|.-
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            578999999875222  2222   379999999999999963   1        149999998753

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

Probab=97.82  E-value=5.3e-06  Score=78.62  Aligned_cols=49  Identities=29%  Similarity=0.645  Sum_probs=43.5

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLK   82 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~   82 (303)
                      -.+|.+|-.+|  .+..+++.|.|.||..||.+++...+.||.|...+...
T Consensus        15 ~itC~LC~GYl--iDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   15 HITCRLCGGYL--IDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             ceehhhcccee--ecchhHHHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence            67899999999  67778889999999999999999999999998776443

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

Probab=97.78  E-value=6e-06  Score=86.83  Aligned_cols=49  Identities=31%  Similarity=0.935  Sum_probs=38.4

Q ss_pred             cccccccccccc--CC-CC-eeeccCCccccHHhHHHHHhc--CCCCCCCcccCc
Q 022060           32 DDACSICLEEFS--ES-DP-STVTSCKHEFHLQCVLEWCQR--SSQCPMCWQPIS   80 (303)
Q Consensus        32 d~~C~ICle~f~--~~-~~-~~vl~C~H~Fc~~CI~~Wl~~--~~~CP~CR~~l~   80 (303)
                      -.+|+||+..+.  +. -| -++..|+|.||..|+.+|++.  +..||+||..+.
T Consensus      1469 ~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1469 HEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             cchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            567999998874  11 12 356789999999999999976  468999997764

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

Probab=97.76  E-value=1.3e-05  Score=79.52  Aligned_cols=49  Identities=33%  Similarity=0.861  Sum_probs=38.5

Q ss_pred             ccccccccccccCC--------------CCeeeccCCccccHHhHHHHHhc-CCCCCCCcccCc
Q 022060           32 DDACSICLEEFSES--------------DPSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPIS   80 (303)
Q Consensus        32 d~~C~ICle~f~~~--------------~~~~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l~   80 (303)
                      ...|+||+..+.-.              ....+++|.|.||..|+..|... +-.||.||.++.
T Consensus       571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP  634 (636)
T KOG0828|consen  571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP  634 (636)
T ss_pred             cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence            55699999887311              11345799999999999999985 558999999875

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

Probab=97.75  E-value=1.7e-05  Score=76.48  Aligned_cols=57  Identities=35%  Similarity=0.867  Sum_probs=42.6

Q ss_pred             CCCCCCccccccccccccCCC-----CeeeccCCccccHHhHHHHHh--c-----CCCCCCCcccCcCC
Q 022060           26 GIQDSCDDACSICLEEFSESD-----PSTVTSCKHEFHLQCVLEWCQ--R-----SSQCPMCWQPISLK   82 (303)
Q Consensus        26 ~~~~~~d~~C~ICle~f~~~~-----~~~vl~C~H~Fc~~CI~~Wl~--~-----~~~CP~CR~~l~~~   82 (303)
                      ..+...+.+|.||++.+....     -..+++|.|.||..||..|-+  +     .+.||.||......
T Consensus       155 a~~~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v  223 (344)
T KOG1039|consen  155 ALQKSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFV  223 (344)
T ss_pred             CcCccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccc
Confidence            345567899999999984322     112367999999999999973  3     36799999877543

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

Probab=97.74  E-value=0.00025  Score=68.96  Aligned_cols=48  Identities=25%  Similarity=0.701  Sum_probs=40.7

Q ss_pred             ccccccccccCCCCeeeccCCccccHHhHHHHHhc--CCCCCCCcccCcCCCc
Q 022060           34 ACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR--SSQCPMCWQPISLKDA   84 (303)
Q Consensus        34 ~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~--~~~CP~CR~~l~~~d~   84 (303)
                      -|-||-|.   .+.+.+-+|||..|..|+..|...  ...||.||..|.....
T Consensus       371 LCKICaen---dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~  420 (563)
T KOG1785|consen  371 LCKICAEN---DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEP  420 (563)
T ss_pred             HHHHhhcc---CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEeccccc
Confidence            49999998   567889999999999999999854  5789999999876543

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

Probab=97.68  E-value=4e-05  Score=53.69  Aligned_cols=42  Identities=29%  Similarity=0.769  Sum_probs=31.8

Q ss_pred             ccccccccccCCCCeeeccCC-----ccccHHhHHHHHhcC--CCCCCCc
Q 022060           34 ACSICLEEFSESDPSTVTSCK-----HEFHLQCVLEWCQRS--SQCPMCW   76 (303)
Q Consensus        34 ~C~ICle~f~~~~~~~vl~C~-----H~Fc~~CI~~Wl~~~--~~CP~CR   76 (303)
                      .|-||++... .+...+.+|.     |.+|..|+.+|+..+  ..||+|+
T Consensus         1 ~CrIC~~~~~-~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEGD-EGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCCCC-CCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4899998433 3344567886     789999999999654  5899994

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

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

Probab=97.64  E-value=2.8e-05  Score=73.02  Aligned_cols=48  Identities=23%  Similarity=0.518  Sum_probs=39.2

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcC-CCCCCCcccCcCC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS-SQCPMCWQPISLK   82 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~-~~CP~CR~~l~~~   82 (303)
                      +.+|.||+...  .- ++.+.|+|.||..||..-++.. ..|++||.+|...
T Consensus         7 ~~eC~IC~nt~--n~-Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    7 KKECLICYNTG--NC-PVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDST   55 (324)
T ss_pred             CCcceeeeccC--Cc-CccccccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence            56799999986  33 4667999999999998877664 5699999999654

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

Probab=97.57  E-value=2.5e-05  Score=80.96  Aligned_cols=51  Identities=27%  Similarity=0.652  Sum_probs=42.6

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHh-cCCCCCCCcccCcCCCcc
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQ-RSSQCPMCWQPISLKDAT   85 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~-~~~~CP~CR~~l~~~d~~   85 (303)
                      -+.|+.|-.-+++   ..++.|+|.||..|+...+. +...||.|...|...|+.
T Consensus       643 ~LkCs~Cn~R~Kd---~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~  694 (698)
T KOG0978|consen  643 LLKCSVCNTRWKD---AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVH  694 (698)
T ss_pred             ceeCCCccCchhh---HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccccc
Confidence            5679999988743   56779999999999999985 567899999999877654

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

Probab=97.45  E-value=2.7e-05  Score=80.73  Aligned_cols=52  Identities=19%  Similarity=0.471  Sum_probs=42.9

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKD   83 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d   83 (303)
                      ...|+||+..|.+.....-..|.|.||..||..|.....+||+||..|...+
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v~  174 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGEVK  174 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhheee
Confidence            4469999998865555555789999999999999999999999999885443

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

Probab=97.39  E-value=0.00011  Score=70.42  Aligned_cols=48  Identities=31%  Similarity=0.733  Sum_probs=39.1

Q ss_pred             CCccccccccccccCCCCeeeccCCcc-ccHHhHHHHHhcCCCCCCCcccCc
Q 022060           30 SCDDACSICLEEFSESDPSTVTSCKHE-FHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C~H~-Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      +.-.+|.||+...   ....+++|.|. .|..|.+..--..+.||+||+++.
T Consensus       288 ~~gkeCVIClse~---rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~  336 (349)
T KOG4265|consen  288 ESGKECVICLSES---RDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIE  336 (349)
T ss_pred             cCCCeeEEEecCC---cceEEecchhhehhHhHHHHHHHhhcCCCccccchH
Confidence            3467899999996   44678899996 588998877666788999999884

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

Probab=97.38  E-value=8e-05  Score=59.64  Aligned_cols=50  Identities=26%  Similarity=0.690  Sum_probs=37.7

Q ss_pred             cccccccccccc------------CCCC--eeeccCCccccHHhHHHHHhcCCCCCCCcccCcC
Q 022060           32 DDACSICLEEFS------------ESDP--STVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISL   81 (303)
Q Consensus        32 d~~C~ICle~f~------------~~~~--~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~   81 (303)
                      -+.|.||.--+-            ..+.  +..-.|.|.||..||.+|++.+..||+|.+.+..
T Consensus        46 vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~~  109 (114)
T KOG2930|consen   46 VDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWVF  109 (114)
T ss_pred             echhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcceeE
Confidence            456999875431            0111  3336799999999999999999999999887754

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

Probab=97.38  E-value=6.6e-05  Score=73.79  Aligned_cols=47  Identities=34%  Similarity=0.846  Sum_probs=35.5

Q ss_pred             ccccccccccccCCCC-eeeccCCccccHHhHHHHHhcCCCCCCCcccCc
Q 022060           32 DDACSICLEEFSESDP-STVTSCKHEFHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        32 d~~C~ICle~f~~~~~-~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      --+|+||||.+.+... +..+.|.|.||..|+..|..  .+||+||.-..
T Consensus       175 LPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~--~scpvcR~~q~  222 (493)
T KOG0804|consen  175 LPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD--SSCPVCRYCQS  222 (493)
T ss_pred             CCCcchhHhhcCccccceeeeecccccchHHHhhccc--CcChhhhhhcC
Confidence            5579999999943322 23458999999999999954  47999987554

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

Probab=97.36  E-value=0.00012  Score=72.14  Aligned_cols=56  Identities=25%  Similarity=0.643  Sum_probs=45.4

Q ss_pred             hhcCCCCCCccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcC
Q 022060           23 VEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISL   81 (303)
Q Consensus        23 ~~~~~~~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~   81 (303)
                      ..++.+...+.+|.||+..|  -.+ ++++|||.||..||.+-+.....||.||..+..
T Consensus        75 ~s~~~~~~sef~c~vc~~~l--~~p-v~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   75 LSGPEEIRSEFECCVCSRAL--YPP-VVTPCGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             hccCccccchhhhhhhHhhc--CCC-ccccccccccHHHHHHHhccCCCCccccccccc
Confidence            33444556688999999998  444 555999999999999988888899999999875

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

Probab=97.33  E-value=5.5e-05  Score=53.91  Aligned_cols=46  Identities=33%  Similarity=0.746  Sum_probs=35.7

Q ss_pred             ccccccccccccCCCCeeeccCCcc-ccHHhHHHHHh-cCCCCCCCcccCc
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHE-FHLQCVLEWCQ-RSSQCPMCWQPIS   80 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~-Fc~~CI~~Wl~-~~~~CP~CR~~l~   80 (303)
                      +++|.||+|-..+   .++..|+|. .|..|-.+.++ .+..||+||+++.
T Consensus         7 ~dECTICye~pvd---sVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    7 SDECTICYEHPVD---SVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             ccceeeeccCcch---HHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            4789999998632   345589996 58899777665 6789999999874

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

Probab=97.24  E-value=0.00027  Score=68.85  Aligned_cols=54  Identities=28%  Similarity=0.791  Sum_probs=40.7

Q ss_pred             CccccccccccccCC--CCeeeccCCccccHHhHHHHHhc--CCCCCCCcccCcCCCc
Q 022060           31 CDDACSICLEEFSES--DPSTVTSCKHEFHLQCVLEWCQR--SSQCPMCWQPISLKDA   84 (303)
Q Consensus        31 ~d~~C~ICle~f~~~--~~~~vl~C~H~Fc~~CI~~Wl~~--~~~CP~CR~~l~~~d~   84 (303)
                      +..+|+||++.+...  ..+..+.|+|.|..+||.+|+-+  ...||.|..+-.....
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katkr~i   60 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKRQI   60 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHHHHH
Confidence            356899999998533  23556899999999999999953  3579999876544443

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

Probab=97.23  E-value=0.0002  Score=68.65  Aligned_cols=53  Identities=21%  Similarity=0.484  Sum_probs=44.6

Q ss_pred             cCCCCCCccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCc
Q 022060           25 GGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        25 ~~~~~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      ...-+.+|..|+||+.--   ......+|+|.-|+.||...+...+.|..|+..+.
T Consensus       415 ~~lp~sEd~lCpICyA~p---i~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~  467 (489)
T KOG4692|consen  415 KDLPDSEDNLCPICYAGP---INAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVI  467 (489)
T ss_pred             CCCCCcccccCcceeccc---chhhccCCCCchHHHHHHHHHhcCCeeeEecceee
Confidence            445667899999999763   33456799999999999999999999999998875

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

Probab=97.22  E-value=0.00016  Score=52.21  Aligned_cols=41  Identities=37%  Similarity=0.829  Sum_probs=30.2

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhc--CCCCCC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR--SSQCPM   74 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~--~~~CP~   74 (303)
                      ...|||.+..|  .+|++-..|+|.|-...|..|++.  ...||.
T Consensus        11 ~~~CPiT~~~~--~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   11 SLKCPITLQPF--EDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             -SB-TTTSSB---SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             ccCCCCcCChh--hCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            67899999999  788888899999999999999944  457998

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

Probab=97.20  E-value=0.00019  Score=69.49  Aligned_cols=47  Identities=26%  Similarity=0.772  Sum_probs=33.5

Q ss_pred             cccccccccccCCCCeeec-cCCccccHHhHHHHHhcC---CCCCCCcccC
Q 022060           33 DACSICLEEFSESDPSTVT-SCKHEFHLQCVLEWCQRS---SQCPMCWQPI   79 (303)
Q Consensus        33 ~~C~ICle~f~~~~~~~vl-~C~H~Fc~~CI~~Wl~~~---~~CP~CR~~l   79 (303)
                      ..|.||.+.+-....+.-+ .|||.||..|+..|+..-   ..||.|+-.+
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~   55 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKL   55 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecc
Confidence            4699996555322233223 499999999999999863   4799998443

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

Probab=97.15  E-value=0.00018  Score=70.81  Aligned_cols=51  Identities=31%  Similarity=0.757  Sum_probs=43.4

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCC
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKD   83 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d   83 (303)
                      ++..|+||...+  .+++..+.|+|.||..|+..|+..+..||.|+..+....
T Consensus        20 ~~l~C~~C~~vl--~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~   70 (391)
T KOG0297|consen   20 ENLLCPICMSVL--RDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAE   70 (391)
T ss_pred             ccccCccccccc--cCCCCCCCCCCcccccccchhhccCcCCcccccccchhh
Confidence            478999999999  566554699999999999999999999999988775443

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

Probab=97.14  E-value=0.00067  Score=61.58  Aligned_cols=64  Identities=27%  Similarity=0.539  Sum_probs=47.4

Q ss_pred             CCccccccccccccCCCCeeeccCCccccHHhHHHHHhc--------CCCCCCCcccCcCCCcchHHHHHHHH
Q 022060           30 SCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR--------SSQCPMCWQPISLKDATSQELLEAVE   94 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~--------~~~CP~CR~~l~~~d~~~~~l~e~~~   94 (303)
                      +++-.|..|--.+..++.+++ .|.|.||+.|+.+|...        ..+||.|..+|.........+.+++.
T Consensus        48 DY~pNC~LC~t~La~gdt~RL-vCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~NlvsPva~aLr  119 (299)
T KOG3970|consen   48 DYNPNCRLCNTPLASGDTTRL-VCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLVSPVAEALR  119 (299)
T ss_pred             CCCCCCceeCCccccCcceee-hhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccccchhHHHHH
Confidence            346679999999877777665 89999999999999754        24699999988765444334444443

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

Probab=97.08  E-value=0.00042  Score=64.50  Aligned_cols=51  Identities=24%  Similarity=0.578  Sum_probs=41.8

Q ss_pred             CCCCccccccccccccCCCCeeeccCCccccHHhHHHHHhc--CCCCCCCcccCc
Q 022060           28 QDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR--SSQCPMCWQPIS   80 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~--~~~CP~CR~~l~   80 (303)
                      ....+.+|++|-+.-  ..|.+..+|+|.||..||..-+..  +..||.|-....
T Consensus       235 ~~t~~~~C~~Cg~~P--tiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  235 TGTSDTECPVCGEPP--TIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cccCCceeeccCCCC--CCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            344588999999996  678888889999999999887654  478999977654

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

Probab=97.01  E-value=0.0002  Score=67.31  Aligned_cols=50  Identities=34%  Similarity=0.824  Sum_probs=39.9

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhc-----------------------CCCCCCCcccCcC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR-----------------------SSQCPMCWQPISL   81 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~-----------------------~~~CP~CR~~l~~   81 (303)
                      ...|.|||--|-++...+++.|.|.||..|+.++|..                       ...||+||..|..
T Consensus       115 ~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~  187 (368)
T KOG4445|consen  115 NGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI  187 (368)
T ss_pred             CCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence            3469999999977777899999999999999877531                       1259999988743

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

Probab=96.79  E-value=0.0011  Score=72.89  Aligned_cols=70  Identities=34%  Similarity=0.655  Sum_probs=48.6

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhcC----------CCCCCCcccCcCC---Ccc--hHHHHHHHHH
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS----------SQCPMCWQPISLK---DAT--SQELLEAVEQ   95 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~----------~~CP~CR~~l~~~---d~~--~~~l~e~~~~   95 (303)
                      -|+.|.||+-+-....|...+.|+|.||..|....|++.          -.||+|+.+|...   |+.  ..++++.+..
T Consensus      3485 ~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH~~LkDLldPiKel~edV~~ 3564 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINHIVLKDLLDPIKELYEDVRR 3564 (3738)
T ss_pred             cCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhhHHHHHHHHHHHHHHHHHHH
Confidence            378899999876555677778999999999998777543          2599999988543   322  2344555554


Q ss_pred             HHhhh
Q 022060           96 ERSIR  100 (303)
Q Consensus        96 er~~r  100 (303)
                      ....|
T Consensus      3565 KA~MR 3569 (3738)
T KOG1428|consen 3565 KALMR 3569 (3738)
T ss_pred             HHhhh
Confidence            44443

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

Probab=96.79  E-value=0.00077  Score=63.34  Aligned_cols=60  Identities=32%  Similarity=0.520  Sum_probs=46.3

Q ss_pred             cccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCcchHHHHHHHHH
Q 022060           33 DACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQ   95 (303)
Q Consensus        33 ~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~~~~~l~e~~~~   95 (303)
                      ..|-||..+|  ..| +++.|+|.||..|...-++....|++|-+.+........+++..+..
T Consensus       242 f~c~icr~~f--~~p-Vvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~~~~akeL~~~L~~  301 (313)
T KOG1813|consen  242 FKCFICRKYF--YRP-VVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGSFNVAKELLVSLKL  301 (313)
T ss_pred             cccccccccc--ccc-hhhcCCceeehhhhccccccCCcceecccccccccchHHHHHHHHHh
Confidence            3499999999  444 55699999999999999999999999988776555444555444443

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

Probab=96.66  E-value=0.0012  Score=59.03  Aligned_cols=48  Identities=25%  Similarity=0.619  Sum_probs=39.4

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLK   82 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~   82 (303)
                      ...|.||-++|  .. ++++.|+|.||..|...-++....|-+|-+.....
T Consensus       196 PF~C~iCKkdy--~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~  243 (259)
T COG5152         196 PFLCGICKKDY--ES-PVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGR  243 (259)
T ss_pred             ceeehhchhhc--cc-hhhhhcchhHHHHHHHHHhccCCcceecchhhccc
Confidence            45799999999  33 45679999999999998888889999997765433

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

Probab=96.31  E-value=0.0017  Score=65.25  Aligned_cols=52  Identities=23%  Similarity=0.682  Sum_probs=40.8

Q ss_pred             CCCCccccccccccccCCCCeeeccCCccccHHhHHHHHhc-----CCCCCCCcccCcCC
Q 022060           28 QDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR-----SSQCPMCWQPISLK   82 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~-----~~~CP~CR~~l~~~   82 (303)
                      ++-.+.+|.+|-+.-   +......|.|.||..||.++...     ..+||.|-..+...
T Consensus       532 enk~~~~C~lc~d~a---ed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD  588 (791)
T KOG1002|consen  532 ENKGEVECGLCHDPA---EDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID  588 (791)
T ss_pred             cccCceeecccCChh---hhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence            334478899999985   44566799999999999998753     46899998877544

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

Probab=96.22  E-value=0.0041  Score=43.37  Aligned_cols=45  Identities=27%  Similarity=0.674  Sum_probs=22.7

Q ss_pred             cccccccccCCCCe-eeccCCccccHHhHHHHHh-cCCCCCCCcccC
Q 022060           35 CSICLEEFSESDPS-TVTSCKHEFHLQCVLEWCQ-RSSQCPMCWQPI   79 (303)
Q Consensus        35 C~ICle~f~~~~~~-~vl~C~H~Fc~~CI~~Wl~-~~~~CP~CR~~l   79 (303)
                      |++|.+.+...+.- .-=+|++.+|..|....+. ....||-||+++
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            78999998333222 2236889999999988886 478899999875

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

Probab=96.12  E-value=0.005  Score=58.13  Aligned_cols=50  Identities=22%  Similarity=0.525  Sum_probs=39.6

Q ss_pred             cccccccccccCCCCeeeccCCccccHHhHHHHHh-cCCCCCCC-cccCcCCCc
Q 022060           33 DACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQ-RSSQCPMC-WQPISLKDA   84 (303)
Q Consensus        33 ~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~-~~~~CP~C-R~~l~~~d~   84 (303)
                      +.|+.|-..+  .+++....|+|.||..||...|. ..+.||.| |+.+....+
T Consensus       275 LkCplc~~Ll--rnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdvlld~l  326 (427)
T COG5222         275 LKCPLCHCLL--RNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLDGL  326 (427)
T ss_pred             ccCcchhhhh--hCcccCccccchHHHHHHhhhhhhccccCCCcccccchhhcc
Confidence            7899999998  77777778999999999987764 56789999 444544433

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

Probab=96.06  E-value=0.0022  Score=62.38  Aligned_cols=51  Identities=25%  Similarity=0.612  Sum_probs=39.5

