Citrus Sinensis ID: 014500

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------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-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420---

MFVLRVHSVDDNHPITIEEAGFCTVSSTATRSRANPNPKFSERRGLVHLFRGTSQSYQQNPNSRSTCIFVVAVPNYLSSDEFVRFCGSHIDHVEELIFIRNDAMEDRYSVLIKLVDQLTADEFYSNLNGKRFSPAEAEVCHMLFMLSVEYTELAEIASTPPAGFTELPTCPICLERLDPDTSGILSTICDHSFQCSCTAKWTVLSCQVCRFCHQQDERPTCSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYVGDNYVHRLNQSKADGKLVEMNSPCMSHEAHCGTCECSEDSGISGALFNSKVEAIVDEYNRLLATQLETQRQYYESLLAEAKSKRESLIPETVEKAVASKMQDIQNELDICEEAKKAVADVNPLTTHFRSVILFFFGGVGGCYLMLLIETF

cEEEEEcccccccccccccccccccccccccccccccccEEEEEEEEEEEccccccccccccccccEEEEEcccccccHHHHHHHHcccccccEEEEEEEccccccEEEEEEEEccHHcHHHHHHHHccccccccccccEEEEEEEEEEEEEccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccEEEEEccEEcccccccHHHHHHHHHccccEEEEccccEEEEcccccEEEEcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHccccEEEEEEEEEcc

cEEEEEEEcccccccccHHccccccccccccccccccccEEEEEEEEEEEccccccccccccccccEEEEEEccccccHHHHHHHHHHHHHHHcEEEEEEcccccccEEEEEEEccHHHHHHHHHHHcccccccccccEEEEEEEEEEEEEcccccccccccccccccccccEEEcccccccEEEEEEccccccHHHHHHcccccccEEEEEcccccccccccccccccEEEEEEEcccccccccccHHHHHHHHcccEEEEEccccEEEEccccccEEEEEEEccccEEEEEcccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEHHHHccccHHHHHHHHHHcc

mfvlrvhsvddnhpitieeagfctvsstatrsranpnpkfserrglVHLFrgtsqsyqqnpnsrstCIFVVavpnylssdEFVRFCGSHIDHVEELIFIRNDAMEDRYSVLIKLVDQLTADEfysnlngkrfspaeAEVCHMLFMLSVEYTELaeiastppagftelptcpiclerldpdtsgilsticdhsfqcsctakwtvlscqvcrfchqqderptcsvcgtvenLWVCLICGfvgcgrykeghavrhwkdtqhwysldLRTQQIWDYVGDNYVHRLNqskadgklvemnspcmsheahcgtcecsedsgisgalfnSKVEAIVDEYNRLLATQLETQRQYYESLLAEAKSKRESLIPETVEKAVASKMQDIQNELDICEEAKKAvadvnpltthFRSVILFFFGGVGGCYLMLLIETF

MFVLRVHsvddnhpitieeagfctvsstatrsranpnpkfserrgLVHLFRGTSqsyqqnpnsrsTCIFVVAVPNYLSSDEFVRFCGSHIDHVEELIFIRNDAMEDRYSVLIKLVDQLTADEFYSNLNGKRFSPAEAEVCHMLFMLSVEYTELAEIASTPPAGFTELPTCPICLERLDPDTSGILSTICDHSFQCSCTAKWTVLSCQVCRFCHQQDERPTCSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYVGDNYVHRLNQSKADGKLVEMNSPCMSHEAHCGTCECSEDSGISGALFNSKVEAIVDEYNRLLATQLETQRQYYESLLAEakskresliPETVEKAVASKMQDIQNELDICEEAKKAVADVNPLTTHFRSVILFFFGGVGGCYLMLLIETF

*****V**VDDNHPITIEEAGFCTV*********************VHLF**************STCIFVVAVPNYLSSDEFVRFCGSHIDHVEELIFIRNDAMEDRYSVLIKLVDQLTADEFYSNLNGKRFSPAEAEVCHMLFMLSVEYTELAEIASTPPAGFTELPTCPICLERLDPDTSGILSTICDHSFQCSCTAKWTVLSCQVCRFCHQQDERPTCSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYVGDNYVHRLNQSKADGKLVEMNSPCMSHEAHCGTCECSEDSGISGALFNSKVEAIVDEYNRLLATQLETQRQYYESLL*************************IQNELDICEEAKKAVADVNPLTTHFRSVILFFFGGVGGCYLMLLIE**

*FV*************************************SERRGLVHL*****************CIFVVAVPNYLSSDEFVRFCGSHIDHVEELIFIRNDAMEDRYSVLIKLVDQLTADEFYSNLNGKRFSPAEAEVCHMLFMLSV***************FTELPTCPICLERLDPDTSGILSTICDHSFQCSCTAKWTVLSCQVCRFCHQQDERPTCSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYVGDNYVHRLNQSKADGKLV**********************************AIVDEYNRLLATQLETQRQY************************************************************FFFGGVGGCYLMLLIETF

MFVLRVHSVDDNHPITIEEAGFCTVS***********PKFSERRGLVHLFRGT*********SRSTCIFVVAVPNYLSSDEFVRFCGSHIDHVEELIFIRNDAMEDRYSVLIKLVDQLTADEFYSNLNGKRFSPAEAEVCHMLFMLSVEYTELAEIASTPPAGFTELPTCPICLERLDPDTSGILSTICDHSFQCSCTAKWTVLSCQVCRFCHQQDERPTCSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYVGDNYVHRLNQSKADGKLVEMNSPCMSHEAHCGTCECSEDSGISGALFNSKVEAIVDEYNRLLATQLETQRQYYESLLAEAKSKRESLIPETVEKAVASKMQDIQNELDICEEAKKAVADVNPLTTHFRSVILFFFGGVGGCYLMLLIETF

MFVLRVHSVD**********************RANPNPKFSERRGLVHLFRGTSQSYQQNPNSRSTCIFVVAVPNYLSSDEFVRFCGSHIDHVEELIFIRNDAMEDRYSVLIKLVDQLTADEFYSNLNGKRFSPAEAEVCHMLFMLSVEYTELAEIASTPPAGFTELPTCPICLERLDPDTSGILSTICDHSFQCSCTAKWTVLSCQVCRFCHQQDERPTCSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYVGDNYVHRLNQSKADGKLVEMNSP********************GALFNSKVEAIVDEYNRLLATQLETQRQYYESLLAEAKSKRESLIPETVEKAVASKMQDIQNELDICEEAKKAVADVNPLTTHFRSVILFFFGGVGGCYLMLLIETF

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiii

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MFVLRVHSVDDNHPITIEEAGFCTVSSTATRSRANPNPKFSERRGLVHLFRGTSQSYQQNPNSRSTCIFVVAVPNYLSSDEFVRFCGSHIDHVEELIFIRNDAMEDRYSVLIKLVDQLTADEFYSNLNGKRFSPAEAEVCHMLFMLSVEYTELAEIASTPPAGFTELPTCPICLERLDPDTSGILSTICDHSFQCSCTAKWTVLSCQVCRFCHQQDERPTCSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYVGDNYVHRLNQSKADGKLVEMNSPCMSHEAHCGTCECSEDSGISGALFNSKVEAIVDEYNRLLxxxxxxxxxxxxxxxxxxxxxRESLIPETVEKAVASKMQDIQNELDICEEAKKAVADVNPLTTHFRSVILFFFGGVGGCYLMLLIETF

no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		423	2.2.26 [Sep-21-2011]
Q99MP8		591	BRCA1-associated protein	yes	no	0.735	0.526	0.373	2e-64
Q7Z569		592	BRCA1-associated protein	yes	no	0.848	0.606	0.338	5e-64
O13747		547	RING finger protein ETP1	yes	no	0.756	0.585	0.359	2e-57
Q95QN6		590	Uncharacterized RING fing	yes	no	0.843	0.605	0.322	3e-51
P38748		585	RING finger protein ETP1	yes	no	0.808	0.584	0.323	1e-50
Q0V9G5		652	Ubiquitin carboxyl-termin	no	no	0.137	0.088	0.431	2e-08
Q9H0E7		712	Ubiquitin carboxyl-termin	no	no	0.200	0.119	0.367	2e-08
Q5XGZ2		690	Ubiquitin carboxyl-termin	N/A	no	0.137	0.084	0.431	2e-08
Q6NTR6		690	Ubiquitin carboxyl-termin	N/A	no	0.137	0.084	0.431	2e-08
D2HBJ8		711	Ubiquitin carboxyl-termin	no	no	0.203	0.120	0.348	4e-08