Q ss_pred             CCCccccccccccccCCC-CeeeccCCccccHHhHHHHHhcC--CCCCCCcccC
Q 022060           29 DSCDDACSICLEEFSESD-PSTVTSCKHEFHLQCVLEWCQRS--SQCPMCWQPI   79 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~~~-~~~vl~C~H~Fc~~CI~~Wl~~~--~~CP~CR~~l   79 (303)
                      ++-++-|..|-+.+...+ ....++|.|+||..|+.+++..+  .+||.||+..
T Consensus       362 ~e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crklr  415 (518)
T KOG1941|consen  362 EETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLR  415 (518)
T ss_pred             HHHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHH
Confidence            334678999999985433 24558999999999999999664  5799999543

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

Probab=95.97  E-value=0.0072  Score=59.24  Aligned_cols=45  Identities=24%  Similarity=0.479  Sum_probs=35.4

Q ss_pred             ccccccccccCCCCeeeccCCccccHHhHHHHHhcC--------CCCCCCccc
Q 022060           34 ACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS--------SQCPMCWQP   78 (303)
Q Consensus        34 ~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~--------~~CP~CR~~   78 (303)
                      .|.||++...-......++|.|.||..|+..++...        -.||-|...
T Consensus       186 ~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~  238 (445)
T KOG1814|consen  186 DCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCG  238 (445)
T ss_pred             cceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCc
Confidence            599999998554677889999999999999998531        248776543

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

Probab=95.96  E-value=0.006  Score=58.66  Aligned_cols=54  Identities=20%  Similarity=0.443  Sum_probs=42.1

Q ss_pred             hhcCCCCCCccccccccccccCCCCeeeccCCccccHHhHHHH--HhcCCCCCCCcccC
Q 022060           23 VEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEW--CQRSSQCPMCWQPI   79 (303)
Q Consensus        23 ~~~~~~~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~W--l~~~~~CP~CR~~l   79 (303)
                      ...+.+|+++..|.||-+.+.   -+.++||+|..|.-|..+.  |-..+.|++||..+
T Consensus        52 sSaddtDEen~~C~ICA~~~T---Ys~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~  107 (493)
T COG5236          52 SSADDTDEENMNCQICAGSTT---YSARYPCGHQICHACAVRLRALYMQKGCPLCRTET  107 (493)
T ss_pred             ccccccccccceeEEecCCce---EEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence            344556777788999999863   3567899999999998654  45678999999876

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

Probab=95.54  E-value=0.0079  Score=52.94  Aligned_cols=51  Identities=33%  Similarity=0.767  Sum_probs=36.0

Q ss_pred             ccccccccccccCCCCe--e--eccCCccccHHhHHHHHhc-----C------CCCCCCcccCcCC
Q 022060           32 DDACSICLEEFSESDPS--T--VTSCKHEFHLQCVLEWCQR-----S------SQCPMCWQPISLK   82 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~--~--vl~C~H~Fc~~CI~~Wl~~-----~------~~CP~CR~~l~~~   82 (303)
                      -..|.||+.+-.++...  +  -..|+..||.-|+..||..     +      ..||+|.+++..|
T Consensus       165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK  230 (234)
T KOG3268|consen  165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK  230 (234)
T ss_pred             hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence            44588888775433221  1  2579999999999999964     1      2599999988644

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.52  E-value=0.012  Score=54.16  Aligned_cols=54  Identities=15%  Similarity=0.355  Sum_probs=45.1

Q ss_pred             ccccccccccccCCCCee-eccCCccccHHhHHHHHhcCCCCCCCcccCcCCCcc
Q 022060           32 DDACSICLEEFSESDPST-VTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDAT   85 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~-vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~~   85 (303)
                      --.|+||.+.+.+..+.. +-+|+|+||..|..++......||+|-+++..+|+.
T Consensus       221 ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI  275 (303)
T KOG3039|consen  221 RYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDII  275 (303)
T ss_pred             ceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceE
Confidence            446999999997666544 458999999999999999899999999999877643

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

Probab=95.43  E-value=0.012  Score=56.23  Aligned_cols=55  Identities=18%  Similarity=0.518  Sum_probs=42.6

Q ss_pred             hhcCCCCCCccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccC
Q 022060           23 VEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPI   79 (303)
Q Consensus        23 ~~~~~~~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l   79 (303)
                      .++++.......|+||+...  .++..+.--|-+||+.||..++...+.||+=-.+.
T Consensus       291 se~e~l~~~~~~CpvClk~r--~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~  345 (357)
T KOG0826|consen  291 SESELLPPDREVCPVCLKKR--QNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPA  345 (357)
T ss_pred             cccccCCCccccChhHHhcc--CCCceEEecceEEeHHHHHHHHHhcCCCCccCCcc
Confidence            34444555577899999987  55555556799999999999999999999865554

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

Probab=95.33  E-value=0.0059  Score=55.97  Aligned_cols=46  Identities=28%  Similarity=0.672  Sum_probs=34.2

Q ss_pred             cccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcC
Q 022060           33 DACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISL   81 (303)
Q Consensus        33 ~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~   81 (303)
                      ..|.-|...- +.++..++.|.|+||..|...-.  ...||+|++.+..
T Consensus         4 VhCn~C~~~~-~~~~f~LTaC~HvfC~~C~k~~~--~~~C~lCkk~ir~   49 (233)
T KOG4739|consen    4 VHCNKCFRFP-SQDPFFLTACRHVFCEPCLKASS--PDVCPLCKKSIRI   49 (233)
T ss_pred             EEeccccccC-CCCceeeeechhhhhhhhcccCC--ccccccccceeee
Confidence            3577777654 36778899999999999964322  2389999998743

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.30  E-value=0.011  Score=56.71  Aligned_cols=53  Identities=21%  Similarity=0.504  Sum_probs=37.4

Q ss_pred             CccccccccccccCCCCe-eeccCCccccHHhHHHHHhc-CCCCCCCcccCcCCC
Q 022060           31 CDDACSICLEEFSESDPS-TVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPISLKD   83 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~-~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l~~~d   83 (303)
                      +|+.|+.|+|.+...+.- .--+||...|.-|+...-+. ...||-||..+....
T Consensus        13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~den   67 (480)
T COG5175          13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDEN   67 (480)
T ss_pred             ccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccc
Confidence            366699999998433332 22478888888887655443 568999999876554

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

Probab=95.29  E-value=0.0091  Score=50.32  Aligned_cols=46  Identities=20%  Similarity=0.523  Sum_probs=32.4

Q ss_pred             CccccccccccccCCCCeeeccCC------ccccHHhHHHHHhcCCCCCCCc
Q 022060           31 CDDACSICLEEFSESDPSTVTSCK------HEFHLQCVLEWCQRSSQCPMCW   76 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~------H~Fc~~CI~~Wl~~~~~CP~CR   76 (303)
                      ...+|.||++.+.+.+-+..+.|+      |.||..|+.+|-.....=|.=|
T Consensus        25 ~~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~rDPfnR   76 (134)
T PF05883_consen   25 CTVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRERNRDPFNR   76 (134)
T ss_pred             cCeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhhccCCCccc
Confidence            467899999999653345555666      8999999999954444434433

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.

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

Probab=95.13  E-value=0.01  Score=62.71  Aligned_cols=46  Identities=37%  Similarity=0.925  Sum_probs=36.0

Q ss_pred             ccccccccccccCCCCe-eeccCCccccHHhHHHHHhcC-------CCCCCCcc
Q 022060           32 DDACSICLEEFSESDPS-TVTSCKHEFHLQCVLEWCQRS-------SQCPMCWQ   77 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~-~vl~C~H~Fc~~CI~~Wl~~~-------~~CP~CR~   77 (303)
                      -.+|.||++.+....++ ....|.|+||..||.+|....       -.||.|..
T Consensus       191 ~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs  244 (950)
T KOG1952|consen  191 KYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS  244 (950)
T ss_pred             ceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence            56799999999665554 236799999999999998542       25999974

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

Probab=95.08  E-value=0.022  Score=53.61  Aligned_cols=48  Identities=27%  Similarity=0.616  Sum_probs=38.8

Q ss_pred             ccccccccccccCCC---CeeeccCCccccHHhHHHHHhc-CCCCCCCcccC
Q 022060           32 DDACSICLEEFSESD---PSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPI   79 (303)
Q Consensus        32 d~~C~ICle~f~~~~---~~~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l   79 (303)
                      ...|-||-++|...+   -++++.|+|.||..|+...+.. ...||.||...
T Consensus         3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CCceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            357999999997553   3577899999999999877765 35799999985

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

Probab=95.08  E-value=0.12  Score=49.30  Aligned_cols=41  Identities=27%  Similarity=0.651  Sum_probs=28.2

Q ss_pred             cccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccC
Q 022060           35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPI   79 (303)
Q Consensus        35 C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l   79 (303)
                      |.-|--.+  ..--++.+|+|+||++|...  ...+.||.|-..+
T Consensus        93 Cd~Cd~PI--~IYGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen   93 CDRCDFPI--AIYGRMIPCKHVFCLECARS--DSDKICPLCDDRV  133 (389)
T ss_pred             ecccCCcc--eeeecccccchhhhhhhhhc--CccccCcCcccHH
Confidence            55565444  22345689999999999643  3467899997655

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

Probab=94.79  E-value=0.016  Score=55.90  Aligned_cols=47  Identities=32%  Similarity=0.659  Sum_probs=33.9

Q ss_pred             CCCCccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCc
Q 022060           28 QDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      ++...+.|.||++.+++   ...++|||.-|  |..-. +....||+||..+.
T Consensus       301 ~~~~p~lcVVcl~e~~~---~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI~  347 (355)
T KOG1571|consen  301 ELPQPDLCVVCLDEPKS---AVFVPCGHVCC--CTLCS-KHLPQCPVCRQRIR  347 (355)
T ss_pred             ccCCCCceEEecCCccc---eeeecCCcEEE--chHHH-hhCCCCchhHHHHH
Confidence            34456679999999743   55669999877  76443 33455999998774

>PHA03096 p28-like protein; Provisional

Probab=94.48  E-value=0.022  Score=53.90  Aligned_cols=45  Identities=29%  Similarity=0.600  Sum_probs=32.0

Q ss_pred             cccccccccccCCC-----CeeeccCCccccHHhHHHHHhcC---CCCCCCcc
Q 022060           33 DACSICLEEFSESD-----PSTVTSCKHEFHLQCVLEWCQRS---SQCPMCWQ   77 (303)
Q Consensus        33 ~~C~ICle~f~~~~-----~~~vl~C~H~Fc~~CI~~Wl~~~---~~CP~CR~   77 (303)
                      .+|.||++......     -..+..|.|.||..||..|-...   ..||.|+.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            67999999975321     12446899999999999997542   34555544

>PF04641 Rtf2: Rtf2 RING-finger

Probab=94.15  E-value=0.043  Score=51.13  Aligned_cols=53  Identities=23%  Similarity=0.461  Sum_probs=40.7

Q ss_pred             CccccccccccccCCCCe-eeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCc
Q 022060           31 CDDACSICLEEFSESDPS-TVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDA   84 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~-~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~   84 (303)
                      ..-.|||....|...... .+-+|||+|+..+|.+.- ....||+|-++|...|.
T Consensus       112 ~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~Di  165 (260)
T PF04641_consen  112 GRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEEDI  165 (260)
T ss_pred             ceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccCCE
Confidence            356799999999443343 345999999999999873 45679999999876654

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

Probab=93.37  E-value=0.028  Score=48.87  Aligned_cols=31  Identities=26%  Similarity=0.564  Sum_probs=26.7

Q ss_pred             CCCccccccccccccCCCCeeeccCCccccH
Q 022060           29 DSCDDACSICLEEFSESDPSTVTSCKHEFHL   59 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~   59 (303)
                      .....+|.||||++..++.+..|+|.++||+
T Consensus       174 ~ddkGECvICLEdL~~GdtIARLPCLCIYHK  204 (205)
T KOG0801|consen  174 KDDKGECVICLEDLEAGDTIARLPCLCIYHK  204 (205)
T ss_pred             cccCCcEEEEhhhccCCCceeccceEEEeec
Confidence            4445689999999998898888999999986

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

Probab=93.35  E-value=0.056  Score=37.38  Aligned_cols=40  Identities=30%  Similarity=0.901  Sum_probs=25.6

Q ss_pred             cccccccccCCCCeeeccCCc-----cccHHhHHHHHhc--CCCCCCC
Q 022060           35 CSICLEEFSESDPSTVTSCKH-----EFHLQCVLEWCQR--SSQCPMC   75 (303)
Q Consensus        35 C~ICle~f~~~~~~~vl~C~H-----~Fc~~CI~~Wl~~--~~~CP~C   75 (303)
                      |-||++.-.+.. ..+.+|..     ..|..|+..|+..  ...|++|
T Consensus         1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            679999864433 34457763     6799999999974  4678887

>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=93.25  E-value=0.035  Score=43.82  Aligned_cols=33  Identities=24%  Similarity=0.579  Sum_probs=26.4

Q ss_pred             CCccccccccccccCCCCeeeccCCccccHHhHH
Q 022060           30 SCDDACSICLEEFSESDPSTVTSCKHEFHLQCVL   63 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~   63 (303)
                      +.+..|++|-..|.. ....+.||+|.||..|+.
T Consensus        76 ~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   76 TESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence            346779999999954 445667999999999974

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 [].

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

Probab=93.24  E-value=0.016  Score=54.62  Aligned_cols=42  Identities=29%  Similarity=0.671  Sum_probs=31.4

Q ss_pred             ccccccccccccCCCCeeeccCCcc-ccHHhHHHHHhcCCCCCCCcccCc
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHE-FHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~-Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      +.-|.||++..  .+ -..|+|||. -|..|-..    -..||+||+.+.
T Consensus       300 ~~LC~ICmDaP--~D-CvfLeCGHmVtCt~CGkr----m~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAP--RD-CVFLECGHMVTCTKCGKR----MNECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCC--cc-eEEeecCcEEeehhhccc----cccCchHHHHHH
Confidence            56799999996  33 456699995 47788644    348999998764

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

Probab=92.93  E-value=0.066  Score=50.42  Aligned_cols=52  Identities=29%  Similarity=0.514  Sum_probs=41.2

Q ss_pred             CCCCccccccccccccCCC-CeeeccCCccccHHhHHHHHhcCCCCCCCcccCc
Q 022060           28 QDSCDDACSICLEEFSESD-PSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~~~-~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      +...+..||||.+.+.... .+.+++|+|..|..|+.+.....-.||+|.+ +.
T Consensus       154 e~~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~-~~  206 (276)
T KOG1940|consen  154 ERSSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK-PG  206 (276)
T ss_pred             hhcccCCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc-hH
Confidence            3334556999999986554 4567899999999999998877789999988 54

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

Probab=92.90  E-value=0.04  Score=38.32  Aligned_cols=31  Identities=32%  Similarity=0.814  Sum_probs=23.0

Q ss_pred             ccCC-ccccHHhHHHHHhcCCCCCCCcccCcC
Q 022060           51 TSCK-HEFHLQCVLEWCQRSSQCPMCWQPISL   81 (303)
Q Consensus        51 l~C~-H~Fc~~CI~~Wl~~~~~CP~CR~~l~~   81 (303)
                      ..|. |..|..|+...+..+..||+|++++..
T Consensus        16 i~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt   47 (50)
T PF03854_consen   16 IKCSDHYLCLNCLTLMLSRSDRCPICGKPLPT   47 (50)
T ss_dssp             EE-SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred             eeecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence            3676 999999999999999999999998754

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.

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=92.90  E-value=0.06  Score=38.59  Aligned_cols=47  Identities=28%  Similarity=0.632  Sum_probs=33.5

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKD   83 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d   83 (303)
                      +..|..|...   .....+++|+|..|..|..-  .+-+-||.|-.++...+
T Consensus         7 ~~~~~~~~~~---~~~~~~~pCgH~I~~~~f~~--~rYngCPfC~~~~~~~~   53 (55)
T PF14447_consen    7 EQPCVFCGFV---GTKGTVLPCGHLICDNCFPG--ERYNGCPFCGTPFEFDD   53 (55)
T ss_pred             ceeEEEcccc---ccccccccccceeeccccCh--hhccCCCCCCCcccCCC
Confidence            3456667665   33456679999999999543  45678999988886543

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=92.75  E-value=0.11  Score=44.98  Aligned_cols=46  Identities=30%  Similarity=0.757  Sum_probs=34.3

Q ss_pred             CccccccccccccCCCCeeeccCCc-----cccHHhHHHHHhcC--CCCCCCcccCc
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKH-----EFHLQCVLEWCQRS--SQCPMCWQPIS   80 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H-----~Fc~~CI~~Wl~~~--~~CP~CR~~l~   80 (303)
                      .+..|-||.+.-  +..  ..+|..     ..|..|+.+|+..+  ..|+.|+.++.
T Consensus         7 ~~~~CRIC~~~~--~~~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~   59 (162)
T PHA02825          7 MDKCCWICKDEY--DVV--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN   59 (162)
T ss_pred             CCCeeEecCCCC--CCc--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence            477899999885  221  236665     45999999999654  57999998774

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

Probab=92.67  E-value=0.031  Score=58.80  Aligned_cols=46  Identities=33%  Similarity=0.796  Sum_probs=36.9

Q ss_pred             cccccccccccCCCCeeeccCCccccHHhHHHHHhcC--CCCCCCcccCcCC
Q 022060           33 DACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS--SQCPMCWQPISLK   82 (303)
Q Consensus        33 ~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~--~~CP~CR~~l~~~   82 (303)
                      ..|.||++ .   +...++.|+|.||..|+...+...  ..||.||..+..+
T Consensus       455 ~~c~ic~~-~---~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~  502 (674)
T KOG1001|consen  455 HWCHICCD-L---DSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEK  502 (674)
T ss_pred             cccccccc-c---ccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHH
Confidence            68999999 3   446677999999999999887653  3699999877544

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

Probab=92.45  E-value=0.036  Score=61.10  Aligned_cols=44  Identities=32%  Similarity=0.713  Sum_probs=36.8

Q ss_pred             cccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCccc
Q 022060           33 DACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQP   78 (303)
Q Consensus        33 ~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~   78 (303)
                      -.|.||++.+..  --.+..|+|.||..|+..|+..+..||.|+..
T Consensus      1154 ~~c~ic~dil~~--~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi 1197 (1394)
T KOG0298|consen 1154 FVCEICLDILRN--QGGIAGCGHEPCCRCDELWLYASSRCPICKSI 1197 (1394)
T ss_pred             cchHHHHHHHHh--cCCeeeechhHhhhHHHHHHHHhccCcchhhh
Confidence            379999999943  23345799999999999999999999999753

>PHA02862 5L protein; Provisional

Probab=92.42  E-value=0.1  Score=44.62  Aligned_cols=47  Identities=23%  Similarity=0.653  Sum_probs=35.0

Q ss_pred             ccccccccccccCCCCeeeccCC-----ccccHHhHHHHHhc--CCCCCCCcccCcCC
Q 022060           32 DDACSICLEEFSESDPSTVTSCK-----HEFHLQCVLEWCQR--SSQCPMCWQPISLK   82 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~-----H~Fc~~CI~~Wl~~--~~~CP~CR~~l~~~   82 (303)
                      .+.|-||++.-  ++.  .-+|.     ..-|..|+.+|+..  ...|++|+.++..+
T Consensus         2 ~diCWIC~~~~--~e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik   55 (156)
T PHA02862          2 SDICWICNDVC--DER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK   55 (156)
T ss_pred             CCEEEEecCcC--CCC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence            46799999985  222  24665     47899999999965  45799999988543

>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=92.14  E-value=0.14  Score=34.72  Aligned_cols=39  Identities=26%  Similarity=0.750  Sum_probs=22.1

Q ss_pred             cccccccccCCCCeeec--cCCccccHHhHHHHHhcCC--CCCCC
Q 022060           35 CSICLEEFSESDPSTVT--SCKHEFHLQCVLEWCQRSS--QCPMC   75 (303)
Q Consensus        35 C~ICle~f~~~~~~~vl--~C~H~Fc~~CI~~Wl~~~~--~CP~C   75 (303)
                      |.+|.+.+.  .-..-.  .|.-.+|..|+..++....  .||.|
T Consensus         1 C~~C~~iv~--~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVT--QGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-S--SSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHe--eeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            678888873  334443  5888999999999997654  69987

; PDB: 3NW0_A 2CT0_A.

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

Probab=92.14  E-value=0.078  Score=56.31  Aligned_cols=43  Identities=26%  Similarity=0.691  Sum_probs=35.5

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPI   79 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l   79 (303)
                      ...|.+|--.+  +.|.+--.|+|.||.+|+.   .....||.|+..+
T Consensus       840 ~skCs~C~~~L--dlP~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  840 VSKCSACEGTL--DLPFVHFLCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeeecccCCcc--ccceeeeecccHHHHHhhc---cCcccCCccchhh
Confidence            35799999998  7777777999999999997   4567899998743

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

Probab=90.56  E-value=0.22  Score=48.84  Aligned_cols=46  Identities=20%  Similarity=0.454  Sum_probs=38.2

Q ss_pred             ccccccccccCCCCeeeccCCccccHHhHHHHHhcC---CCCCCCcccC
Q 022060           34 ACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS---SQCPMCWQPI   79 (303)
Q Consensus        34 ~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~---~~CP~CR~~l   79 (303)
                      .|||=.+--.+.+|+..+.|||+.+.+-|.+..+..   ..||+|-...
T Consensus       336 ~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~  384 (394)
T KOG2817|consen  336 ICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ  384 (394)
T ss_pred             ecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence            599988887778888889999999999999988654   4699995443

>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=90.48  E-value=0.079  Score=48.80  Aligned_cols=52  Identities=23%  Similarity=0.474  Sum_probs=36.5

Q ss_pred             CCccccccccccccCCCCee--e-ccCCccccHHhHHHHHhc-CCCCC--CCcccCcC
Q 022060           30 SCDDACSICLEEFSESDPST--V-TSCKHEFHLQCVLEWCQR-SSQCP--MCWQPISL   81 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~--v-l~C~H~Fc~~CI~~Wl~~-~~~CP--~CR~~l~~   81 (303)
                      ..|..||||..+..-.-.+.  + ..|.|..|-+|+.+.+.. ...||  -|-+.+..
T Consensus         8 ~~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK   65 (314)
T COG5220           8 MEDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRK   65 (314)
T ss_pred             hhcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHH
Confidence            34678999997743222222  3 349999999999999876 46899  68665543

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

Probab=90.26  E-value=0.16  Score=49.55  Aligned_cols=32  Identities=25%  Similarity=0.790  Sum_probs=24.7

Q ss_pred             CCccccHHhHHHHHhcC-------------CCCCCCcccCcCCCc
Q 022060           53 CKHEFHLQCVLEWCQRS-------------SQCPMCWQPISLKDA   84 (303)
Q Consensus        53 C~H~Fc~~CI~~Wl~~~-------------~~CP~CR~~l~~~d~   84 (303)
                      |...+|..|+-+|+..+             ..||+||+.+...|.
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilDV  355 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILDV  355 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeeee
Confidence            55677999999998532             359999999876653

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

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

Probab=89.24  E-value=0.28  Score=46.87  Aligned_cols=43  Identities=30%  Similarity=0.651  Sum_probs=33.3

Q ss_pred             CccccccccccccCCCCeeeccC--CccccHHhHHHHHhcCCCCCCCcccCc
Q 022060           31 CDDACSICLEEFSESDPSTVTSC--KHEFHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C--~H~Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      +-++||||.+.+  ..|+.  .|  ||..|..|-.   +....||.||.++.
T Consensus        47 ~lleCPvC~~~l--~~Pi~--QC~nGHlaCssC~~---~~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   47 DLLDCPVCFNPL--SPPIF--QCDNGHLACSSCRT---KVSNKCPTCRLPIG   91 (299)
T ss_pred             hhccCchhhccC--cccce--ecCCCcEehhhhhh---hhcccCCccccccc
Confidence            356799999998  44443  56  5999999954   45678999999986

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

Probab=89.12  E-value=0.25  Score=49.12  Aligned_cols=34  Identities=18%  Similarity=0.541  Sum_probs=27.4

Q ss_pred             CCccccccccccccCCCCeeeccCCccccHHhHHHHH
Q 022060           30 SCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWC   66 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl   66 (303)
                      ++++.|+||...|  .+| .+++|+|..|..|....+
T Consensus         2 eeelkc~vc~~f~--~ep-iil~c~h~lc~~ca~~~~   35 (699)
T KOG4367|consen    2 EEELKCPVCGSFY--REP-IILPCSHNLCQACARNIL   35 (699)
T ss_pred             cccccCceehhhc--cCc-eEeecccHHHHHHHHhhc
Confidence            3588999999999  555 455999999999987544

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

Probab=87.90  E-value=0.39  Score=40.51  Aligned_cols=48  Identities=21%  Similarity=0.418  Sum_probs=35.1

Q ss_pred             ccccccccccccCCCCeee---ccCCccccHHhHHHHHhc---CCCCCCCcccCcC
Q 022060           32 DDACSICLEEFSESDPSTV---TSCKHEFHLQCVLEWCQR---SSQCPMCWQPISL   81 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~v---l~C~H~Fc~~CI~~Wl~~---~~~CP~CR~~l~~   81 (303)
                      --+|.||.|...+  .-.+   .-||-..|..|-...++.   ...||.|+..+..
T Consensus        80 lYeCnIC~etS~e--e~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs  133 (140)
T PF05290_consen   80 LYECNICKETSAE--ERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS  133 (140)
T ss_pred             ceeccCcccccch--hhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence            4479999999633  2222   249999999997766554   5789999988754

>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=86.26  E-value=0.75  Score=32.15  Aligned_cols=43  Identities=21%  Similarity=0.544  Sum_probs=23.3

Q ss_pred             cccccccccccCCCCeeeccCCccccHHhHHHHHhc---C--CCCCCCccc
Q 022060           33 DACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR---S--SQCPMCWQP   78 (303)
Q Consensus        33 ~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~---~--~~CP~CR~~   78 (303)
                      +.|+|....+  ..|++...|.|.-|++- ..|+..   .  -.||+|.++
T Consensus         3 L~CPls~~~i--~~P~Rg~~C~H~~CFDl-~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRI--RIPVRGKNCKHLQCFDL-ESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB---SSEEEETT--SS--EEH-HHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEE--EeCccCCcCcccceECH-HHHHHHhhccCCeECcCCcCc
Confidence            5799999998  77899999999877553 344432   2  369999763

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.

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

Probab=85.63  E-value=0.29  Score=48.31  Aligned_cols=37  Identities=30%  Similarity=0.652  Sum_probs=27.1

Q ss_pred             cccccccc-ccccCCCCeeeccCCccccHHhHHHHHhc
Q 022060           32 DDACSICL-EEFSESDPSTVTSCKHEFHLQCVLEWCQR   68 (303)
Q Consensus        32 d~~C~ICl-e~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~   68 (303)
                      ..+|.||+ +.....+-..+..|+|.||..|+..++..
T Consensus       146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev  183 (384)
T KOG1812|consen  146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEV  183 (384)
T ss_pred             cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhh
Confidence            56799999 44432222235789999999999998864

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

Probab=85.39  E-value=0.23  Score=52.06  Aligned_cols=46  Identities=30%  Similarity=0.702  Sum_probs=36.1

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhc---CCCCCCCcccCc
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR---SSQCPMCWQPIS   80 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~---~~~CP~CR~~l~   80 (303)
                      +.+|+||+..+.  .+ ..+.|.|.||..|+..-+..   ...||+|+..+.
T Consensus        21 ~lEc~ic~~~~~--~p-~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e   69 (684)
T KOG4362|consen   21 ILECPICLEHVK--EP-SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIE   69 (684)
T ss_pred             hccCCceeEEee--cc-chhhhhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence            788999999983  44 55699999999998765543   467999986553

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

Probab=85.20  E-value=0.61  Score=49.66  Aligned_cols=54  Identities=31%  Similarity=0.705  Sum_probs=40.0

Q ss_pred             CCCccccccccccccCCCCeeeccCCc-----cccHHhHHHHHhcC--CCCCCCcccCcCCC
Q 022060           29 DSCDDACSICLEEFSESDPSTVTSCKH-----EFHLQCVLEWCQRS--SQCPMCWQPISLKD   83 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~~~~~~vl~C~H-----~Fc~~CI~~Wl~~~--~~CP~CR~~l~~~d   83 (303)
                      .+++..|-||..+=..++|..- ||++     ..|.+|+.+|+..+  ..|-+|..++..++
T Consensus         9 N~d~~~CRICr~e~~~d~pLfh-PCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~   69 (1175)
T COG5183           9 NEDKRSCRICRTEDIRDDPLFH-PCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKD   69 (1175)
T ss_pred             CccchhceeecCCCCCCCcCcc-cccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeee
Confidence            3456889999988655555444 7774     57999999999764  56999998875543

>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=85.11  E-value=1  Score=42.70  Aligned_cols=52  Identities=21%  Similarity=0.411  Sum_probs=36.5

Q ss_pred             ccccccccccCC--CCeeeccCCccccHHhHHHHHhc-CCCCCCCcccCcCCCcc
Q 022060           34 ACSICLEEFSES--DPSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPISLKDAT   85 (303)
Q Consensus        34 ~C~ICle~f~~~--~~~~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l~~~d~~   85 (303)
                      .|++|.-...-.  --..+-+|+|..|..|+...+.. ...||.|-..+....+.
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nfr   56 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNNFR   56 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhcccc
Confidence            588887653211  12334589999999999998865 56899998776554443

>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=85.06  E-value=0.94  Score=39.34  Aligned_cols=33  Identities=24%  Similarity=0.537  Sum_probs=20.6

Q ss_pred             CccccccccccccCCCCeeeccCC------------c-cccHHhHHHHH
Q 022060           31 CDDACSICLEEFSESDPSTVTSCK------------H-EFHLQCVLEWC   66 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~------------H-~Fc~~CI~~Wl   66 (303)
                      +|..|+||||..  .+ .++|-|.            . .-|.-||..+-
T Consensus         1 ed~~CpICme~P--HN-AVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfk   46 (162)
T PF07800_consen    1 EDVTCPICMEHP--HN-AVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFK   46 (162)
T ss_pred             CCccCceeccCC--Cc-eEEEEeccccCCccccccCCccchhHHHHHHH
Confidence            378899999986  33 3333333            1 23467888774

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.

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=83.94  E-value=0.79  Score=42.74  Aligned_cols=57  Identities=19%  Similarity=0.511  Sum_probs=38.3

Q ss_pred             CCCccccccccccccCCCCe-eeccCC-----ccccHHhHHHHHhcC--------CCCCCCcccCcCCCcc
Q 022060           29 DSCDDACSICLEEFSESDPS-TVTSCK-----HEFHLQCVLEWCQRS--------SQCPMCWQPISLKDAT   85 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~~~~~-~vl~C~-----H~Fc~~CI~~Wl~~~--------~~CP~CR~~l~~~d~~   85 (303)
                      .+.|..|-||+..=++.... -+-||.     |..|..|+..|+..+        ..||.|+..+...-+.
T Consensus        17 ~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~   87 (293)
T KOG3053|consen   17 QELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQ   87 (293)
T ss_pred             cccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeeccc
Confidence            33477899999885332222 234665     788999999998532        2599999877544333

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

Probab=83.41  E-value=0.12  Score=50.67  Aligned_cols=51  Identities=22%  Similarity=0.514  Sum_probs=41.0

Q ss_pred             ccccccccccccCC-CCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCC
Q 022060           32 DDACSICLEEFSES-DPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLK   82 (303)
Q Consensus        32 d~~C~ICle~f~~~-~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~   82 (303)
                      ...|.||.+.++.. +....+.|+|.+|..||..|+.....||.|+..+...
T Consensus       196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~  247 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPKN  247 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhhh
Confidence            45699999998533 3344568999999999999999988899999887543

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=83.34  E-value=0.53  Score=44.67  Aligned_cols=31  Identities=26%  Similarity=0.701  Sum_probs=24.3

Q ss_pred             CCccccHHhHHHHHhc-------------CCCCCCCcccCcCCC
Q 022060           53 CKHEFHLQCVLEWCQR-------------SSQCPMCWQPISLKD   83 (303)
Q Consensus        53 C~H~Fc~~CI~~Wl~~-------------~~~CP~CR~~l~~~d   83 (303)
                      |...+|.+|+-.|+..             +-+||+||+.+...|
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~d  368 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRD  368 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEee
Confidence            5677889999988743             347999999987655

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

Probab=83.01  E-value=0.61  Score=42.29  Aligned_cols=46  Identities=24%  Similarity=0.544  Sum_probs=38.3

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPI   79 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l   79 (303)
                      -..|.+|-...  -...+.-.|+-.||..|+.+++++...||.|---|
T Consensus       181 lk~Cn~Ch~Lv--Iqg~rCg~c~i~~h~~c~qty~q~~~~cphc~d~w  226 (235)
T KOG4718|consen  181 LKNCNLCHCLV--IQGIRCGSCNIQYHRGCIQTYLQRRDICPHCGDLW  226 (235)
T ss_pred             HHHHhHhHHHh--heeeccCcccchhhhHHHHHHhcccCcCCchhccc
Confidence            45699999987  55567778888999999999999999999995433

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

Probab=82.72  E-value=0.64  Score=49.88  Aligned_cols=34  Identities=29%  Similarity=0.661  Sum_probs=28.5

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHH
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWC   66 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl   66 (303)
                      .+.|.+|...|. ..+-.+-+|+|.||+.||.+..
T Consensus       817 ~d~C~~C~~~ll-~~pF~vf~CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  817 QDSCDHCGRPLL-IKPFYVFPCGHCFHRDCLIRHV  850 (911)
T ss_pred             ccchHHhcchhh-cCcceeeeccchHHHHHHHHHH
Confidence            677999999984 4576778999999999998764

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=80.91  E-value=1.5  Score=31.32  Aligned_cols=33  Identities=21%  Similarity=0.606  Sum_probs=26.3

Q ss_pred             ccccccccccccCCCCee-eccCCccccHHhHHH
Q 022060           32 DDACSICLEEFSESDPST-VTSCKHEFHLQCVLE   64 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~-vl~C~H~Fc~~CI~~   64 (303)
                      ...|.+|-+.|++++.++ ...|+-.||..|...
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            456999999998666654 478999999999643

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

Probab=80.40  E-value=0.64  Score=48.33  Aligned_cols=40  Identities=28%  Similarity=0.532  Sum_probs=29.2

Q ss_pred             ccccccccccccCCC-CeeeccCCccccHHhHHHHHhcCCCCC
Q 022060           32 DDACSICLEEFSESD-PSTVTSCKHEFHLQCVLEWCQRSSQCP   73 (303)
Q Consensus        32 d~~C~ICle~f~~~~-~~~vl~C~H~Fc~~CI~~Wl~~~~~CP   73 (303)
                      -+.|.||+..|.... .++-+.|+|..|..|+...+..  +||
T Consensus        11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn~--scp   51 (861)
T KOG3161|consen   11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYNA--SCP   51 (861)
T ss_pred             HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhhc--cCC
Confidence            457999987775332 3455699999999999876544  566

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	303
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		2e-06
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		7e-05

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 17/47 (36%), Positives = 29/47 (61%)
Query: 33 DACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPI 79
          + C++CLE+F   D   +  CKH FH +C+++W +    CP+C  P+
Sbjct: 16 ELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPV 62

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 18/41 (43%), Positives = 23/41 (56%)
Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMC 75
          C IC  E+ + D +T   C H FH  CV  W Q+S  CP+C
Sbjct: 43 CPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVC 83

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	303
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	7e-18
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	9e-15
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	4e-14
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	2e-13
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	3e-13
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	4e-13
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-12
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	2e-12
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	3e-12
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	4e-12
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	5e-12
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	1e-11
2ect_A	78	Ring finger protein 126; metal binding protein, st	5e-11
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	8e-11
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	3e-10
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	5e-10
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	7e-10
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	9e-10
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	3e-09
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	6e-09
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	7e-09
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	5e-08
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	1e-07
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-07
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-04
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	2e-07
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	3e-07
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	5e-07
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	9e-06
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	1e-05
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	1e-05
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	1e-05
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	2e-05
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	2e-05
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	3e-05
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	6e-05
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	6e-05
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	6e-05
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	7e-05
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	9e-05
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	2e-04
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	2e-04
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	2e-04
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	2e-04
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	3e-04
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	3e-04
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	3e-04
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	4e-04
1z6u_A	150	NP95-like ring finger protein isoform B; structura	4e-04

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

 Score = 75.5 bits (186), Expect = 7e-18
 Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 2/52 (3%)

Query: 29 DSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPIS 80
           +  + C ICLE+ S  + S    C H F   C+  W +++  CP+C  P+ 
Sbjct: 2  ATVAERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE 51

>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 = 67.2 bits (164), Expect = 9e-15
 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 4/62 (6%)

Query: 26 GIQDSCDDACSICLEEFSE----SDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISL 81
          G++ S   +C IC++ +SE          T C H F  QC+ +  + ++ CP C + I+ 
Sbjct: 4  GLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH 63

Query: 82 KD 83
          K 
Sbjct: 64 KR 65

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

 Score = 65.2 bits (159), Expect = 4e-14
 Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 4/53 (7%)

Query: 35 CSICLEEFSE----SDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKD 83
          C IC++ +SE          T C H F  QC+ +  + ++ CP C + I+ K 
Sbjct: 6  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR 58

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

 Score = 63.6 bits (155), Expect = 2e-13
 Identities = 18/59 (30%), Positives = 32/59 (54%)

Query: 28 QDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATS 86
          + +  + C++CLE+F   D   +  CKH FH +C+++W +    CP+C  P+      S
Sbjct: 11 ELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLS 69

>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 = 62.3 bits (152), Expect = 3e-13
 Identities = 18/52 (34%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 30 SCDDACSICLEEFSESD-PSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPIS 80
          S    C ICLE+   S   + V  C H  H  C  E  +   +CP+C  P S
Sbjct: 3  SGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS 54

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

 Score = 62.4 bits (152), Expect = 4e-13
 Identities = 18/63 (28%), Positives = 30/63 (47%)

Query: 24 EGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKD 83
          E G ++  ++ C+ICL    E +      C H FH  CV +W   + +CP+C   I  + 
Sbjct: 6  EEGTEEDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQL 65

Query: 84 ATS 86
           + 
Sbjct: 66 PSE 68

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

 Score = 60.7 bits (147), Expect = 2e-12
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 4/61 (6%)

Query: 26 GIQDSCDDACSICLEEFSE----SDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISL 81
          G++ S   +C IC++ +SE          T C H F  QC+ +  + ++ CP C + I+ 
Sbjct: 9  GLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH 68

Query: 82 K 82
          K
Sbjct: 69 K 69

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

 Score = 61.1 bits (148), Expect = 2e-12
 Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 28 QDSCDDACSICLEEFSESD-PSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLK 82
          +    DAC  C  E  + D       C H FH  C+  W +++++CP+C Q   ++
Sbjct: 22 RVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQ 77

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

 Score = 60.1 bits (146), Expect = 3e-12
 Identities = 13/55 (23%), Positives = 28/55 (50%), Gaps = 4/55 (7%)

Query: 32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATS 86
          ++ C IC++  ++     +  C H F  +C+ +W  R   CP+C   ++  + +S
Sbjct: 15 EEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANESS 65

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

 Score = 60.4 bits (147), Expect = 4e-12
 Identities = 19/54 (35%), Positives = 25/54 (46%)

Query: 22 FVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMC 75
            E       +  C IC  E+ + D +T   C H FH  CV  W Q+S  CP+C
Sbjct: 30 VTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVC 83

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

 Score = 59.9 bits (145), Expect = 5e-12
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 3/70 (4%)

Query: 29 DSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQE 88
          +     C IC + F   +P  VT C+H F   C LE  + + +C +C QP       ++E
Sbjct: 12 EEIPFRCFICRQAFQ--NP-VVTKCRHYFCESCALEHFRATPRCYICDQPTGGIFNPAKE 68

Query: 89 LLEAVEQERS 98
          L+  +++   
Sbjct: 69 LMAKLQKSGP 78

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

 Score = 58.5 bits (142), Expect = 1e-11
 Identities = 15/49 (30%), Positives = 23/49 (46%)

Query: 32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPIS 80
             C +C+ +F       V  C HEFH +CV +W + +  CP+C     
Sbjct: 23 QTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSG 71

>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 = 57.1 bits (138), Expect = 5e-11
 Identities = 12/61 (19%), Positives = 28/61 (45%)

Query: 28 QDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQ 87
                 C +C E+++  +      C H FH  C++ W ++   CP+C + ++ ++  + 
Sbjct: 11 HVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATN 70

Query: 88 E 88
           
Sbjct: 71 P 71

>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 = 57.2 bits (138), Expect = 8e-11
 Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 3/63 (4%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS-SQCPMCWQPISLKDATSQELLEAV 93
          C IC+E+    D      C       C+  W     +QCP C  P+ L++  +    E V
Sbjct: 25 CFICMEKLR--DARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVNCRWAEEV 82

Query: 94 EQE 96
           Q+
Sbjct: 83 TQQ 85

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus} Length = 117

 Score = 56.0 bits (134), Expect = 3e-10
 Identities = 15/69 (21%), Positives = 21/69 (30%), Gaps = 15/69 (21%)

Query: 29  DSCDDACSICLEEF---------------SESDPSTVTSCKHEFHLQCVLEWCQRSSQCP 73
           D   D C+IC                   SE        C H FH  C+  W +    CP
Sbjct: 45  DIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCP 104

Query: 74  MCWQPISLK 82
           +  +    +
Sbjct: 105 LDNREWEFQ 113

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

 Score = 53.7 bits (129), Expect = 5e-10
 Identities = 15/63 (23%), Positives = 22/63 (34%), Gaps = 3/63 (4%)

Query: 18 SAAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQ 77
           ++              C+ICL+      P +   CKH F   CV        +C +C Q
Sbjct: 1  GSSGSSGNTAPSLTVPECAICLQTCV--HPVS-LPCKHVFCYLCVKGASWLGKRCALCRQ 57

Query: 78 PIS 80
           I 
Sbjct: 58 EIP 60

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A Length = 106

 Score = 54.4 bits (130), Expect = 7e-10
 Identities = 15/69 (21%), Positives = 21/69 (30%), Gaps = 15/69 (21%)

Query: 29  DSCDDACSICLEEF---------------SESDPSTVTSCKHEFHLQCVLEWCQRSSQCP 73
           D   D C+IC                   SE        C H FH  C+  W +    CP
Sbjct: 34  DIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCP 93

Query: 74  MCWQPISLK 82
           +  +    +
Sbjct: 94  LDNREWEFQ 102

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

 Score = 53.2 bits (128), Expect = 9e-10
 Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 2/46 (4%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPIS 80
          CSIC       D +T+T C H F   C++     S++CP C   + 
Sbjct: 18 CSICKGYLI--DATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVH 61

>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 = 52.9 bits (127), Expect = 3e-09
 Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 2/49 (4%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKD 83
          C +C   F   D +T+  C H F   C++ + + S  CP+C   +    
Sbjct: 18 CVLCGGYFI--DATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTR 64