>sp\|Q99MP8\|BRAP_MOUSE BRCA1-associated protein OS=Mus musculus GN=Brap PE=1 SV=1	Back alignment and function desciption

 Score =  246 bits (629), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 127/340 (37%), Positives = 193/340 (56%), Gaps = 29/340 (8%)

Query: 37  NPKFSERRGLVHLFRGTSQSYQQNPNSRSTCIFVVAVPNYLSSDEFVRFCGSHIDHVEEL 96
           NP      G++HL++    +  +    RS  + V+ VP  ++S + ++F     D +E++
Sbjct: 131 NPSVEIVHGIMHLYKTNKMTSLKEDVRRSAMLCVLTVPATMTSHDLMKFVAPFNDVIEQM 190

Query: 97  IFIRNDAMEDRYSVLIKLVDQLTADEFYSNLNGKRFSPAEAEVCHMLFMLSVEYTELAEI 156
             IR D+  ++Y VLIK   Q  AD FY   NG++F+  E +VC ++++   E  +  + 
Sbjct: 191 KIIR-DSTPNQYMVLIKFSAQADADSFYMACNGRQFNSIEDDVCQLVYVERAEVLKSEDG 249

Query: 157 ASTPPAGFTELPTCPICLERLDPDTSGILSTICDHSFQCSCTAKWTVLSCQVCRFCHQQD 216
           AS P    TELP C +CLER+D   +GIL+T+C+HSF   C  +W   +C VCR+C   +
Sbjct: 250 ASLPVMDLTELPKCTVCLERMDESVNGILTTLCNHSFHSQCLQRWDDTTCPVCRYCQTPE 309

Query: 217 --ERPTCSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYVG 274
             E   C  CG  ENLW+CLICG +GCGRY   HA +H+++TQH Y++ L   ++WDY G
Sbjct: 310 PVEENKCFECGVQENLWICLICGHIGCGRYVSRHAYKHFEETQHTYAMQLTNHRVWDYAG 369

Query: 275 DNYVHRLNQSKADGKLVEMNSPCMSHEAHCGTCECSEDSGISGALFNSKVEAIVDEYNRL 334
           DNYVHRL  SK DGK+V+       +E    TC+              K++A+  EY+ L
Sbjct: 370 DNYVHRLVASKTDGKIVQ-------YECEGDTCQ------------EEKIDALQLEYSYL 410

Query: 335 LATQLETQRQYYESLL-------AEAKSKRESLIPETVEK 367
           L +QLE+QR Y+E+ +       AE  +  ++   ET+EK
Sbjct: 411 LTSQLESQRIYWENKIVRIEKDTAEEINNMKTKFKETIEK 450

Negatively regulates MAP kinase activation by limiting the formation of Raf/MEK complexes probably by inactivation of the KSR1 scaffold protein. Also acts as a Ras responsive E3 ubiquitin ligase that, on activation of Ras, is modified by auto-polyubiquitination resulting in the release of inhibition of Raf/MEK complex formation. May also act as a cytoplasmic retention protein with a role in regulating nuclear transport.
Mus musculus (taxid: 10090)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp\|Q7Z569\|BRAP_HUMAN BRCA1-associated protein OS=Homo sapiens GN=BRAP PE=1 SV=2	Back alignment and function description

>sp\|O13747\|EPT1_SCHPO RING finger protein ETP1 homolog OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC16E8.13 PE=3 SV=1	Back alignment and function description

>sp\|Q95QN6\|YQOE_CAEEL Uncharacterized RING finger protein EEED8.16 OS=Caenorhabditis elegans GN=EEED8.16 PE=4 SV=1	Back alignment and function description

>sp\|P38748\|ETP1_YEAST RING finger protein ETP1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ETP1 PE=1 SV=1	Back alignment and function description

>sp\|Q0V9G5\|UBP44_XENTR Ubiquitin carboxyl-terminal hydrolase 44 OS=Xenopus tropicalis GN=usp44 PE=2 SV=1	Back alignment and function description