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

 Score = 51.7 bits (124), Expect = 6e-09
 Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 3/67 (4%)

Query: 35  CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELL-EAV 93
           C IC E F+      +  C H +   C+ ++    +QCP C   ++  D  +  +L E V
Sbjct: 25  CGICFEYFN--IAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLKNNRILDELV 82

Query: 94  EQERSIR 100
           +     R
Sbjct: 83  KSLNFAR 89

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

 Score = 50.3 bits (121), Expect = 7e-09
 Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 1/42 (2%)

Query: 35 CSICLEEFSESDPSTV-TSCKHEFHLQCVLEWCQRSSQCPMC 75
          C++CL E  + + +     C H FH +CV  W    S CP+C
Sbjct: 8  CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLC 49

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

 Score = 50.4 bits (120), Expect = 5e-08
 Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 3/52 (5%)

Query: 32  DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKD 83
           +  C IC E F   +  T  +C H F   C+ EW +R  +CP+C + I  K 
Sbjct: 64  ELQCIICSEYFI--EAVT-LNCAHSFCSYCINEWMKRKIECPICRKDIKSKT 112

>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 = 48.7 bits (116), Expect = 1e-07
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKD 83
          CS C       +P  +  C+H F   CV +     + CP+C+ P  ++D
Sbjct: 25 CSRCTNILR--EPVCLGGCEHIFCSNCVSDCI--GTGCPVCYTPAWIQD 69

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

 Score = 49.0 bits (116), Expect = 1e-07
 Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 4/53 (7%)

Query: 35 CSICLEEFSESDPS----TVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKD 83
          C IC++ +SE   +      T C H F  QC+ +  + ++ CP C + I+ K 
Sbjct: 10 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR 62

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

 Score = 39.4 bits (91), Expect = 2e-04
 Identities = 18/81 (22%), Positives = 29/81 (35%), Gaps = 4/81 (4%)

Query: 7   EEGKKPEDHMTSAAAFVEGGIQDSCDDACSICLEEFSE----SDPSTVTSCKHEFHLQCV 62
                P                 S   +C IC++ +SE          T C H F  QC+
Sbjct: 47  NANTCPTCRKKINHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCL 106

Query: 63  LEWCQRSSQCPMCWQPISLKD 83
            +  + ++ CP C + I+ K 
Sbjct: 107 RDSLKNANTCPTCRKKINHKR 127

>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 = 50.9 bits (121), Expect = 2e-07
 Identities = 13/57 (22%), Positives = 18/57 (31%), Gaps = 4/57 (7%)

Query: 28  QDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQ-RSSQCPMCWQPISLKD 83
             S    C IC E   +     +  C H     C+  W +     CP C   I   +
Sbjct: 328 MGSTFQLCKICAENDKDV---KIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE 381

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

 Score = 50.6 bits (120), Expect = 3e-07
 Identities = 14/71 (19%), Positives = 24/71 (33%), Gaps = 16/71 (22%)

Query: 28  QDSCDDACSICLEEFSESDPSTV-----TSCKHEFHLQCVLEWCQRSS-----------Q 71
           +D+ +  C+IC     +     +       C  + H  C+ EW +              Q
Sbjct: 304 EDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQ 363

Query: 72  CPMCWQPISLK 82
           CP C   +S  
Sbjct: 364 CPFCKAKLSTS 374

>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 = 46.8 bits (110), Expect = 5e-07
 Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 20/64 (31%)

Query: 32 DDACSICLEEFSESDPST---------------VTSCKHEFHLQCVLEWCQRSS-----Q 71
          ++ C IC+E+ + +   +               +T C H FHL C+L      +     Q
Sbjct: 25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQ 84

Query: 72 CPMC 75
          CP C
Sbjct: 85 CPSC 88

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

 Score = 41.7 bits (98), Expect = 9e-06
 Identities = 13/50 (26%), Positives = 16/50 (32%), Gaps = 4/50 (8%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSS-QCPMCWQPISLKD 83
          C  C        P   T C H F   C+      SS +C  C + I    
Sbjct: 18 CEKCHLVLC--SPKQ-TECGHRFCESCMAALLSSSSPKCTACQESIVKDK 64

>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 = 43.4 bits (102), Expect = 1e-05
 Identities = 17/93 (18%), Positives = 30/93 (32%), Gaps = 7/93 (7%)

Query: 7   EEGKKPEDHMTSAAAFVEGGIQDSCDD-ACSICLEEFSESDPSTVTSCKHEFHLQCVLE- 64
            E         ++ +  +  +    +   C  C E      P T T C+H     C+   
Sbjct: 26  NEVLASLKDRPASGSPFQLFLSKVEETFQCICCQELVF--RPIT-TVCQHNVCKDCLDRS 82

Query: 65  WCQRSSQCPMCWQPISLKDA--TSQELLEAVEQ 95
           +  +   CP C   +    A   +Q L   + Q
Sbjct: 83  FRAQVFSCPACRYDLGRSYAMQVNQPLQTVLNQ 115

>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 = 44.6 bits (104), Expect = 1e-05
 Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 6/78 (7%)

Query: 35  CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSS--QCPM--CWQPISLKDATSQELL 90
           C I  + +    P     C H F    +  + Q  +   CP   C Q +S++D     ++
Sbjct: 184 CPITCKPYE--APLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFVRDPIM 241

Query: 91  EAVEQERSIRANPPRNAT 108
           E   +   ++ +  ++  
Sbjct: 242 ELRCKIAKMKESQEQDKR 259

>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 = 41.5 bits (97), Expect = 2e-05
 Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 4/47 (8%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS--SQCPMCWQPI 79
          C+IC     +    +  +C    HL CV ++ Q +   +CP C    
Sbjct: 18 CNICHSLLIQG--QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYW 62

>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 = 43.4 bits (102), Expect = 2e-05
 Identities = 16/70 (22%), Positives = 26/70 (37%), Gaps = 8/70 (11%)

Query: 35  CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS-SQCPMCWQPISLK-----DATSQE 88
           C ICL+     +  T   C H F   C++   +    +CP C + +  K     D     
Sbjct: 57  CPICLDMLK--NTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDA 114

Query: 89  LLEAVEQERS 98
           L+  +   R 
Sbjct: 115 LISKIYPSRD 124

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

 Score = 41.4 bits (97), Expect = 3e-05
 Identities = 19/50 (38%), Positives = 22/50 (44%), Gaps = 4/50 (8%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPISLKD 83
          C IC    +  DP   TSCKH F   C+L   +   S CP C  P    D
Sbjct: 26 CQICEHILA--DP-VETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTD 72

>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 = 40.2 bits (94), Expect = 6e-05
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 10/73 (13%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQ--------RSSQCPM--CWQPISLKDA 84
          C +CL E+     +T+  C+  F   C+ ++ +         +  CP   C +   L++ 
Sbjct: 8  CKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQEN 67

Query: 85 TSQELLEAVEQER 97
            + ++ A   +R
Sbjct: 68 EIECMVAAEIMQR 80

>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 = 39.7 bits (93), Expect = 6e-05
 Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 4/52 (7%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQ--CPMCWQPISLKDA 84
          C IC +  +  D   +  C + +  +C+      S +  CP C Q     DA
Sbjct: 18 CLICKDIMT--DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA 67

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

 Score = 40.1 bits (94), Expect = 6e-05
 Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 4/56 (7%)

Query: 35 CSICLEEFSESD-PSTVTSCKHEFHLQCVLEWCQRSS---QCPMCWQPISLKDATS 86
          C IC+E F+E      +  C H    QC+ +    S    +CP C +   +   T 
Sbjct: 18 CPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITSLTQ 73

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

 Score = 40.7 bits (95), Expect = 7e-05
 Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 4/63 (6%)

Query: 19 AAAFVEGGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSS-QCPMCWQ 77
          + A  +  I    +  C IC+E     +P T   C H     C     +++S  CP C +
Sbjct: 2  SMALPKDAIPSLSECQCGICMEILV--EPVT-LPCNHTLCKPCFQSTVEKASLCCPFCRR 58

Query: 78 PIS 80
           +S
Sbjct: 59 RVS 61

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

 Score = 39.3 bits (91), Expect = 9e-05
 Identities = 12/60 (20%), Positives = 21/60 (35%), Gaps = 2/60 (3%)

Query: 32 DDACSICLEEFSESDPS-TVTSCKHEFHLQCVLEW-CQRSSQCPMCWQPISLKDATSQEL 89
             C +C+E     D +    +C ++    C        +  CP C +P     A  + L
Sbjct: 11 PVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAVYKPL 70

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

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 6/52 (11%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWC---QRSSQCPMCWQPISLKD 83
          C ICL+      P T   C H F L+C+ +         +CP+C   +    
Sbjct: 23 CPICLDIL--QKPVT-IDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA 71

>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 = 40.5 bits (94), Expect = 2e-04
 Identities = 11/50 (22%), Positives = 20/50 (40%), Gaps = 4/50 (8%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQ-CPMCWQPISLKD 83
          C ICL      +    T C H F   C+++  + +   CP+  + +    
Sbjct: 21 CPICLMALR--EA-VQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQ 67

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

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 4/51 (7%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS--SQCPMCWQPISLKD 83
          C IC +  +  D   +  C + +  +C+      S    CP C Q     D
Sbjct: 16 CLICKDIMT--DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD 64

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

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 11/50 (22%), Positives = 20/50 (40%), Gaps = 4/50 (8%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQ-CPMCWQPISLKD 83
          C ICL      +    T C H F   C+++  + +   CP+  + +    
Sbjct: 21 CPICLMALR--EA-VQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQ 67

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

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 10/75 (13%)

Query: 16 MTSAAAFVEGGIQDSCDDA-CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS----- 69
           + ++    G + +  ++  C ICLE    + P +   C H F   C+    ++S     
Sbjct: 2  SSGSSGMASGILVNVKEEVTCPICLELL--TQPLS-LDCGHSFCQACLTANHKKSMLDKG 58

Query: 70 -SQCPMCWQPISLKD 83
           S CP+C      ++
Sbjct: 59 ESSCPVCRISYQPEN 73

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

 Score = 37.6 bits (88), Expect = 3e-04
 Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 10/56 (17%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS-------SQCPMCWQPISLKD 83
          C ICLE    ++P +   C H     C+    + +       S CP+C    S + 
Sbjct: 15 CPICLELL--TEPLS-LDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEH 67

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

 Score = 37.0 bits (86), Expect = 3e-04
 Identities = 15/47 (31%), Positives = 17/47 (36%), Gaps = 6/47 (12%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISL 81
          C  C  E     P  +  C H     C LE      QCP+C  P  L
Sbjct: 9  CQQCQAEA--KCP-KLLPCLHTLCSGC-LE--ASGMQCPICQAPWPL 49

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

 Score = 36.9 bits (86), Expect = 4e-04
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 7/61 (11%)

Query: 19 AAAFVEGGIQDSCDDA-CSICLEEFSESDPSTVTSCKHEFHLQCVLEWC---QRSSQCPM 74
           ++   G +++   +A CS+CLE     +P     C H F   C+  W    +R   CP+
Sbjct: 1  GSSGSSGALENLQVEASCSVCLEYL--KEPVI-IECGHNFCKACITRWWEDLERDFPCPV 57

Query: 75 C 75
          C
Sbjct: 58 C 58

>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 = 39.2 bits (91), Expect = 4e-04
 Identities = 12/51 (23%), Positives = 15/51 (29%), Gaps = 4/51 (7%)

Query: 35  CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSS-QCPMCWQPISLKDA 84
           C  C E      P T T C H     C+    +     CP C   +     
Sbjct: 81  CVCCQELVY--QPVT-TECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYI 128

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	303
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.42
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.41
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.4
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.38
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.38
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.36
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.36
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.34
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.32
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.31
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.3
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.3
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.3
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.29
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.29
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.27
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.27
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.26
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.26
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.23
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.23
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.22
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.22
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.22
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.21
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.21
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.21
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.19
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.19
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.18
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.14
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.14
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.14
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.13
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.12
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.12
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.12
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.12
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.09
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.09
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.08
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.06
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.04
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.03
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.02
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.01
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	98.99
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	98.99
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.98
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	98.95
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.95
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.92
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.89
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.86
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.84
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.83
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.82
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.78
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.77
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.76
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.75
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.59
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.54
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.49
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.47
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.46
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.45
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.45
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.24
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.05
3nw0_A	238	Non-structural maintenance of chromosomes element	97.66
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	95.87
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	95.51
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	93.15
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	88.6
3i2d_A	371	E3 SUMO-protein ligase SIZ1; signal transduction,	87.95
4fo9_A	360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	86.54
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	84.53
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	83.03
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	82.4
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	82.06
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	81.61
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	81.24
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	80.26

>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=99.42  E-value=1.8e-13  Score=100.08  Aligned_cols=55  Identities=29%  Similarity=0.765  Sum_probs=47.6

Q ss_pred             CCCCccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCC
Q 022060           28 QDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLK   82 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~   82 (303)
                      .++.+..|+||++.|.....+..++|+|.||..||..|+..+..||+||+.+...
T Consensus        10 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           10 EEDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             STTCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             cCCCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            3445778999999997667778889999999999999999999999999998654

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

Probab=99.41  E-value=1.7e-13  Score=102.57  Aligned_cols=56  Identities=21%  Similarity=0.723  Sum_probs=48.0

Q ss_pred             CCCccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCc
Q 022060           29 DSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDA   84 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~   84 (303)
                      ...+..|+||++.|.....+.+++|+|.||..||..|++.+..||+||+.+...+.
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   67 (78)
T 2ect_A           12 VGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNT   67 (78)
T ss_dssp             SSSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCCCSCS
T ss_pred             CCCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccCCccc
Confidence            34477899999999665666778999999999999999999999999999976543

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

Probab=99.40  E-value=1.2e-13  Score=107.10  Aligned_cols=53  Identities=34%  Similarity=0.731  Sum_probs=46.2

Q ss_pred             CCCccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcC
Q 022060           29 DSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISL   81 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~   81 (303)
                      .+.+..|+||++.|..++.+..++|+|.||..||..|+..+..||+||+.+..
T Consensus        37 ~~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           37 VGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFPP   89 (91)
T ss_dssp             SSSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTCBCTTTCCBSSC
T ss_pred             cCCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCCcCcCcCccCCC
Confidence            34577899999999766667778999999999999999999999999998753

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

Probab=99.38  E-value=3.5e-13  Score=99.84  Aligned_cols=54  Identities=31%  Similarity=0.864  Sum_probs=46.6

Q ss_pred             CCCccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCC
Q 022060           29 DSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLK   82 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~   82 (303)
                      ...+..|+||++.|.....+.+++|+|.||..||..|++.+..||+||+.+...
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (74)
T 2ep4_A           12 LNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQL   65 (74)
T ss_dssp             CCCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCSBCTTTCCBCSSC
T ss_pred             CCCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCCcCCCcCcccccc
Confidence            344778999999997666677789999999999999999989999999988643

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

Probab=99.38  E-value=2.3e-13  Score=95.03  Aligned_cols=50  Identities=30%  Similarity=0.802  Sum_probs=43.6

Q ss_pred             CccccccccccccCCCCeeecc-CCccccHHhHHHHHhcCCCCCCCcccCc
Q 022060           31 CDDACSICLEEFSESDPSTVTS-CKHEFHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~-C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      ++.+|+||++.|..++.+..++ |+|.||..||..|++.+..||+||+.+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            3778999999997666666666 9999999999999999999999999874

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

Probab=99.36  E-value=2.6e-13  Score=100.99  Aligned_cols=53  Identities=30%  Similarity=0.767  Sum_probs=46.1

Q ss_pred             CCCccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcC
Q 022060           29 DSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISL   81 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~   81 (303)
                      .+++..|+||++.|...+.+..++|+|.||..||..|++.+..||+||+.+..
T Consensus        20 ~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~   72 (75)
T 1x4j_A           20 QSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGP   72 (75)
T ss_dssp             SSSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCSSCTTTCCCCCC
T ss_pred             cCCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCCcCcCcCCcCCC
Confidence            34577899999999666666778999999999999999999999999998864

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

Probab=99.36  E-value=4.6e-13  Score=99.00  Aligned_cols=53  Identities=28%  Similarity=0.561  Sum_probs=46.1

Q ss_pred             CCccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCc
Q 022060           30 SCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDA   84 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~   84 (303)
                      +++..|+||++.|  .+++++++|+|.||..||..|++.+..||+||+.+...++
T Consensus        13 ~~~~~C~IC~~~~--~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~   65 (72)
T 2djb_A           13 TPYILCSICKGYL--IDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQP   65 (72)
T ss_dssp             CGGGSCTTTSSCC--SSCEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSCS
T ss_pred             CCCCCCCCCChHH--HCcCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCcccc
Confidence            3478899999999  5666667999999999999999989999999999976654

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

Probab=99.34  E-value=5.1e-13  Score=97.83  Aligned_cols=57  Identities=30%  Similarity=0.610  Sum_probs=47.3

Q ss_pred             CCCCccccccccccccCC----CCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCc
Q 022060           28 QDSCDDACSICLEEFSES----DPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDA   84 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~~----~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~   84 (303)
                      ..+++..|+||++.|.+.    ..+.+++|+|.||..||..|+..+..||+||+.+...+.
T Consensus         6 ~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   66 (71)
T 3ng2_A            6 RPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   66 (71)
T ss_dssp             CCTTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCCCSC
T ss_pred             CCCCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccChhhe
Confidence            445588899999998542    334778999999999999999999999999999976654

>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=99.32  E-value=3.7e-13  Score=106.08  Aligned_cols=60  Identities=27%  Similarity=0.660  Sum_probs=49.0

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcC-CCCCCCcccCcCCCcchHHHHHHH
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS-SQCPMCWQPISLKDATSQELLEAV   93 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~-~~CP~CR~~l~~~d~~~~~l~e~~   93 (303)
                      +..|+||++.|  .+++.+++|+|.||..||..|+... ..||+||..+...++.....+..+
T Consensus        22 ~~~C~IC~~~~--~~p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~l~~~~~~~~i   82 (100)
T 3lrq_A           22 VFRCFICMEKL--RDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVNCRWAEEV   82 (100)
T ss_dssp             HTBCTTTCSBC--SSEEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEECTTHHHH
T ss_pred             CCCCccCCccc--cCccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHHHhHhhHHHHHH
Confidence            78899999999  5565548999999999999999887 699999999987666554444443

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

Probab=99.31  E-value=1.2e-12  Score=97.88  Aligned_cols=63  Identities=19%  Similarity=0.326  Sum_probs=49.8

Q ss_pred             CCCccccccccccccCCCCeeeccCCccccHHhHHHHHhc-CCCCCCCcccCcCCCcchHHHHHHHH
Q 022060           29 DSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPISLKDATSQELLEAVE   94 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l~~~d~~~~~l~e~~~   94 (303)
                      -.++..|+||++.|  .+++. ++|+|.||..||..|+.. ...||+||+.+...++..+..+..+.
T Consensus         5 ~~~~~~C~IC~~~~--~~Pv~-~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~l~~n~~l~~~i   68 (78)
T 1t1h_A            5 FPEYFRCPISLELM--KDPVI-VSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNYVLKSLI   68 (78)
T ss_dssp             CSSSSSCTTTSCCC--SSEEE-ETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEECTTTHHHH
T ss_pred             CcccCCCCCccccc--cCCEE-cCCCCeecHHHHHHHHHHCcCCCCCCcCCCChhhCccCHHHHHHH
Confidence            34588999999999  55544 599999999999999987 78899999999877665554444433

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

Probab=99.30  E-value=1e-12  Score=102.89  Aligned_cols=61  Identities=23%  Similarity=0.592  Sum_probs=50.2

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCcchHHHHHHHH
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVE   94 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~~~~~l~e~~~   94 (303)
                      +..|+||++.|  .+++.+++|+|.||..||..|+.....||+||..+...++..+..+..+.
T Consensus        22 ~~~C~IC~~~~--~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~l~~n~~l~~~i   82 (99)
T 2y43_A           22 LLRCGICFEYF--NIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLKNNRILDELV   82 (99)
T ss_dssp             HTBCTTTCSBC--SSEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCEECHHHHHHH
T ss_pred             CCCcccCChhh--CCcCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCChhhCCcCHHHHHHH
Confidence            67899999999  55555569999999999999999889999999999876666555555443

>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=99.30  E-value=1.6e-12  Score=90.62  Aligned_cols=50  Identities=34%  Similarity=0.705  Sum_probs=43.1

Q ss_pred             CccccccccccccCC-CCeeeccCCccccHHhHHHHHhcCCCCCCCcccCc
Q 022060           31 CDDACSICLEEFSES-DPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        31 ~d~~C~ICle~f~~~-~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      .+..|+||++.|.+. ..+.+++|+|.||..||..|+.....||+||+.+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            467899999998543 35777899999999999999998899999999874

>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=99.30  E-value=2.4e-12  Score=103.07  Aligned_cols=54  Identities=33%  Similarity=0.700  Sum_probs=42.3

Q ss_pred             CCCccccccccccccCCC---------------CeeeccCCccccHHhHHHHH-----hcCCCCCCCcccCcCC
Q 022060           29 DSCDDACSICLEEFSESD---------------PSTVTSCKHEFHLQCVLEWC-----QRSSQCPMCWQPISLK   82 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~~~---------------~~~vl~C~H~Fc~~CI~~Wl-----~~~~~CP~CR~~l~~~   82 (303)
                      ...+..|+||++.|....               .+.+++|+|.||..||..|+     ..+..||+||+.+..+
T Consensus        22 ~~~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           22 VAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             SCCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCCCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            334678999999994321               23378999999999999999     4467899999988643

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

Probab=99.29  E-value=2.1e-12  Score=93.77  Aligned_cols=52  Identities=31%  Similarity=0.659  Sum_probs=43.6

Q ss_pred             CCccccccccccccCC----CCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcC
Q 022060           30 SCDDACSICLEEFSES----DPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISL   81 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~----~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~   81 (303)
                      .++..|+||++.|.+.    ..+.+++|+|.||..||..|+..+..||+||+.+..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            4478899999999542    224678999999999999999999999999998854

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

Probab=99.29  E-value=1.5e-12  Score=98.82  Aligned_cols=52  Identities=29%  Similarity=0.723  Sum_probs=41.9

Q ss_pred             CccccccccccccC-----------CC-CeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCC
Q 022060           31 CDDACSICLEEFSE-----------SD-PSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLK   82 (303)
Q Consensus        31 ~d~~C~ICle~f~~-----------~~-~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~   82 (303)
                      +++.|+||++.|.+           ++ .+.+++|+|.||..||.+|+..+.+||+||+.+...
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   77 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQ   77 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchh
Confidence            46779999998843           12 334556999999999999999999999999988643

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

Probab=99.27  E-value=5.2e-12  Score=95.27  Aligned_cols=49  Identities=35%  Similarity=0.765  Sum_probs=42.6

Q ss_pred             CCCccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCc
Q 022060           29 DSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      .+.+..|+||++.|  .++ .+++|+|.||..||..|+.....||+||+.+.
T Consensus        12 ~~~~~~C~IC~~~~--~~p-~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           12 EEIPFRCFICRQAF--QNP-VVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCCSBCSSSCSBC--CSE-EECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCCcCCCchh--cCe-eEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            34477899999999  444 45799999999999999998899999999986

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

Probab=99.27  E-value=2e-12  Score=94.04  Aligned_cols=48  Identities=33%  Similarity=0.887  Sum_probs=43.2

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCc
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      .+..|+||++.+  .+++..++|+|.||..||..|+..+..||+||+.+.
T Consensus         4 ~~~~C~IC~~~~--~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~   51 (68)
T 1chc_A            4 VAERCPICLEDP--SNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCCSSCCSCC--CSCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCCeeCCccc--cCCcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhH
Confidence            467899999998  566678899999999999999998999999999885

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

Probab=99.26  E-value=2e-12  Score=92.49  Aligned_cols=54  Identities=30%  Similarity=0.623  Sum_probs=45.2

Q ss_pred             CccccccccccccCC----CCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCc
Q 022060           31 CDDACSICLEEFSES----DPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDA   84 (303)
Q Consensus        31 ~d~~C~ICle~f~~~----~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~   84 (303)
                      ++.+|+||++.|.+.    +.+.+++|+|.||..||..|+..+..||+||+.+...+.
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   59 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   59 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTTTCE
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCccce
Confidence            367899999998531    334678999999999999999999999999999876553

>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=3.3e-12  Score=101.55  Aligned_cols=50  Identities=26%  Similarity=0.628  Sum_probs=44.3

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCC
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLK   82 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~   82 (303)
                      ++..|+||++.|  .+++++++|+|.||..||..|+.....||+||..+...
T Consensus        14 ~~~~C~IC~~~~--~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           14 PHLMCVLCGGYF--IDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GGTBCTTTSSBC--SSEEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             CcCCCccCChHH--hCcCEeCCCCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            378899999999  56666669999999999999999999999999998765

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

Probab=99.23  E-value=4.5e-12  Score=93.38  Aligned_cols=50  Identities=30%  Similarity=0.595  Sum_probs=42.6

Q ss_pred             CCCccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcC
Q 022060           29 DSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISL   81 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~   81 (303)
                      ..++..|+||++.|  .++ +.++|+|.||..||..|+.....||+||+.+..
T Consensus        12 ~~~~~~C~IC~~~~--~~~-~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   61 (71)
T 2d8t_A           12 SLTVPECAICLQTC--VHP-VSLPCKHVFCYLCVKGASWLGKRCALCRQEIPE   61 (71)
T ss_dssp             SSSCCBCSSSSSBC--SSE-EEETTTEEEEHHHHHHCTTCSSBCSSSCCBCCH
T ss_pred             CCCCCCCccCCccc--CCC-EEccCCCHHHHHHHHHHHHCCCcCcCcCchhCH
Confidence            34577899999998  444 556999999999999999999999999999863

>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=99.23  E-value=1.1e-12  Score=111.86  Aligned_cols=62  Identities=23%  Similarity=0.585  Sum_probs=47.8

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhc-CCCCCCCcccCcCC-CcchHHHHHHHH
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPISLK-DATSQELLEAVE   94 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l~~~-d~~~~~l~e~~~   94 (303)
                      ++..|+||++.|  .+++.+++|+|.||..||..|+.. ...||+||..+... .+..+..+..+.
T Consensus        53 ~~~~C~IC~~~~--~~p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~l~~~~~l~~~i  116 (165)
T 2ckl_B           53 SELMCPICLDML--KNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALI  116 (165)
T ss_dssp             HHHBCTTTSSBC--SSEEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCSGGGEEECHHHHHHH
T ss_pred             CCCCCcccChHh--hCcCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCCcccCCcCHHHHHHH
Confidence            366899999999  566666699999999999999987 77899999998543 334444444443

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 4f52_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A

Probab=99.22  E-value=5.3e-12  Score=101.12  Aligned_cols=51  Identities=24%  Similarity=0.635  Sum_probs=43.0

Q ss_pred             CccccccccccccCC---------------CCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcC
Q 022060           31 CDDACSICLEEFSES---------------DPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISL   81 (303)
Q Consensus        31 ~d~~C~ICle~f~~~---------------~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~   81 (303)
                      +++.|+||++.|...               ..+.+++|+|.||..||..|+..+..||+||+.+..
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~~  101 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEF  101 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCCE
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcCCcCcCCCCccee
Confidence            477899999998532               125668999999999999999999999999998754

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

Probab=99.22  E-value=1e-11  Score=94.38  Aligned_cols=54  Identities=26%  Similarity=0.583  Sum_probs=44.3

Q ss_pred             CCccccccccccccCCCC-eeeccCCccccHHhHHHHHhcC---CCCCCCcccCcCCC
Q 022060           30 SCDDACSICLEEFSESDP-STVTSCKHEFHLQCVLEWCQRS---SQCPMCWQPISLKD   83 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~-~~vl~C~H~Fc~~CI~~Wl~~~---~~CP~CR~~l~~~d   83 (303)
                      .++.+|+||++.|.+.+. +.+++|+|.||..||..|+...   ..||+||+.+...+
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   70 (88)
T 2ct2_A           13 REVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITS   70 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCSS
T ss_pred             cCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccchh
Confidence            347889999999954332 6677999999999999999875   78999999886543

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

Probab=99.22  E-value=8.4e-12  Score=90.51  Aligned_cols=50  Identities=24%  Similarity=0.527  Sum_probs=42.3

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHh-cCCCCCCCcccCcCCC
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQ-RSSQCPMCWQPISLKD   83 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~-~~~~CP~CR~~l~~~d   83 (303)
                      ++..|+||++.+  .+++. ++|+|.||..||..|+. ....||+||+.+...+
T Consensus        14 ~~~~C~IC~~~~--~~p~~-~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   64 (66)
T 2ecy_A           14 DKYKCEKCHLVL--CSPKQ-TECGHRFCESCMAALLSSSSPKCTACQESIVKDK   64 (66)
T ss_dssp             CCEECTTTCCEE--SSCCC-CSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTT
T ss_pred             cCCCCCCCChHh--cCeeE-CCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChhh
Confidence            478899999999  55555 69999999999999994 5678999999987654

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

Probab=99.21  E-value=1.4e-11  Score=94.79  Aligned_cols=62  Identities=21%  Similarity=0.424  Sum_probs=47.2

Q ss_pred             CCccccccccccccCCCCeeecc-CCccccHHhHHHHHhcC--CCCCCCcccC-cCCCcchHHHHHHHH
Q 022060           30 SCDDACSICLEEFSESDPSTVTS-CKHEFHLQCVLEWCQRS--SQCPMCWQPI-SLKDATSQELLEAVE   94 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~-C~H~Fc~~CI~~Wl~~~--~~CP~CR~~l-~~~d~~~~~l~e~~~   94 (303)
                      .++..|+||++.|  .++++ ++ |+|.||..||..|+...  ..||+||+.+ ...++..+..+..+.
T Consensus        11 ~~~~~C~IC~~~~--~~p~~-~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~~~~~n~~l~~~i   76 (92)
T 3ztg_A           11 PDELLCLICKDIM--TDAVV-IPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDALIANKFLRQAV   76 (92)
T ss_dssp             CTTTEETTTTEEC--SSCEE-CTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSCCTTSCEECHHHHHHH
T ss_pred             CcCCCCCCCChhh--cCceE-CCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCCCccccCcCHHHHHHH
Confidence            3478999999999  56655 47 99999999999999643  5899999997 444555555444443

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

Probab=99.21  E-value=9.5e-12  Score=92.52  Aligned_cols=51  Identities=24%  Similarity=0.484  Sum_probs=42.1

Q ss_pred             CCccccccccccccCCCCeeecc-CCccccHHhHHHHHhcC--CCCCCCcccCcCCC
Q 022060           30 SCDDACSICLEEFSESDPSTVTS-CKHEFHLQCVLEWCQRS--SQCPMCWQPISLKD   83 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~-C~H~Fc~~CI~~Wl~~~--~~CP~CR~~l~~~d   83 (303)
                      .++..|+||++.|  .+++. ++ |+|.||..||..|+...  ..||+||+.+...+
T Consensus        13 ~~~~~C~IC~~~~--~~p~~-~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2yur_A           13 PDELLCLICKDIM--TDAVV-IPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD   66 (74)
T ss_dssp             CGGGSCSSSCCCC--TTCEE-CSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTT
T ss_pred             CCCCCCcCCChHH--hCCeE-cCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCcc
Confidence            3478899999999  56655 57 99999999999999865  68999999865443

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

Probab=99.21  E-value=9.7e-12  Score=91.52  Aligned_cols=51  Identities=25%  Similarity=0.691  Sum_probs=42.3

Q ss_pred             CCccccccccccccCCCCeeeccCCccccHHhHHHHHh---cCCCCCCCcccCcCCC
Q 022060           30 SCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQ---RSSQCPMCWQPISLKD   83 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~---~~~~CP~CR~~l~~~d   83 (303)
                      .++..|+||++.|  .++ .+++|+|.||..||..|+.   ....||+||+.+...+
T Consensus        18 ~~~~~C~IC~~~~--~~~-~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           18 QEEVICPICLDIL--QKP-VTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCCBCTTTCSBC--SSE-EECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             ccCCEeccCCccc--CCe-EEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            3478899999998  444 4569999999999999997   4568999999987654

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

Probab=99.19  E-value=4.7e-12  Score=105.21  Aligned_cols=49  Identities=35%  Similarity=0.828  Sum_probs=42.8

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKD   83 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d   83 (303)
                      +..|+||++.|  .++ ++++|+|.||..||..|+..+..||+||+.+....
T Consensus        53 ~~~C~iC~~~~--~~~-~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~  101 (138)
T 4ayc_A           53 ELQCIICSEYF--IEA-VTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKT  101 (138)
T ss_dssp             HSBCTTTCSBC--SSE-EEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCCEE
T ss_pred             cCCCcccCccc--CCc-eECCCCCCccHHHHHHHHHcCCcCCCCCCcCCCCC
Confidence            67899999999  444 55699999999999999999999999999987554

>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=99.19  E-value=1.2e-11  Score=100.70  Aligned_cols=60  Identities=22%  Similarity=0.398  Sum_probs=47.6

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcC-CCCCCCcccCcC-CCcchHHHHHHHH
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS-SQCPMCWQPISL-KDATSQELLEAVE   94 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~-~~CP~CR~~l~~-~d~~~~~l~e~~~   94 (303)
                      +..|+||++.|  .++ +.++|+|.||..||..|+... ..||+||+.+.. .++..+..+..+.
T Consensus        52 ~~~C~IC~~~~--~~p-~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~n~~l~~~i  113 (124)
T 3fl2_A           52 TFQCICCQELV--FRP-ITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGRSYAMQVNQPLQTVL  113 (124)
T ss_dssp             HTBCTTTSSBC--SSE-EECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTTCCCCCCHHHHHHH
T ss_pred             CCCCCcCChHH--cCc-EEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCCCCCCCCCHHHHHHH
Confidence            67899999999  454 445999999999999999854 489999999976 5555555555544

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

Probab=99.18  E-value=4.1e-12  Score=93.03  Aligned_cols=50  Identities=26%  Similarity=0.833  Sum_probs=43.1

Q ss_pred             CCccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCC
Q 022060           30 SCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKD   83 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d   83 (303)
                      .++..|+||++.+.  +  .+++|+|.||..||..|+.....||+||+.+...+
T Consensus        13 ~~~~~C~IC~~~~~--~--~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (70)
T 2ecn_A           13 TDEEECCICMDGRA--D--LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGAN   62 (70)
T ss_dssp             CCCCCCSSSCCSCC--S--EEETTTEEECHHHHHHSSCCCSSCHHHHHCTTCCC
T ss_pred             CCCCCCeeCCcCcc--C--cccCCCCcccHHHHHHHHHCcCcCCCcCCcccCCC
Confidence            34778999999983  3  66799999999999999999999999999887543

>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=99.14  E-value=4.6e-11  Score=94.54  Aligned_cols=64  Identities=13%  Similarity=0.028  Sum_probs=53.5

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCcchHHHHHHHHHHH
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQER   97 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~~~~~l~e~~~~er   97 (303)
                      ++..|+||++.|  .+|+++ +|||.||..||..|+.....||+|+.++...++.++..+.......
T Consensus        28 ~~~~CpI~~~~m--~dPV~~-~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~L~pn~~Lk~~I~~~   91 (100)
T 2kre_A           28 DEFRDPLMDTLM--TDPVRL-PSGTIMDRSIILRHLLNSPTDPFNRQTLTESMLEPVPELKEQIQAW   91 (100)
T ss_dssp             TTTBCTTTCSBC--SSEEEE-TTTEEEEHHHHHHHTTSCSBCSSSCCBCCTTSSEECHHHHHHHHHH
T ss_pred             HhhCCcCccCcc--cCCeEC-CCCCEEchHHHHHHHHcCCCCCCCCCCCChhhceECHHHHHHHHHH
Confidence            478899999999  566554 8999999999999999888999999999988888776666555443

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

Probab=99.14  E-value=2.2e-11  Score=91.55  Aligned_cols=50  Identities=28%  Similarity=0.743  Sum_probs=42.5

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhc------CCCCCCCcccCcCCC
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR------SSQCPMCWQPISLKD   83 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~------~~~CP~CR~~l~~~d   83 (303)
                      ++..|+||++.|  .+++ +++|+|.||..||..|+..      ...||+||..+...+
T Consensus        18 ~~~~C~IC~~~~--~~p~-~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~   73 (85)
T 2ecw_A           18 EEVTCPICLELL--KEPV-SADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGN   73 (85)
T ss_dssp             TTTSCTTTCSCC--SSCE-ECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTC
T ss_pred             cCCCCcCCChhh--Ccce-eCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHh
Confidence            478899999999  5554 5699999999999999987      678999999987554

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

Probab=99.14  E-value=4.6e-11  Score=94.16  Aligned_cols=66  Identities=11%  Similarity=0.061  Sum_probs=54.4

Q ss_pred             CccccccccccccCCCCeeeccCC-ccccHHhHHHHHhcCCCCCCCcccCcCCCcchHHHHHHHHHHHhh
Q 022060           31 CDDACSICLEEFSESDPSTVTSCK-HEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQERSI   99 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~-H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~~~~~l~e~~~~er~~   99 (303)
                      ++..|+||++.|  .+|++ ++|+ |.||..||..|+.....||+|+.++...++.++..+.........
T Consensus        21 ~~~~CpI~~~~m--~dPV~-~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~L~pn~~Lk~~I~~~~~   87 (98)
T 1wgm_A           21 DEFLDPIMSTLM--CDPVV-LPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRPNTELKEKIQRWLA   87 (98)
T ss_dssp             TTTBCTTTCSBC--SSEEE-CTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEECHHHHHHHHHHHH
T ss_pred             HhcCCcCccccc--cCCeE-CCCCCeEECHHHHHHHHHhCCCCCCCCCCCChhhceEcHHHHHHHHHHHH
Confidence            478899999999  55554 5999 999999999999988899999999998888877666665554433

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

Probab=99.13  E-value=8.2e-12  Score=93.17  Aligned_cols=50  Identities=28%  Similarity=0.663  Sum_probs=42.2

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhc-------CCCCCCCcccCcCCC
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR-------SSQCPMCWQPISLKD   83 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~-------~~~CP~CR~~l~~~d   83 (303)
                      ++..|+||++.|  .+++. ++|+|.||..||..|+..       ...||+||..+...+
T Consensus        11 ~~~~C~IC~~~~--~~p~~-l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~   67 (79)
T 2egp_A           11 EEVTCPICLELL--TEPLS-LDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEH   67 (79)
T ss_dssp             CCCEETTTTEEC--SSCCC-CSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSG
T ss_pred             cCCCCcCCCccc--CCeeE-CCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhh
Confidence            478899999999  45544 699999999999999976       568999999987544

>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=99.12  E-value=3.9e-11  Score=101.48  Aligned_cols=62  Identities=21%  Similarity=0.443  Sum_probs=49.2

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhcCC-CCCCCcccCcCC-CcchHHHHHHHHH
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSS-QCPMCWQPISLK-DATSQELLEAVEQ   95 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~-~CP~CR~~l~~~-d~~~~~l~e~~~~   95 (303)
                      ++..|+||++.|  .+++ +++|+|.||..||..|+.... .||+||..+... .+..+..+..+..
T Consensus        77 ~~~~C~IC~~~~--~~pv-~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~l~~n~~l~~lv~  140 (150)
T 1z6u_A           77 QSFMCVCCQELV--YQPV-TTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYIMIPNEILQTLLD  140 (150)
T ss_dssp             HHTBCTTTSSBC--SSEE-ECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTTCCCCBCHHHHHHHH
T ss_pred             cCCEeecCChhh--cCCE-EcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCCCCCCCCHHHHHHHH
Confidence            367899999999  4554 469999999999999998754 899999999876 5555555555544

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

Probab=99.12  E-value=3.5e-11  Score=92.27  Aligned_cols=62  Identities=13%  Similarity=0.011  Sum_probs=51.2

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCcchHHHHHHHHH
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQ   95 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~~~~~l~e~~~~   95 (303)
                      ++..|+||++.|  .+|++ ++|||.||..||..|+.....||+|+..+...++.++..+.....
T Consensus        13 ~~~~CpI~~~~m--~dPV~-~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~l~pn~~L~~~i~   74 (85)
T 2kr4_A           13 DEFRDPLMDTLM--TDPVR-LPSGTVMDRSIILRHLLNSPTDPFNRQMLTESMLEPVPELKEQIQ   74 (85)
T ss_dssp             TTTBCTTTCSBC--SSEEE-CTTSCEEEHHHHHHHHHHCSBCTTTCCBCCGGGCEECHHHHHHHH
T ss_pred             hheECcccCchh--cCCeE-CCCCCEECHHHHHHHHhcCCCCCCCcCCCChHhcchHHHHHHHHH
Confidence            478899999999  55555 589999999999999998889999999998877776655554443

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

Probab=99.12  E-value=3e-11  Score=87.28  Aligned_cols=53  Identities=25%  Similarity=0.576  Sum_probs=41.7

Q ss_pred             ccccccccc-cccCCC-CeeeccCCccccHHhHHHHHhc-CCCCCCCcccCcCCCc
Q 022060           32 DDACSICLE-EFSESD-PSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPISLKDA   84 (303)
Q Consensus        32 d~~C~ICle-~f~~~~-~~~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l~~~d~   84 (303)
                      +..|+||++ .|.+.. ...+++|||.||..||..|+.. ...||+||+.+...++
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   58 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNF   58 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCC
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccccc
Confidence            678999999 774322 1245799999999999999765 4679999999976654

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

Probab=99.12  E-value=2.7e-11  Score=91.07  Aligned_cols=51  Identities=27%  Similarity=0.660  Sum_probs=42.8

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhc------CCCCCCCcccCcCCCc
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR------SSQCPMCWQPISLKDA   84 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~------~~~CP~CR~~l~~~d~   84 (303)
                      ++..|+||++.|  .+++ .++|+|.||..||..|+..      ...||+||..+...++
T Consensus        18 ~~~~C~IC~~~~--~~p~-~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~   74 (85)
T 2ecv_A           18 EEVTCPICLELL--TQPL-SLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENI   74 (85)
T ss_dssp             CCCCCTTTCSCC--SSCB-CCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSSC
T ss_pred             CCCCCCCCCccc--CCce-eCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHhc
Confidence            378899999999  4554 4599999999999999976      6789999999876543

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

Probab=99.09  E-value=2.6e-11  Score=97.91  Aligned_cols=58  Identities=26%  Similarity=0.637  Sum_probs=47.6

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCcchHHHHHHH
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAV   93 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~~~~~l~e~~   93 (303)
                      +..|+||++.|  .+++.+.+|+|.||..||..|+.  ..||+||..+...++..+..+..+
T Consensus        22 ~~~C~IC~~~~--~~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~~~~n~~l~~l   79 (117)
T 1jm7_B           22 LLRCSRCTNIL--REPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLKINRQLDSM   79 (117)
T ss_dssp             TTSCSSSCSCC--SSCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCCCCHHHHHH
T ss_pred             CCCCCCCChHh--hCccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCccccccccHHHHHH
Confidence            78899999999  56655559999999999999998  789999999977766655544443