>sp\|Q9H0E7\|UBP44_HUMAN Ubiquitin carboxyl-terminal hydrolase 44 OS=Homo sapiens GN=USP44 PE=1 SV=2	Back alignment and function description

>sp\|Q5XGZ2\|UP44B_XENLA Ubiquitin carboxyl-terminal hydrolase 44-B OS=Xenopus laevis GN=usp44-b PE=2 SV=1	Back alignment and function description

>sp\|Q6NTR6\|UP44A_XENLA Ubiquitin carboxyl-terminal hydrolase 44-A OS=Xenopus laevis GN=usp44-a PE=2 SV=1	Back alignment and function description

>sp\|D2HBJ8\|UBP44_AILME Ubiquitin carboxyl-terminal hydrolase 44 OS=Ailuropoda melanoleuca GN=USP44 PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		423
224144167		486	predicted protein [Populus trichocarpa]	0.926	0.806	0.740	1e-172
255572491		477	brca1-associated protein, putative [Rici	0.914	0.811	0.746	1e-171
42569859		488	zinc finger (ubiquitin-hydrolase) domain	0.931	0.807	0.650	1e-159
297827885		488	zinc finger (ubiquitin-hydrolase) domain	0.929	0.805	0.656	1e-159
225445567		470	PREDICTED: BRCA1-associated protein [Vit	0.895	0.806	0.708	1e-159
147766280		438	hypothetical protein VITISV_012708 [Viti	0.895	0.865	0.708	1e-159
449517888		487	PREDICTED: BRCA1-associated protein-like	0.931	0.809	0.675	1e-158
449443061		487	PREDICTED: BRCA1-associated protein-like	0.931	0.809	0.675	1e-157
2673908		506	hypothetical protein [Arabidopsis thalia	0.931	0.778	0.625	1e-156
356562985		470	PREDICTED: BRCA1-associated protein-like	0.893	0.804	0.666	1e-154

>gi\|224144167\|ref\|XP_002325207.1\| predicted protein [Populus trichocarpa] gi\|222866641\|gb\|EEF03772.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  610 bits (1574), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 294/397 (74%), Positives = 330/397 (83%), Gaps = 5/397 (1%)

Query: 1   MFVLRVHSVDDNHPITIEEAGFCTVSSTATRSRANPNPKFSERRGLVHLFRGTSQSY--- 57
           MF LRVHSVD NHP+T+EE  F  +S+ AT S      KF+ERRG+ HL+R  SQ     
Sbjct: 1   MFSLRVHSVDSNHPLTLEETTF--ISAAATTSTTAATTKFNERRGISHLYRNASQKSSLP 58

Query: 58  QQNPNSRSTCIFVVAVPNYLSSDEFVRFCGSHIDHVEELIFIRNDAMEDRYSVLIKLVDQ 117
             NPNSRST +FVVAVPNY S D+F+RFCGSHIDHV  L+FIRND MEDRYSVLIKL +Q
Sbjct: 59  NPNPNSRSTSLFVVAVPNYFSEDDFIRFCGSHIDHVHVLLFIRNDGMEDRYSVLIKLDNQ 118

Query: 118 LTADEFYSNLNGKRFSPAEAEVCHMLFMLSVEYTELAEIASTPPAGFTELPTCPICLERL 177
           +TAD FY++ N KRFSP+EAE+CH+L++LSVE+TE AEIASTPP  FTELP CPICLERL
Sbjct: 119 VTADRFYNSFNEKRFSPSEAEICHILYVLSVEFTESAEIASTPPENFTELPACPICLERL 178

Query: 178 DPDTSGILSTICDHSFQCSCTAKWTVLSCQVCRFCHQQDERPTCSVCGTVENLWVCLICG 237
           DPDTSGI +T+CDHSFQCSCT+KWT LSCQVCR C QQDE+P CSVCGT ENLWVCLICG
Sbjct: 179 DPDTSGIRNTLCDHSFQCSCTSKWTHLSCQVCRLCQQQDEKPACSVCGTSENLWVCLICG 238