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus}

Probab=99.09  E-value=1.2e-11  Score=100.75  Aligned_cols=51  Identities=24%  Similarity=0.635  Sum_probs=1.0

Q ss_pred             CccccccccccccCC---------------CCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcC
Q 022060           31 CDDACSICLEEFSES---------------DPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISL   81 (303)
Q Consensus        31 ~d~~C~ICle~f~~~---------------~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~   81 (303)
                      .++.|+||++.|...               ..+..++|+|.||..||..|+..+..||+||+.+..
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~~  112 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEF  112 (117)
T ss_dssp             CC----------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeeee
Confidence            367899999999431               123446899999999999999999999999998754

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

Probab=99.08  E-value=8e-11  Score=84.40  Aligned_cols=43  Identities=33%  Similarity=0.845  Sum_probs=36.2

Q ss_pred             CCccccccccccccCCCCeeeccCCccccHHhHHHHHh---cCCCCCCC
Q 022060           30 SCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQ---RSSQCPMC   75 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~---~~~~CP~C   75 (303)
                      .++..|+||++.|  .+++. ++|+|.||..||..|+.   ....||+|
T Consensus        18 ~~~~~C~IC~~~~--~~p~~-~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           18 QEEVICPICLDIL--QKPVT-IDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCBCTTTCSBC--SSCEE-CTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             ccCCCCCcCCchh--CCeEE-eCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            3478899999999  45544 59999999999999997   45689998

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

Probab=99.08  E-value=5e-11  Score=96.66  Aligned_cols=55  Identities=31%  Similarity=0.628  Sum_probs=45.6

Q ss_pred             CCccccccccccccCC----CCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCc
Q 022060           30 SCDDACSICLEEFSES----DPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDA   84 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~----~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~   84 (303)
                      .++.+|+||++.|.+.    ..+++++|+|.||..||..|+..+..||+||+.+...+.
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l   63 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   63 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCE
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCccccc
Confidence            3478899999999432    234778999999999999999999999999999875543

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

Probab=99.06  E-value=8.2e-11  Score=89.55  Aligned_cols=54  Identities=30%  Similarity=0.684  Sum_probs=44.0

Q ss_pred             CCCCccccccccccccCCCCeeeccCC-----ccccHHhHHHHHhcC--CCCCCCcccCcCC
Q 022060           28 QDSCDDACSICLEEFSESDPSTVTSCK-----HEFHLQCVLEWCQRS--SQCPMCWQPISLK   82 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~~~~~~vl~C~-----H~Fc~~CI~~Wl~~~--~~CP~CR~~l~~~   82 (303)
                      ..+++..|.||++.|.+++++ +++|.     |.||..||.+|+..+  ..||+||..+...
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~l-~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~   71 (80)
T 2d8s_A           11 TPSSQDICRICHCEGDDESPL-ITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIME   71 (80)
T ss_dssp             CCTTSCCCSSSCCCCCSSSCE-ECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCC
T ss_pred             CCCCCCCCeEcCccccCCCee-EeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecC
Confidence            444577899999998665655 57996     999999999999765  4899999988643

>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=99.04  E-value=4.5e-11  Score=94.90  Aligned_cols=50  Identities=36%  Similarity=0.759  Sum_probs=41.8

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcC---CCCCCCcccCcCCCc
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS---SQCPMCWQPISLKDA   84 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~---~~CP~CR~~l~~~d~   84 (303)
                      +..|+||++.|  .+++. ++|+|.||..||..|+...   ..||+||..+...++
T Consensus        21 ~~~C~IC~~~~--~~p~~-~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~   73 (112)
T 1jm7_A           21 ILECPICLELI--KEPVS-TKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL   73 (112)
T ss_dssp             HTSCSSSCCCC--SSCCB-CTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTC
T ss_pred             CCCCcccChhh--cCeEE-CCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhhc
Confidence            67899999998  45544 6999999999999999865   489999999876543

>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=99.03  E-value=7.7e-11  Score=95.20  Aligned_cols=61  Identities=18%  Similarity=0.439  Sum_probs=48.0

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhcCC-CCCCCcccCcCCCcchHHHHHHHH
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSS-QCPMCWQPISLKDATSQELLEAVE   94 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~-~CP~CR~~l~~~d~~~~~l~e~~~   94 (303)
                      ++..|+||++.|  .++ +.++|+|.||..||..|+.... .||+||..+...+......+....
T Consensus        17 ~~~~C~IC~~~~--~~p-~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~l~~~i   78 (118)
T 3hct_A           17 SKYECPICLMAL--REA-VQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKREI   78 (118)
T ss_dssp             GGGBCTTTCSBC--SSE-EECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGCEECHHHHHHH
T ss_pred             CCCCCCcCChhh--cCe-EECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHHhcccCHHHHHHH
Confidence            378899999999  455 4569999999999999998765 999999999876655544444433

>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=99.02  E-value=2.8e-10  Score=88.66  Aligned_cols=66  Identities=21%  Similarity=0.445  Sum_probs=51.9

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhcC------CCCCC--Cccc-CcCCCcchHHHHHHHHHHHh
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS------SQCPM--CWQP-ISLKDATSQELLEAVEQERS   98 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~------~~CP~--CR~~-l~~~d~~~~~l~e~~~~er~   98 (303)
                      .+..|+||++.|  .+|++...|+|.||..||..|+...      ..||+  |++. +...++.++..+..+.....
T Consensus         6 ~~~~CPI~~~~~--~dPV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~~~L~pn~~L~~~I~~~~   80 (94)
T 2yu4_A            6 SGFTCPITKEEM--KKPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSDLIQDEALRRAIENHN   80 (94)
T ss_dssp             SCCBCTTTCSBC--SSEEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCGGGEEECHHHHHHHHHHH
T ss_pred             cEeECcCcCchh--cCCEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCHhhCcCCHHHHHHHHHHH
Confidence            378899999999  5666653599999999999999753      48999  9887 77777777766666555443

>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=99.01  E-value=3.4e-11  Score=96.63  Aligned_cols=49  Identities=29%  Similarity=0.681  Sum_probs=41.3

Q ss_pred             CCccccccccccccCCCCeeeccCCccccHHhHHHHHhc-CCCCCCCcccCcC
Q 022060           30 SCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPISL   81 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l~~   81 (303)
                      .++..|+||++.|  .++++ ++|+|.||..||..|+.. ...||+||+.+..
T Consensus        13 ~~~~~C~iC~~~~--~~p~~-~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           13 LSECQCGICMEIL--VEPVT-LPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHHBCTTTCSBC--SSCEE-CTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCCccCCccc--CceeE-cCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            3478899999999  55554 599999999999999976 6789999999853

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

Probab=98.99  E-value=2.7e-10  Score=79.86  Aligned_cols=42  Identities=36%  Similarity=1.074  Sum_probs=35.0

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHh---cCCCCCCC
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQ---RSSQCPMC   75 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~---~~~~CP~C   75 (303)
                      ++..|+||++.|  .++ ++++|+|.||..||..|+.   ....||+|
T Consensus        14 ~~~~C~IC~~~~--~~p-~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           14 VEASCSVCLEYL--KEP-VIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCBCSSSCCBC--SSC-CCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cCCCCccCCccc--Ccc-EeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            477899999999  455 4469999999999999954   46789998

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

Probab=98.99  E-value=3.5e-10  Score=85.55  Aligned_cols=53  Identities=19%  Similarity=0.434  Sum_probs=41.2

Q ss_pred             CCccccccccccccCCCCeeecc--CCccccHHhHHHHHhc-CCCCCCCcccCcCCC
Q 022060           30 SCDDACSICLEEFSESDPSTVTS--CKHEFHLQCVLEWCQR-SSQCPMCWQPISLKD   83 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~--C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l~~~d   83 (303)
                      +++.+|+||++.+...+ +..++  |||.||..||..|+.. ...||.||+.+....
T Consensus         9 ~~~~~CpICle~~~~~d-~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~   64 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDD-INFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDP   64 (78)
T ss_dssp             CCCCBCTTTCCBCCTTT-TTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCS
T ss_pred             ccCCcCCccCccCcccc-ccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCc
Confidence            44789999999984323 33334  9999999999998854 568999999987554

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

Probab=98.98  E-value=8e-11  Score=94.56  Aligned_cols=50  Identities=38%  Similarity=0.696  Sum_probs=42.7

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhc-CCCCCCCcccCcCCCc
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPISLKDA   84 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l~~~d~   84 (303)
                      +..|+||++.|  .+++ .++|+|.||..||..|+.. ...||+||..+...+.
T Consensus        23 ~~~C~IC~~~~--~~p~-~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   73 (116)
T 1rmd_A           23 SISCQICEHIL--ADPV-ETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDL   73 (116)
T ss_dssp             HTBCTTTCSBC--SSEE-ECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGC
T ss_pred             CCCCCCCCcHh--cCcE-EcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhhc
Confidence            67899999999  4554 4699999999999999987 6789999999876554

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

Probab=98.95  E-value=6.7e-10  Score=83.37  Aligned_cols=49  Identities=24%  Similarity=0.603  Sum_probs=41.5

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcC--CCCCCCcccCcCC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS--SQCPMCWQPISLK   82 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~--~~CP~CR~~l~~~   82 (303)
                      ..+|.||++.|..  ......|+|.||..||.+||+.+  ..||+||..|...
T Consensus        15 i~~C~IC~~~i~~--g~~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~   65 (74)
T 2ct0_A           15 VKICNICHSLLIQ--GQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE   65 (74)
T ss_dssp             SCBCSSSCCBCSS--SEECSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSC
T ss_pred             CCcCcchhhHccc--CCccCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCC
Confidence            5679999999943  34556899999999999999877  7899999998654

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

Probab=98.95  E-value=3e-10  Score=91.98  Aligned_cols=56  Identities=30%  Similarity=0.630  Sum_probs=46.3

Q ss_pred             CCCccccccccccccC----CCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCc
Q 022060           29 DSCDDACSICLEEFSE----SDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDA   84 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~----~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~   84 (303)
                      ++++..|+||++.|..    ......++|+|.||..||.+|++..+.||+||..+..++.
T Consensus        69 ~~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~  128 (133)
T 4ap4_A           69 GSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY  128 (133)
T ss_dssp             SSSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGGGE
T ss_pred             CCCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChhcc
Confidence            4457889999999853    1234677999999999999999999999999999976553

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

Probab=98.92  E-value=5.7e-10  Score=101.17  Aligned_cols=66  Identities=15%  Similarity=0.130  Sum_probs=52.7

Q ss_pred             CCCccccccccccccCCCCeeeccCCccccHHhHHHHHhcC-CCCCCCcccCcCCCcchHHHHHHHHHHH
Q 022060           29 DSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS-SQCPMCWQPISLKDATSQELLEAVEQER   97 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~-~~CP~CR~~l~~~d~~~~~l~e~~~~er   97 (303)
                      ...+..|+||++.|  .+|++ ++|||.||..||..|+... ..||+||.++...++.++..+..+...-
T Consensus       205 ~~~~~~c~i~~~~~--~dPv~-~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~l~~n~~l~~~i~~~  271 (281)
T 2c2l_A          205 IPDYLCGKISFELM--REPCI-TPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAMKEVIDAF  271 (281)
T ss_dssp             CCSTTBCTTTCSBC--SSEEE-CSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEECHHHHHHHHHH
T ss_pred             CCcccCCcCcCCHh--cCCeE-CCCCCEECHHHHHHHHHHCCCCCcCCCCCCchhcCcccHHHHHHHHHH
Confidence            34578899999999  56554 5899999999999999764 4599999999888877776666655443

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

Probab=98.89  E-value=9.2e-10  Score=79.88  Aligned_cols=49  Identities=24%  Similarity=0.555  Sum_probs=41.2

Q ss_pred             CCCccccccccccccCCCCeeec--cCCcc-ccHHhHHHHHhcCCCCCCCcccCc
Q 022060           29 DSCDDACSICLEEFSESDPSTVT--SCKHE-FHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~~~~~~vl--~C~H~-Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      ++++.+|.||++.+  .+ +.++  +|+|. ||..|+..|......||+||+.+.
T Consensus         5 ~~~~~~C~IC~~~~--~~-~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            5 LNAIEPCVICQGRP--KN-GCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             CGGGSCCTTTSSSC--SC-EEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CCCcCCCCcCCCCC--CC-EEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            34577899999997  33 3444  99999 899999999998899999999885

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

Probab=98.86  E-value=4.9e-10  Score=78.99  Aligned_cols=48  Identities=27%  Similarity=0.528  Sum_probs=39.2

Q ss_pred             CCCccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCC
Q 022060           29 DSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLK   82 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~   82 (303)
                      +.++..|+||++.|  .++ ++++|+|.||..||..|   ...||+||+.+...
T Consensus         3 e~~~~~C~IC~~~~--~~p-~~l~CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T 1bor_A            3 EFQFLRCQQCQAEA--KCP-KLLPCLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             SCCCSSCSSSCSSC--BCC-SCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             cccCCCceEeCCcc--CCe-EEcCCCCcccHHHHccC---CCCCCcCCcEeecC
Confidence            45578899999999  444 55699999999999774   66899999988654

>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=98.84  E-value=1e-09  Score=100.61  Aligned_cols=62  Identities=23%  Similarity=0.505  Sum_probs=52.1

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcC--CCCCC--CcccCcCCCcchHHHHHHHHH
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS--SQCPM--CWQPISLKDATSQELLEAVEQ   95 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~--~~CP~--CR~~l~~~d~~~~~l~e~~~~   95 (303)
                      +..|+||++.|  .+|++.+.|||.||..||..|+...  ..||+  |++.+...++.++..+..+.+
T Consensus       181 el~CPIcl~~f--~DPVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL~pN~~L~~lve  246 (267)
T 3htk_C          181 ELTCPITCKPY--EAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFVRDPIMELRCK  246 (267)
T ss_dssp             CSBCTTTSSBC--SSEEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGEEECHHHHHHHH
T ss_pred             eeECcCccCcc--cCCeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhCCcCHHHHHHHH
Confidence            66799999999  7888877999999999999999764  47999  999998888887766655443

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

Probab=98.83  E-value=7e-10  Score=92.81  Aligned_cols=48  Identities=19%  Similarity=0.455  Sum_probs=40.5

Q ss_pred             CCccccccccccccCCCCeeeccCCccccHHhHHHHHhcCC-CCCCCcccCc
Q 022060           30 SCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSS-QCPMCWQPIS   80 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~-~CP~CR~~l~   80 (303)
                      +++..|+||++.|  .++ +.++|+|.||..||..|+.... .||+||.++.
T Consensus        29 ~~~~~C~IC~~~~--~~p-v~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~   77 (141)
T 3knv_A           29 EAKYLCSACRNVL--RRP-FQAQCGHRYCSFCLASILSSGPQNCAACVHEGI   77 (141)
T ss_dssp             CGGGBCTTTCSBC--SSE-EECTTSCEEEHHHHHHHGGGSCEECHHHHHTTC
T ss_pred             CcCcCCCCCChhh--cCc-EECCCCCccCHHHHHHHHhcCCCCCCCCCCccc
Confidence            3478999999999  555 4469999999999999998654 8999999764

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

Probab=98.82  E-value=1.4e-09  Score=92.96  Aligned_cols=61  Identities=18%  Similarity=0.431  Sum_probs=47.8

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhcC-CCCCCCcccCcCCCcchHHHHHHHH
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS-SQCPMCWQPISLKDATSQELLEAVE   94 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~-~~CP~CR~~l~~~d~~~~~l~e~~~   94 (303)
                      ++..|+||++.|  .+++ .++|+|.||..||..|+... ..||+||..+...+......++...
T Consensus        17 ~~~~C~IC~~~~--~~pv-~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~i   78 (170)
T 3hcs_A           17 SKYECPICLMAL--REAV-QTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKREI   78 (170)
T ss_dssp             GGGBCTTTCSBC--SSEE-ECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGCEECHHHHHHH
T ss_pred             CCCCCCCCChhh--cCcE-ECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchhhhhhhHHHHHHH
Confidence            478999999999  5554 46999999999999999764 4999999999876655444444433

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

Probab=98.78  E-value=3.3e-09  Score=76.69  Aligned_cols=48  Identities=21%  Similarity=0.500  Sum_probs=40.1

Q ss_pred             CCccccccccccccCCCCeeec--cCCcc-ccHHhHHHHHhcCCCCCCCcccCc
Q 022060           30 SCDDACSICLEEFSESDPSTVT--SCKHE-FHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl--~C~H~-Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      +.+..|.||++.+  .+ ..++  +|+|. ||..|+..|.+....||+||+++.
T Consensus         5 ~~~~~C~IC~~~~--~~-~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            5 NLLKPCSLCEKRP--RD-GNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GGGSBCTTTSSSB--SC-EEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             CcCCCCcccCCcC--CC-eEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            3467899999987  33 3344  99998 999999999988889999999885

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

Probab=98.77  E-value=3.6e-09  Score=92.10  Aligned_cols=65  Identities=15%  Similarity=0.141  Sum_probs=52.5

Q ss_pred             CCccccccccccccCCCCeeeccCCccccHHhHHHHHhcC-CCCCCCcccCcCCCcchHHHHHHHHHHH
Q 022060           30 SCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS-SQCPMCWQPISLKDATSQELLEAVEQER   97 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~-~~CP~CR~~l~~~d~~~~~l~e~~~~er   97 (303)
                      ..+..|+||++.|  .+|++ ++|||.||..||..|+... .+||+|+.++...++.++..+.......
T Consensus       104 p~~f~CPI~~elm--~DPV~-~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~L~pN~~Lk~~Ie~~  169 (179)
T 2f42_A          104 PDYLCGKISFELM--REPCI-TPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPNLAMKEVIDAF  169 (179)
T ss_dssp             CGGGBCTTTCSBC--SSEEE-CTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEECHHHHHHHHHH
T ss_pred             cHhhcccCccccC--CCCeE-CCCCCEECHHHHHHHHHhCCCCCCCCcCCCChhhCcchHHHHHHHHHH
Confidence            4578899999999  55554 5999999999999999764 4699999999888888776666655444

>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=98.76  E-value=4.5e-09  Score=101.35  Aligned_cols=48  Identities=27%  Similarity=0.656  Sum_probs=41.3

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHh-cCCCCCCCcccCcCC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQ-RSSQCPMCWQPISLK   82 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~-~~~~CP~CR~~l~~~   82 (303)
                      ...|+||++.+  .+ +..++|+|.||..||..|+. ....||+||+.+...
T Consensus       332 ~~~C~ICle~~--~~-pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          332 FQLCKICAEND--KD-VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             SSBCTTTSSSB--CC-EEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCCccCcCC--CC-eEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            46899999998  33 56679999999999999998 678999999988643

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

Probab=98.75  E-value=2e-09  Score=80.14  Aligned_cols=43  Identities=28%  Similarity=0.714  Sum_probs=36.9

Q ss_pred             ccccccccccccCCCCeeeccCCcc-ccHHhHHHHHhcCCCCCCCcccCcC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHE-FHLQCVLEWCQRSSQCPMCWQPISL   81 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~-Fc~~CI~~Wl~~~~~CP~CR~~l~~   81 (303)
                      +..|+||++.+  .+ +..++|+|. ||..|+..|    ..||+||+.+..
T Consensus        24 ~~~C~iC~~~~--~~-~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           24 EKLCKICMDRN--IA-IVFVPCGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HTBCTTTSSSB--CC-EEEETTCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             CCCCCCCCCCC--CC-EEEcCCCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            67899999998  44 455699999 999999998    789999998853

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

Probab=98.59  E-value=1.2e-08  Score=75.96  Aligned_cols=43  Identities=28%  Similarity=0.726  Sum_probs=35.6

Q ss_pred             ccccccccccccCCCCeeeccCCcc-ccHHhHHHHHhcCCCCCCCcccCcC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHE-FHLQCVLEWCQRSSQCPMCWQPISL   81 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~-Fc~~CI~~Wl~~~~~CP~CR~~l~~   81 (303)
                      +..|+||++.+  .+ +.+++|+|. ||..|+..    ...||+||+.+..
T Consensus        25 ~~~C~IC~~~~--~~-~~~~pCgH~~~C~~C~~~----~~~CP~Cr~~i~~   68 (75)
T 2ecg_A           25 EKLCKICMDRN--IA-IVFVPCGHLVTCKQCAEA----VDKCPMCYTVITF   68 (75)
T ss_dssp             HHSCSSSCSSC--CC-BCCSSSCCCCBCHHHHHH----CSBCTTTCCBCCC
T ss_pred             CCCCCcCCCCC--CC-EEEecCCCHHHHHHHhhC----CCCCccCCceecC
Confidence            67899999998  34 455799999 99999954    3789999998864

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

Probab=98.54  E-value=4.9e-08  Score=71.62  Aligned_cols=47  Identities=26%  Similarity=0.539  Sum_probs=38.2

Q ss_pred             CCCCccccccccccccCCCCeeeccCCcc-ccHHhHHHHHhcCCCCCCCcccCcC
Q 022060           28 QDSCDDACSICLEEFSESDPSTVTSCKHE-FHLQCVLEWCQRSSQCPMCWQPISL   81 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~~~~~~vl~C~H~-Fc~~CI~~Wl~~~~~CP~CR~~l~~   81 (303)
                      .++++..|.||++.+   ..+.+++|+|. ||..|+..    ...||+||..+..
T Consensus        11 ~~~~~~~C~IC~~~~---~~~v~~pCgH~~~C~~C~~~----~~~CP~CR~~i~~   58 (68)
T 2ea5_A           11 SEENSKDCVVCQNGT---VNWVLLPCRHTCLCDGCVKY----FQQCPMCRQFVQE   58 (68)
T ss_dssp             SCCCSSCCSSSSSSC---CCCEETTTTBCCSCTTHHHH----CSSCTTTCCCCCC
T ss_pred             cCCCCCCCCCcCcCC---CCEEEECCCChhhhHHHHhc----CCCCCCCCcchhc
Confidence            444578899999997   33667799999 99999974    4789999998854

>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=98.49  E-value=3.9e-08  Score=76.08  Aligned_cols=48  Identities=23%  Similarity=0.654  Sum_probs=37.0

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhc--------CCCCCC--Cccc
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR--------SSQCPM--CWQP   78 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~--------~~~CP~--CR~~   78 (303)
                      +..+|+||++.+.......+++|+|.||..||..|+..        ...||.  |+..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            46789999999843332334579999999999999853        136999  9988

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

Probab=98.47  E-value=3e-08  Score=93.92  Aligned_cols=53  Identities=26%  Similarity=0.612  Sum_probs=40.0

Q ss_pred             CCCccccccccccccCCCCe---e--eccCCccccHHhHHHHHhcC-----------CCCCCCcccCcC
Q 022060           29 DSCDDACSICLEEFSESDPS---T--VTSCKHEFHLQCVLEWCQRS-----------SQCPMCWQPISL   81 (303)
Q Consensus        29 ~~~d~~C~ICle~f~~~~~~---~--vl~C~H~Fc~~CI~~Wl~~~-----------~~CP~CR~~l~~   81 (303)
                      ++...+|+||++.+.+...+   .  .+.|+|.||..||.+|++..           ..||+||+++..
T Consensus       305 ee~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~  373 (381)
T 3k1l_B          305 DNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLST  373 (381)
T ss_dssp             CCSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEG
T ss_pred             ccCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCc
Confidence            34567899999998652221   1  24899999999999999752           359999998864

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

Probab=98.46  E-value=5e-08  Score=70.23  Aligned_cols=52  Identities=13%  Similarity=0.280  Sum_probs=43.0

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCcc
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDAT   85 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~~   85 (303)
                      ...|+||++.|  .+|+...+|||.|+..||.+|+..+..||++++++...++.
T Consensus         3 ~~~CpIs~~~m--~dPV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~Li   54 (61)
T 2bay_A            3 HMLCAISGKVP--RRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIV   54 (61)
T ss_dssp             -CCCTTTCSCC--SSEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCE
T ss_pred             eEEecCCCCCC--CCCEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhhcE
Confidence            35799999999  55544448999999999999998888899999999766643

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

Probab=98.45  E-value=1.3e-07  Score=67.97  Aligned_cols=51  Identities=24%  Similarity=0.570  Sum_probs=39.8

Q ss_pred             CCCCccccccccccccCCCCeeeccCC--c---cccHHhHHHHHhc--CCCCCCCcccCcC
Q 022060           28 QDSCDDACSICLEEFSESDPSTVTSCK--H---EFHLQCVLEWCQR--SSQCPMCWQPISL   81 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~~~~~~vl~C~--H---~Fc~~CI~~Wl~~--~~~CP~CR~~l~~   81 (303)
                      +++++..|.||++..  +++. +++|.  +   .||..||.+|+..  +..||+|+..+..
T Consensus         2 e~~~~~~CrIC~~~~--~~~l-~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            2 EDEDVPVCWICNEEL--GNER-FRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             TTCSCCEETTTTEEC--SCCC-CCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCCEeEEeecCC--CCce-ecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            455678899999985  4444 56865  4   9999999999964  5789999998753

>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=98.45  E-value=3.9e-08  Score=74.20  Aligned_cols=43  Identities=28%  Similarity=0.635  Sum_probs=35.9

Q ss_pred             ccccccccccccCCCCeeeccCCcc-ccHHhHHHHHhcCCCCCCCcccCcC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHE-FHLQCVLEWCQRSSQCPMCWQPISL   81 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~-Fc~~CI~~Wl~~~~~CP~CR~~l~~   81 (303)
                      +..|.||++.+  .+ +..++|+|. ||..|+..|    ..||+||..+..
T Consensus        18 ~~~C~IC~~~~--~~-~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   61 (79)
T 2yho_A           18 AMLCMVCCEEE--IN-STFCPCGHTVCCESCAAQL----QSCPVCRSRVEH   61 (79)
T ss_dssp             HTBCTTTSSSB--CC-EEEETTCBCCBCHHHHTTC----SBCTTTCCBCCE
T ss_pred             CCEeEEeCccc--Cc-EEEECCCCHHHHHHHHHhc----CcCCCCCchhhC
Confidence            67899999997  33 566799999 999999877    389999998853

>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=98.24  E-value=1.9e-07  Score=88.92  Aligned_cols=43  Identities=21%  Similarity=0.625  Sum_probs=36.8

Q ss_pred             ccccccccccccCCCCeeeccCCcc-ccHHhHHHHHhcCCCCCCCcccCcC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHE-FHLQCVLEWCQRSSQCPMCWQPISL   81 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~-Fc~~CI~~Wl~~~~~CP~CR~~l~~   81 (303)
                      +..|+||++.+  .+ +..++|+|. ||..|+..|    ..||+||..+..
T Consensus       295 ~~~C~IC~~~~--~~-~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          295 ERTCKVCMDKE--VS-VVFIPCGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             TCBCTTTSSSB--CC-EEEETTCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             CCCCCccCCcC--Cc-eEEcCCCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            67899999998  44 455699999 999999988    789999998853

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

Probab=98.05  E-value=2.2e-06  Score=67.39  Aligned_cols=46  Identities=24%  Similarity=0.569  Sum_probs=38.6

Q ss_pred             ccccccccccCCCCeeeccCCccccHHhHHHHHhc-CCCCCCCcccCcC
Q 022060           34 ACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPISL   81 (303)
Q Consensus        34 ~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l~~   81 (303)
                      .|.+|--.+  ....++.+|+|.||.+|+..|.+. .+.||.|+.++..
T Consensus         3 fC~~C~~Pi--~iygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~r   49 (101)
T 3vk6_A            3 FCDKCGLPI--KVYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQR   49 (101)
T ss_dssp             BCTTTCSBC--SEEEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCSE
T ss_pred             ecCccCCCe--EEEeeeccccccHHHHHHHHHHhccCCCCcCcCCeeee
Confidence            488888887  455678899999999999999854 6899999998853

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

Probab=97.66  E-value=3e-05  Score=70.08  Aligned_cols=50  Identities=24%  Similarity=0.560  Sum_probs=41.1

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcC--CCCCCCcccCcCCC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS--SQCPMCWQPISLKD   83 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~--~~CP~CR~~l~~~d   83 (303)
                      -..|.||.+.+.  .......|+|.||..|+..|++.+  ..||.|+..|....
T Consensus       180 i~~C~iC~~iv~--~g~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~~  231 (238)
T 3nw0_A          180 VKICNICHSLLI--QGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEI  231 (238)
T ss_dssp             CCBCTTTCSBCS--SCEECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSCC
T ss_pred             CCcCcchhhHHh--CCcccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCCC
Confidence            567999999984  345666699999999999999765  48999999886554

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

Probab=95.51  E-value=0.0084  Score=46.09  Aligned_cols=34  Identities=18%  Similarity=0.429  Sum_probs=25.8

Q ss_pred             CccccccccccccCCCCe-eeccCCccccHHhHHHH
Q 022060           31 CDDACSICLEEFSESDPS-TVTSCKHEFHLQCVLEW   65 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~-~vl~C~H~Fc~~CI~~W   65 (303)
                      ++..|.||++.+. ..++ ..+.|+|.||..|+..|
T Consensus         2 ee~~C~~C~~~~~-~~av~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            2 EKVLCQFCDQDPA-QDAVKTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CCCBCTTCCSSSC-CBCCEEETTTTEEECHHHHHHH
T ss_pred             CCCCCcCCCCCCC-CCceEECCcCChHHhHHHCHHH
Confidence            4788999998642 2333 33899999999999984

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

Probab=93.15  E-value=0.071  Score=38.48  Aligned_cols=52  Identities=21%  Similarity=0.471  Sum_probs=36.9

Q ss_pred             cCCCCCCccccccccccccCCCCeeeccCCccccHHhHHHHHhcC----CCCCCCcccC
Q 022060           25 GGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS----SQCPMCWQPI   79 (303)
Q Consensus        25 ~~~~~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~----~~CP~CR~~l   79 (303)
                      ++.....+..|.||.+.   ++-+..-.|...||..|+...+...    -.||.|....
T Consensus         5 ~~~~~~~~~~C~vC~~~---~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C            5 GQQNLAPGARCGVCGDG---TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             TTTCCCTTCCCTTTSCC---TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             cccCCCCCCCcCCCCCC---CeEEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            33334446679999865   4445556799999999998877653    3699997643

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

Probab=88.60  E-value=0.21  Score=35.20  Aligned_cols=50  Identities=20%  Similarity=0.598  Sum_probs=35.2

Q ss_pred             cCCCCCCccccccccccccCCCCeeeccCCccccHHhHHHHHhc----CCCCCCCcc
Q 022060           25 GGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR----SSQCPMCWQ   77 (303)
Q Consensus        25 ~~~~~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~----~~~CP~CR~   77 (303)
                      ...++..+..|.||.+.   ++-+..-.|...||..|+..-+..    .-.||.|.+
T Consensus         4 ~~~~~~~~~~C~vC~~~---g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A            4 GSYETDHQDYCEVCQQG---GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             SCCSSCCCSSCTTTSCC---SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CcccCCCCCCCccCCCC---CcEEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            34456668889999874   333444678899999999875433    236999965

>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication, ring E3, PIAS, ubiquitin, UBC9, metal-binding, nucleus; 2.60A {Saccharomyces cerevisiae}

Probab=87.95  E-value=0.32  Score=46.42  Aligned_cols=60  Identities=25%  Similarity=0.470  Sum_probs=44.0

Q ss_pred             cccccccccccCCCCeeeccCCccccHHh--HHHHHhc--CCCCCCCcccCcCCCcchHHHHHHHH
Q 022060           33 DACSICLEEFSESDPSTVTSCKHEFHLQC--VLEWCQR--SSQCPMCWQPISLKDATSQELLEAVE   94 (303)
Q Consensus        33 ~~C~ICle~f~~~~~~~vl~C~H~Fc~~C--I~~Wl~~--~~~CP~CR~~l~~~d~~~~~l~e~~~   94 (303)
                      +.|||-+..|  ..|++...|.|.-|++-  ++.+...  .-.||+|.+.+...++.....+..+.
T Consensus       250 L~CPlS~~ri--~~PvRg~~C~HlQCFDl~sfL~~~~~~~~W~CPIC~k~~~~~dL~ID~~~~~IL  313 (371)
T 3i2d_A          250 LQCPISYTRM--KYPSKSINCKHLQCFDALWFLHSQLQIPTWQCPVCQIDIALENLAISEFVDDIL  313 (371)
T ss_dssp             SBCTTTSSBC--SSEEEETTCCSSCCEEHHHHHHHHHHSCCCBCTTTCCBCCGGGEEEBHHHHHHH
T ss_pred             ecCCCccccc--cccCcCCcCCCcceECHHHHHHHhhcCCceeCCCCCcccCHHHeeEcHHHHHHH
Confidence            4599988888  78899999999966654  3333333  34699999999888887766555544

>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=86.54  E-value=0.5  Score=44.86  Aligned_cols=60  Identities=15%  Similarity=0.329  Sum_probs=43.8

Q ss_pred             cccccccccccCCCCeeeccCCccccHHh--HHHHHhcC--CCCCCCcccCcCCCcchHHHHHHHH
Q 022060           33 DACSICLEEFSESDPSTVTSCKHEFHLQC--VLEWCQRS--SQCPMCWQPISLKDATSQELLEAVE   94 (303)
Q Consensus        33 ~~C~ICle~f~~~~~~~vl~C~H~Fc~~C--I~~Wl~~~--~~CP~CR~~l~~~d~~~~~l~e~~~   94 (303)
                      +.|||-+..|  ..|++...|.|.-|++-  +..+....  -.||+|.+.+...++.....+..+.
T Consensus       216 L~CPlS~~ri--~~P~Rg~~C~HlqCFDl~sfL~~~~~~~~W~CPiC~k~~~~~dL~ID~~~~~IL  279 (360)
T 4fo9_A          216 LMCPLGKMRL--TIPCRAVTCTHLQCFDAALYLQMNEKKPTWICPVCDKKAAYESLILDGLFMEIL  279 (360)
T ss_dssp             SBCTTTCSBC--SSEEEETTCCCCCCEEHHHHHHHHHHSCCCBCTTTCSBCCGGGEEEBHHHHHHH
T ss_pred             eeCCCcccee--ccCCcCCCCCCCccCCHHHHHHHHhhCCCeECCCCCcccCHHHeEEcHHHHHHH
Confidence            4599988888  78899999999966544  33333333  4699999999888887666555554

>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=84.53  E-value=0.71  Score=49.05  Aligned_cols=64  Identities=16%  Similarity=0.119  Sum_probs=50.7

Q ss_pred             CCccccccccccccCCCCeeeccCC-ccccHHhHHHHHhcCCCCCCCcccCcCCCcchHHHHHHHHHH
Q 022060           30 SCDDACSICLEEFSESDPSTVTSCK-HEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQE   96 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C~-H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~~~~~l~e~~~~e   96 (303)
                      .++..|||-++.+  .+|++ ++-| +.|=..+|.+|+..+.+||.=|.++...+..++..+.....+
T Consensus       889 P~~F~cPIs~~lM--~DPVi-lpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~liPN~~Lk~~I~~  953 (968)
T 3m62_A          889 PDEFLDPLMYTIM--KDPVI-LPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTPNEELRQKILC  953 (968)
T ss_dssp             CGGGBCTTTCSBC--SSEEE-CTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCEECHHHHHHHHH
T ss_pred             cHHhCCcchhhHH--hCCeE-cCCCCEEECHHHHHHHHhcCCCCCCCCCCCCcccccccHHHHHHHHH
Confidence            3467799999998  56555 5776 699999999999989999999999988877776655554433

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

Probab=83.03  E-value=0.52  Score=35.90  Aligned_cols=52  Identities=27%  Similarity=0.533  Sum_probs=37.0

Q ss_pred             cCCCCCCccccccccccccCCCCeeeccCCccccHHhHHHHHhcC----CCCCCCcccC
Q 022060           25 GGIQDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS----SQCPMCWQPI   79 (303)
Q Consensus        25 ~~~~~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~----~~CP~CR~~l   79 (303)
                      ....++.+..|.||.+.   ++-+..-.|.-.||..|+..-+...    -.||.|...-
T Consensus        18 ~~~~d~n~~~C~vC~~~---g~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~   73 (88)
T 1fp0_A           18 FGTLDDSATICRVCQKP---GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   73 (88)
T ss_dssp             CCSSSSSSSCCSSSCSS---SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             ccccCCCCCcCcCcCCC---CCEEECCCCCCceecccCCCCCCCCcCCCcCCccccCCC
Confidence            34456668889999975   4445556788999999997655432    3699997543

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=82.40  E-value=0.32  Score=41.46  Aligned_cols=47  Identities=21%  Similarity=0.505  Sum_probs=34.0

Q ss_pred             CCccccccccccccCCCCeeeccCCccccHHhHHHHHhcC----CCCCCCcccC
Q 022060           30 SCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS----SQCPMCWQPI   79 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~----~~CP~CR~~l   79 (303)
                      ..++.|.||.+.   ++-+..-.|...||..|+...+...    -.||.|+..-
T Consensus         2 ~~~~~C~~C~~~---g~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A            2 PNEDWCAVCQNG---GELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             CSCSSCTTTCCC---SSCEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCccccCCCC---CeeeecCCCCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            347789999865   4444556799999999987665432    3699998654

>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=82.06  E-value=1.4  Score=33.13  Aligned_cols=43  Identities=30%  Similarity=0.626  Sum_probs=30.8

Q ss_pred             CCccccccccccccCCCCeeeccC----CccccHHhHHHHHhcC-----CCCCCC
Q 022060           30 SCDDACSICLEEFSESDPSTVTSC----KHEFHLQCVLEWCQRS-----SQCPMC   75 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C----~H~Fc~~CI~~Wl~~~-----~~CP~C   75 (303)
                      ...+.|.+|.+.+++  ...+ .|    .|.||+.|-...+++.     ..||.=
T Consensus        13 ~a~l~CtlC~erLEd--tHFV-QCPsv~~HkFCFpCsr~sIk~q~~~~EvyCPSG   64 (93)
T 2cs3_A           13 SGPLCCTICHERLED--THFV-QCPSVPSHKFCFPCSRESIKAQGATGEVYCPSG   64 (93)
T ss_dssp             CCSCCCSSSCSCCSS--TTSE-ECSSCSSCEECHHHHHHHHHHHHSSSCCCCTTS
T ss_pred             CCeeEeecchhhhcc--Ccee-eCCCccCCeeeccccHHHHHhcCCCCcEECCCC
Confidence            446789999999943  3333 44    5999999999888652     357764

>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A

Probab=81.61  E-value=0.4  Score=33.73  Aligned_cols=49  Identities=20%  Similarity=0.550  Sum_probs=33.8

Q ss_pred             CCCCccccccccccccCCCCeeeccCCccccHHhHHHHHhc----CCCCCCCcccC
Q 022060           28 QDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR----SSQCPMCWQPI   79 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~----~~~CP~CR~~l   79 (303)
                      ++..+..|.||.+.   ++-+..-.|...||..|+..-+..    .-.||.|....
T Consensus         5 ~d~~~~~C~vC~~~---g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            5 SDHHMEFCRVCKDG---GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SCSSCSSCTTTCCC---SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             ccCCCCcCCCCCCC---CCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            34557889999864   343444579999999999754433    23699997643

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=81.24  E-value=0.23  Score=43.24  Aligned_cols=49  Identities=24%  Similarity=0.500  Sum_probs=34.3

Q ss_pred             CCCCccccccccccccCCCCeeeccCCccccHHhHHHHHhcC----CCCCCCcccC
Q 022060           28 QDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS----SQCPMCWQPI   79 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~----~~CP~CR~~l   79 (303)
                      ++..+..|.+|.+.   ++-+..-.|...||..|+...+...    -.||.|+..-
T Consensus         3 ~d~~~~~C~~C~~~---g~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A            3 DDPNEDWCAVCQNG---GDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             CCSSCSSBTTTCCC---EEEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCCCCCCCCCCC---CceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            34557889999865   3323345788999999987665432    3699997643

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=80.26  E-value=1.5  Score=36.16  Aligned_cols=47  Identities=23%  Similarity=0.551  Sum_probs=34.3

Q ss_pred             CCCCccccccccccccCCCCeeeccCCccccHHhHHHHHh-----------cCCCCCCCcc
Q 022060           28 QDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQ-----------RSSQCPMCWQ   77 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~-----------~~~~CP~CR~   77 (303)
                      ++..++.|.||.+-   ++-+-.-.|-..||..||..-+.           ..-.||.|+.
T Consensus        59 ~Dg~~d~C~vC~~G---G~LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~  116 (142)
T 2lbm_A           59 SDGMDEQCRWCAEG---GNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHP  116 (142)
T ss_dssp             TTSCBCSCSSSCCC---SSEEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCC
T ss_pred             CCCCCCeecccCCC---CcEEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccC
Confidence            46678899999976   44344457899999999986542           1236999974

---

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	303
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	1e-13
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	3e-13
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	2e-12
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	5e-11
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	1e-10
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	2e-08
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	2e-08
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	3e-08
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	3e-08
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	1e-07
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	3e-07
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	4e-07
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	5e-06
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	1e-05

>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 = 62.3 bits (151), Expect = 1e-13
 Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 2/51 (3%)

Query: 30 SCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPIS 80
          +  + C ICLE+ S  + S    C H F   C+  W +++  CP+C  P+ 
Sbjct: 3  TVAERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE 51

>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 = 61.0 bits (148), Expect = 3e-13
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 32 DDACSICLEEFSESD-PSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPI 79
             C++CL E  + +    +  C H FH +CV  W    S CP+C   +
Sbjct: 5  GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>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 = 60.1 bits (145), Expect = 2e-12
 Identities = 13/69 (18%), Positives = 20/69 (28%), Gaps = 15/69 (21%)

Query: 29 DSCDDACSICLEEFSES---------------DPSTVTSCKHEFHLQCVLEWCQRSSQCP 73
          D   D C+IC     +                       C H FH  C+  W +    CP
Sbjct: 18 DIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCP 77

Query: 74 MCWQPISLK 82
          +  +    +
Sbjct: 78 LDNREWEFQ 86

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 5e-11
 Identities = 17/74 (22%), Positives = 25/74 (33%), Gaps = 5/74 (6%)

Query: 12 PEDHMTSAAAFVEGGIQ-DSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQ-RS 69
          P+DH+       E   +  S    C IC E   +     +  C H     C+  W +   
Sbjct: 2  PQDHIKVTQEQYELYCEMGSTFQLCKICAENDKDV---KIEPCGHLMCTSCLTSWQESEG 58

Query: 70 SQCPMCWQPISLKD 83
            CP C   I   +
Sbjct: 59 QGCPFCRCEIKGTE 72

>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 = 54.4 bits (130), Expect = 1e-10
 Identities = 13/59 (22%), Positives = 17/59 (28%), Gaps = 3/59 (5%)

Query: 32 DDACSICLEEFSESDPS--TVTSCKHEFHLQCVLEWCQ-RSSQCPMCWQPISLKDATSQ 87
          D  C  C      +      V  C H     CV       +  CP C  P+   +   Q
Sbjct: 3  DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQ 61

>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 = 47.6 bits (113), Expect = 2e-08
 Identities = 13/51 (25%), Positives = 16/51 (31%), Gaps = 6/51 (11%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDAT 85
          C  C  E        +  C H     C+        QCP+C  P  L   T
Sbjct: 9  CQQCQAEAKCP---KLLPCLHTLCSGCLEAS---GMQCPICQAPWPLGADT 53

>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 = 48.4 bits (115), Expect = 2e-08
 Identities = 18/53 (33%), Positives = 22/53 (41%), Gaps = 4/53 (7%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQ-RSSQCPMCWQPISLKDATS 86
          C IC    ++      TSCKH F   C+L   +   S CP C  P    D  S
Sbjct: 26 CQICEHILADP---VETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLES 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 = 47.0 bits (111), Expect = 3e-08
 Identities = 10/48 (20%), Positives = 18/48 (37%), Gaps = 2/48 (4%)

Query: 35 CSICLEEFSESDPS-TVTSCKHEFHLQCVLEW-CQRSSQCPMCWQPIS 80
          C +C+E     D +    +C ++    C        +  CP C +P  
Sbjct: 3  CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYP 50

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.5 bits (115), Expect = 3e-08
 Identities = 21/71 (29%), Positives = 29/71 (40%), Gaps = 7/71 (9%)

Query: 35  CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSS---QCPMCWQPISLKD-ATSQELL 90
           C ICLE   E      T C H F   C+L+   +     QCP+C   I+ +    S    
Sbjct: 24  CPICLELIKEP---VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFS 80

Query: 91  EAVEQERSIRA 101
           + VE+   I  
Sbjct: 81  QLVEELLKIIC 91

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

 Score = 45.6 bits (107), Expect = 1e-07
 Identities = 13/60 (21%), Positives = 20/60 (33%), Gaps = 4/60 (6%)

Query: 27 IQDSCDDACSICLEEFSESD--PSTVTSCKHEFHLQCVLEWCQRS--SQCPMCWQPISLK 82
          ++D     C IC EE           T      H  C+  W   S  + C +C    + +
Sbjct: 1  MEDEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNTR 60

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 44.7 bits (105), Expect = 3e-07
 Identities = 7/49 (14%), Positives = 21/49 (42%), Gaps = 2/49 (4%)

Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKD 83
          C+I  +      P      +  F    + ++ + +   P+  +P+S+++
Sbjct: 3  CAISGKVPR--RPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEE 49

>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 = 45.5 bits (107), Expect = 4e-07
 Identities = 16/67 (23%), Positives = 27/67 (40%), Gaps = 5/67 (7%)

Query: 35  CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELL-EAV 93
           CS C       +P  +  C+H F   CV +       CP+C+ P  ++D      L   +
Sbjct: 25  CSRCTNILR--EPVCLGGCEHIFCSNCVSDCIGT--GCPVCYTPAWIQDLKINRQLDSMI 80

Query: 94  EQERSIR 100
           +    +R
Sbjct: 81  QLCSKLR 87

>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 = 42.0 bits (98), Expect = 5e-06
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 10/76 (13%)

Query: 32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQ--------CPM--CWQPISL 81
             C +CL E+     +T+  C+  F   C+ ++ +   +        CP   C +   L
Sbjct: 5  SSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHL 64

Query: 82 KDATSQELLEAVEQER 97
          ++   + ++ A   +R
Sbjct: 65 QENEIECMVAAEIMQR 80

>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 = 41.6 bits (96), Expect = 1e-05
 Identities = 18/80 (22%), Positives = 28/80 (35%), Gaps = 20/80 (25%)

Query: 27 IQDSCDDACSICLEEF---------------SESDPSTVTSCKHEFHLQCVLEWCQRSS- 70
          ++ + ++ C IC+E+                       +T C H FHL C+L      + 
Sbjct: 20 LKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNK 79

Query: 71 ----QCPMCWQPISLKDATS 86
              QCP C      K  T 
Sbjct: 80 DGSLQCPSCKTIYGEKTGTQ 99

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	303
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.47
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.39
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.32
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.29
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.27
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.25
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.24
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.23
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.23
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.2
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.2
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.16
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.11
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.09
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.01
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.98
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.3
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	87.84
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	86.63
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	84.61
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	82.21
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	82.19

>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=99.47  E-value=8.7e-15  Score=102.28  Aligned_cols=49  Identities=31%  Similarity=0.845  Sum_probs=43.0

Q ss_pred             ccccccccccccCCCCeee-ccCCccccHHhHHHHHhcCCCCCCCcccCc
Q 022060           32 DDACSICLEEFSESDPSTV-TSCKHEFHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~v-l~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      +.+|+||++.|..++.+.. +.|+|.||..||..|++.+..||+||+.+.
T Consensus         5 ~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           5 GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             SCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            6679999999977666655 469999999999999999999999999874

>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=99.39  E-value=7e-14  Score=101.41  Aligned_cols=47  Identities=34%  Similarity=0.906  Sum_probs=42.3

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCc
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPIS   80 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~   80 (303)
                      .++|+||++.|  .+++++++|+|.||..||.+|++.+..||+||.++.
T Consensus         5 ~d~C~IC~~~~--~~~~~~~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~   51 (68)
T d1chca_           5 AERCPICLEDP--SNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCSSCCSCC--CSCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCccCCcCc--cCCcEEeCCCCcCcHHHHHHHHHhCCcCCCCCcchH
Confidence            45699999999  567788899999999999999999999999999874

>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=99.32  E-value=6.3e-13  Score=95.53  Aligned_cols=54  Identities=24%  Similarity=0.448  Sum_probs=42.8

Q ss_pred             CccccccccccccCC--CCeeeccCCccccHHhHHHHHhc-CCCCCCCcccCcCCCc
Q 022060           31 CDDACSICLEEFSES--DPSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPISLKDA   84 (303)
Q Consensus        31 ~d~~C~ICle~f~~~--~~~~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l~~~d~   84 (303)
                      ++.+|+||++.+...  ..+.+++|+|.||..||..|+.. +..||+||+.+...++
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~~   58 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNF   58 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCC
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCcccccc
Confidence            378899999976322  33566799999999999999965 5679999999876553

>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=99.29  E-value=1.4e-12  Score=97.32  Aligned_cols=49  Identities=27%  Similarity=0.657  Sum_probs=41.4

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhc-CCCCCCCcccCcCCC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPISLKD   83 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l~~~d   83 (303)
                      ...|+||++.+  .+ +++++|+|.||..||..|+.. .+.||+||+.+....
T Consensus        23 ~~~C~IC~~~~--~~-~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~   72 (79)
T d1fbva4          23 FQLCKICAEND--KD-VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE   72 (79)
T ss_dssp             TTBCTTTSSSB--CC-EECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCC
T ss_pred             CCCCccCCCcC--CC-eEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCc
Confidence            45799999998  33 667899999999999999974 578999999997544

>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=99.27  E-value=5.3e-13  Score=93.20  Aligned_cols=50  Identities=14%  Similarity=0.288  Sum_probs=44.1

Q ss_pred             cccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCc
Q 022060           33 DACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDA   84 (303)
Q Consensus        33 ~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~   84 (303)
                      +.|+||++.|  .+++..+.|||.||..||.+|++.+..||+||+++...++
T Consensus         1 l~C~Ic~~~~--~~Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dL   50 (56)
T d2baya1           1 MLCAISGKVP--RRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEI   50 (56)
T ss_dssp             CCCTTTCSCC--SSEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGC
T ss_pred             CCCccCCchH--HhcCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhc
Confidence            3699999999  6676666899999999999999999999999999977654

>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=99.25  E-value=1.1e-12  Score=90.29  Aligned_cols=49  Identities=20%  Similarity=0.459  Sum_probs=40.1

Q ss_pred             cccccccccccCCCC-eeeccCCccccHHhHHHHHhc-CCCCCCCcccCcC
Q 022060           33 DACSICLEEFSESDP-STVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPISL   81 (303)
Q Consensus        33 ~~C~ICle~f~~~~~-~~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l~~   81 (303)
                      ++|+||++.|...+. +.+++|+|.||..||..|++. +..||+||+++..
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            479999999964433 455689999999999999986 4579999998864

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.24  E-value=2.1e-12  Score=102.00  Aligned_cols=55  Identities=31%  Similarity=0.637  Sum_probs=42.7

Q ss_pred             CCCCccccccccccccC---------------CCCeeeccCCccccHHhHHHHHhcC-----CCCCCCcccCcCC
Q 022060           28 QDSCDDACSICLEEFSE---------------SDPSTVTSCKHEFHLQCVLEWCQRS-----SQCPMCWQPISLK   82 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~---------------~~~~~vl~C~H~Fc~~CI~~Wl~~~-----~~CP~CR~~l~~~   82 (303)
                      +...+..|+||++.|..               ...+.+++|+|.||..||..|++..     ..||+||..+..+
T Consensus        21 ~~~~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          21 KVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             SSCCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             cccccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            44446789999999842               1234678999999999999999753     4799999988654

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=2.6e-12  Score=97.49  Aligned_cols=51  Identities=24%  Similarity=0.645  Sum_probs=42.2

Q ss_pred             ccccccccccccCCC---------------CeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCC
Q 022060           32 DDACSICLEEFSESD---------------PSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLK   82 (303)
Q Consensus        32 d~~C~ICle~f~~~~---------------~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~   82 (303)
                      ++.|+||++.+.+..               .+.+++|+|.||..||..|++.+.+||+||+++..+
T Consensus        21 ~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   86 (88)
T d3dplr1          21 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQ   86 (88)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCCEE
T ss_pred             CCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCCcCCCCCCccccc
Confidence            556999998874321               356689999999999999999999999999998643

>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=99.23  E-value=1.2e-12  Score=100.99  Aligned_cols=58  Identities=26%  Similarity=0.637  Sum_probs=48.1

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCcchHHHHHHH
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAV   93 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~~~~~l~e~~   93 (303)
                      +.+|+||++.|  .+|+++++|+|.||..||..|+.  ..||.||..+...++..+..+..+
T Consensus        22 ~l~C~IC~~~~--~~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~l~~n~~l~~l   79 (97)
T d1jm7b_          22 LLRCSRCTNIL--REPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLKINRQLDSM   79 (97)
T ss_dssp             TTSCSSSCSCC--SSCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCCCCHHHHHH
T ss_pred             cCCCccCCchh--hcCceeCCCCCchhHHHHHHHHh--ccccccCCcCchhhCcccHHHHHH
Confidence            67899999999  67877779999999999999985  359999999988777665554443

>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=99.20  E-value=1.1e-12  Score=102.23  Aligned_cols=50  Identities=36%  Similarity=0.759  Sum_probs=41.9

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcC---CCCCCCcccCcCCCc
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS---SQCPMCWQPISLKDA   84 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~---~~CP~CR~~l~~~d~   84 (303)
                      .+.|+||++.|  .+|++ ++|+|.||..||..|+...   ..||+||+.+...++
T Consensus        21 ~l~CpIC~~~~--~~pv~-~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l   73 (103)
T d1jm7a_          21 ILECPICLELI--KEPVS-TKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL   73 (103)
T ss_dssp             HTSCSSSCCCC--SSCCB-CTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTC
T ss_pred             CcCCCccCchh--CCeEE-cCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhC
Confidence            67899999999  56655 5899999999999999764   479999999865543

>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=99.20  E-value=3.3e-12  Score=96.88  Aligned_cols=51  Identities=35%  Similarity=0.641  Sum_probs=42.5

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhc-CCCCCCCcccCcCCCcc
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPISLKDAT   85 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l~~~d~~   85 (303)
                      +..|+||++.|  .+ +++++|+|.||..||.+|++. ...||+||.++...+..
T Consensus        23 ~l~C~IC~~~~--~~-pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l~   74 (86)
T d1rmda2          23 SISCQICEHIL--AD-PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE   74 (86)
T ss_dssp             HTBCTTTCSBC--SS-EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCB
T ss_pred             CcCCccCCcch--hc-ceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChhhcc
Confidence            57899999998  44 456799999999999999975 46899999998766543

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.16  E-value=1.2e-11  Score=91.50  Aligned_cols=64  Identities=19%  Similarity=0.352  Sum_probs=50.6

Q ss_pred             CCCCccccccccccccCCCCeeeccCCccccHHhHHHHHhcC-CCCCCCcccCcCCCcchHHHHHHHH
Q 022060           28 QDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS-SQCPMCWQPISLKDATSQELLEAVE   94 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~-~~CP~CR~~l~~~d~~~~~l~e~~~   94 (303)
                      +-.++..|+||++.|  .+|+ +++|+|.||..||..|+... ..||.|+.++...++.++..+..+.
T Consensus         4 eiP~~l~CpIc~~~m--~dPV-~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~l~pN~~L~~~I   68 (78)
T d1t1ha_           4 EFPEYFRCPISLELM--KDPV-IVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNYVLKSLI   68 (78)
T ss_dssp             CCSSSSSCTTTSCCC--SSEE-EETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEECTTTHHHH
T ss_pred             CCCccCCCcCcCchh--hCce-EccCCCcchHHHHHHHHHHCCCCCCcccccCCcccccchHHHHHHH
Confidence            344589999999999  6665 55999999999999999764 5799999999887766554444433

>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=99.11  E-value=2.1e-11  Score=90.65  Aligned_cols=64  Identities=16%  Similarity=0.197  Sum_probs=51.3

Q ss_pred             CCccccccccccccCCCCeeeccCCccccHHhHHHHHhc-CCCCCCCcccCcCCCcchHHHHHHHHHH
Q 022060           30 SCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR-SSQCPMCWQPISLKDATSQELLEAVEQE   96 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~-~~~CP~CR~~l~~~d~~~~~l~e~~~~e   96 (303)
                      .++..|+||++.|  .+|+ +++|||.||..||..|+.. ...||.|+.++...++.++..+....++
T Consensus         5 P~~l~CpIc~~l~--~dPv-~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~l~pN~~L~~~I~~   69 (80)
T d2c2la2           5 PDYLCGKISFELM--REPC-ITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAMKEVIDA   69 (80)
T ss_dssp             CSTTBCTTTCSBC--SSEE-ECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEECHHHHHHHHH
T ss_pred             CccccCcCcCchh--hhhc-ccCCcCeecHHHHHHHHhcCCccCCCccccccccccccHHHHHHHHHH
Confidence            3488999999999  5665 5699999999999999975 5679999999987777766555554433

>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=99.09  E-value=5.2e-11  Score=92.04  Aligned_cols=64  Identities=13%  Similarity=0.126  Sum_probs=51.6

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCCCcchHHHHHHHHHH
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVEQE   96 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~d~~~~~l~e~~~~e   96 (303)
                      ++..|+||++.|  .+|+++..|+|.||..||..|+..+..||+|++++...++.++..+.....+
T Consensus        21 ~~f~CPI~~~lm--~dPV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L~pN~~Lr~~I~~   84 (98)
T d1wgma_          21 DEFLDPIMSTLM--CDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRPNTELKEKIQR   84 (98)
T ss_dssp             TTTBCTTTCSBC--SSEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEECHHHHHHHHH
T ss_pred             HHhCCcCchhHH--HHHHhcccccchhhHHHHHHHHHhcCCcccccccccchhhcchHHHHHHHHH
Confidence            378999999999  6666553345689999999999999999999999998888877665554443

>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=99.01  E-value=2.1e-11  Score=85.03  Aligned_cols=46  Identities=28%  Similarity=0.552  Sum_probs=37.8

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCCcccCcCC
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLK   82 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~CR~~l~~~   82 (303)
                      +.++|+||++.|  .++ ++++|+|.||..||..|   ...||+||+.+...
T Consensus         5 ~~l~C~IC~~~~--~~p-~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T d1bora_           5 QFLRCQQCQAEA--KCP-KLLPCLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CCSSCSSSCSSC--BCC-SCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             CCCCCcccCccc--CCC-EEecCCCHHhHHHHHcC---CCcCcCCCCcccCC
Confidence            457899999999  444 55699999999999765   66899999998654

>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=98.98  E-value=1.4e-10  Score=81.42  Aligned_cols=54  Identities=24%  Similarity=0.474  Sum_probs=40.0

Q ss_pred             CCCCccccccccccccCCCCe--eeccCCccccHHhHHHHHh--cCCCCCCCcccCcC
Q 022060           28 QDSCDDACSICLEEFSESDPS--TVTSCKHEFHLQCVLEWCQ--RSSQCPMCWQPISL   81 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~~~~~--~vl~C~H~Fc~~CI~~Wl~--~~~~CP~CR~~l~~   81 (303)
                      +++++..|.||++.+.+....  ....|+|.||..||..|+.  .+..||+||+++..
T Consensus         2 eded~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           2 EDEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             TTCSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            566788999999998422111  1233569999999999995  45689999998864

>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=98.30  E-value=1.1e-07  Score=71.77  Aligned_cols=46  Identities=22%  Similarity=0.577  Sum_probs=36.1

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcC--------CCCCCCcc
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS--------SQCPMCWQ   77 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~--------~~CP~CR~   77 (303)
                      ..+|+||++.+...+.+.+++|+|.||..||..|+..+        -.||.|+.
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            56799999998654556677999999999999998531        14998654

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.84  E-value=0.11  Score=35.80  Aligned_cols=47  Identities=26%  Similarity=0.562  Sum_probs=32.9

Q ss_pred             CccccccccccccCCCCeeeccCCccccHHhHHHHHhcC----CCCCCCcccCc
Q 022060           31 CDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS----SQCPMCWQPIS   80 (303)
Q Consensus        31 ~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~----~~CP~CR~~l~   80 (303)
                      ....|.||.+.   ++-+..-.|...||..|+...+...    -.||.|+....
T Consensus         6 ~c~~C~~C~~~---~~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   56 (70)
T d1fp0a1           6 SATICRVCQKP---GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   56 (70)
T ss_dssp             SSSCCSSSCSS---SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             CCCCCCCCCCc---CEEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCc
Confidence            45668888754   4444556899999999998776443    35999976443

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.63  E-value=0.065  Score=36.04  Aligned_cols=49  Identities=20%  Similarity=0.550  Sum_probs=33.9

Q ss_pred             CCCCccccccccccccCCCCeeeccCCccccHHhHHHHHhc----CCCCCCCcccC
Q 022060           28 QDSCDDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQR----SSQCPMCWQPI   79 (303)
Q Consensus        28 ~~~~d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~----~~~CP~CR~~l   79 (303)
                      .++.++.|.||.+.   ++-+..-.|.-.||..|+...+..    .-.||.|+...
T Consensus         5 ~d~~~~~C~~C~~~---g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           5 SDHHMEFCRVCKDG---GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SCSSCSSCTTTCCC---SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             ccCCcCCCcCCCCC---CeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            34556789999864   343445679999999998655443    23699997543

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.61  E-value=0.21  Score=32.00  Aligned_cols=44  Identities=25%  Similarity=0.578  Sum_probs=29.0

Q ss_pred             ccccccccccCCCCeeeccCCccccHHhHHHHHhcC----CCCCCCcc
Q 022060           34 ACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRS----SQCPMCWQ   77 (303)
Q Consensus        34 ~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~----~~CP~CR~   77 (303)
                      .|.||...-....-+.--.|...||..|+..-+...    -.||.|+.
T Consensus         2 ~C~vC~~~~~~~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            378887653222223346799999999998765432    25999974

>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=82.21  E-value=0.8  Score=31.78  Aligned_cols=43  Identities=33%  Similarity=0.641  Sum_probs=30.7

Q ss_pred             CCccccccccccccCCCCeeeccC----CccccHHhHHHHHhcC-----CCCCCC
Q 022060           30 SCDDACSICLEEFSESDPSTVTSC----KHEFHLQCVLEWCQRS-----SQCPMC   75 (303)
Q Consensus        30 ~~d~~C~ICle~f~~~~~~~vl~C----~H~Fc~~CI~~Wl~~~-----~~CP~C   75 (303)
                      ...+.|.||.|-+.  +...+ .|    .|.||+.|-...++.+     ..||.-
T Consensus         6 ~~~l~CtlC~erLE--dtHFV-QCPsv~~HkFCFpCsr~sik~q~~~~evyCPSG   57 (80)
T d2cs3a1           6 SGPLCCTICHERLE--DTHFV-QCPSVPSHKFCFPCSRESIKAQGATGEVYCPSG   57 (80)
T ss_dssp             CCSCCCSSSCSCCS--STTSE-ECSSCSSCEECHHHHHHHHHHHHSSSCCCCTTS
T ss_pred             CCceeeeeehhhhc--CCceE-eCCCCcCCceeccccHHHHHhcCCCCcEECCCC
Confidence            34578999999994  33333 44    5999999999988642     357765

>d1z60a1 g.49.1.2 (A:328-386) TFIIH p44 subunit cysteine-rich domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: TFIIH p44 subunit cysteine-rich domain
domain: TFIIH p44 subunit cysteine-rich domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.19  E-value=0.25  Score=33.23  Aligned_cols=44  Identities=20%  Similarity=0.517  Sum_probs=31.2

Q ss_pred             ccccccccccccCCCCeeeccCCccccHHhHHHHHhcCCCCCCC
Q 022060           32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMC   75 (303)
Q Consensus        32 d~~C~ICle~f~~~~~~~vl~C~H~Fc~~CI~~Wl~~~~~CP~C   75 (303)
                      ...|--|...|.+........|++.||.+|=.-.-+.-..||-|
T Consensus        15 ~~~C~gC~~~l~~~~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          15 ERFCYGCQGELKDQHVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             CCEETTTTEECTTSEEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCccCCCCcCCCCceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            56799999998543334568899999999943222334679987