Query: 238 FVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYVGDNYVHRLNQSKADGKLVEMNSPC 297
           FVGCGRYKEGHA RHW+DTQH YSLDLRTQQIWDYVGDNYVHRLNQSK DGK ++ NS C
Sbjct: 239 FVGCGRYKEGHAKRHWQDTQHCYSLDLRTQQIWDYVGDNYVHRLNQSKTDGKSIDTNSCC 298

Query: 298 MSHEAHCGTCECSEDSGISGALFNSKVEAIVDEYNRLLATQLETQRQYYESLLAEAKSKR 357
           +S E  CGTC CSEDSGISGALF+SKVEAI DEYNRLLATQLE QRQ+YESL+ EAKSKR
Sbjct: 299 VSFEGDCGTCGCSEDSGISGALFSSKVEAIADEYNRLLATQLEAQRQHYESLIIEAKSKR 358

Query: 358 ESLIPETVEKAVASKMQDIQNELDICEEAKKAVADVN 394
           +S I E VE AV S MQDIQN+L+ CE  K AVAD+N
Sbjct: 359 QSSISEAVENAVTSTMQDIQNKLEKCELEKNAVADIN 395

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|255572491\|ref\|XP_002527180.1\| brca1-associated protein, putative [Ricinus communis] gi\|223533445\|gb\|EEF35193.1\| brca1-associated protein, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|42569859\|ref\|NP_181746.2\| zinc finger (ubiquitin-hydrolase) domain-containing protein [Arabidopsis thaliana] gi\|312274868\|gb\|ADQ57814.1\| BRIZ1 [Arabidopsis thaliana] gi\|330254987\|gb\|AEC10081.1\| zinc finger (ubiquitin-hydrolase) domain-containing protein [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|297827885\|ref\|XP_002881825.1\| zinc finger (ubiquitin-hydrolase) domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi\|297327664\|gb\|EFH58084.1\| zinc finger (ubiquitin-hydrolase) domain-containing protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|225445567\|ref\|XP_002285333.1\| PREDICTED: BRCA1-associated protein [Vitis vinifera] gi\|297738981\|emb\|CBI28226.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|147766280\|emb\|CAN74457.1\| hypothetical protein VITISV_012708 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449517888\|ref\|XP_004165976.1\| PREDICTED: BRCA1-associated protein-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449443061\|ref\|XP_004139299.1\| PREDICTED: BRCA1-associated protein-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|2673908\|gb\|AAB88642.1\| hypothetical protein [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|356562985\|ref\|XP_003549748.1\| PREDICTED: BRCA1-associated protein-like [Glycine max]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		423
TAIR\|locus:2060045		488	BRIZ1 "AT2G42160" [Arabidopsis	0.931	0.807	0.650	1e-148
TAIR\|locus:2057469		479	BRIZ2 "AT2G26000" [Arabidopsis	0.843	0.745	0.495	3.1e-99
DICTYBASE\|DDB_G0270200		687	DDB_G0270200 "BRCA1-associated	0.463	0.285	0.431	1.4e-66
MGI\|MGI:1919649		591	Brap "BRCA1 associated protein	0.602	0.431	0.406	2.6e-63
UNIPROTKB\|F1PGI5		592	BRAP "Uncharacterized protein"	0.820	0.586	0.336	2.6e-59
ZFIN\|ZDB-GENE-040718-168		578	brap "BRCA1 associated protein	0.817	0.598	0.334	6.6e-58
UNIPROTKB\|F1NJH4		556	BRAP "Uncharacterized protein"	0.829	0.631	0.328	1.4e-57
UNIPROTKB\|F1NR06		585	BRAP "Uncharacterized protein"	0.829	0.6	0.328	1.4e-57
UNIPROTKB\|A6H716		592	BRAP "BRAP protein" [Bos tauru	0.820	0.586	0.338	2.2e-57
UNIPROTKB\|J3KNN7		562	BRAP "BRCA1-associated protein	0.768	0.578	0.346	4.6e-57

TAIR\|locus:2060045 BRIZ1 "AT2G42160" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1452 (516.2 bits), Expect = 1.0e-148, P = 1.0e-148
 Identities = 259/398 (65%), Positives = 321/398 (80%)

Query:     1 MFVLRVHSVDDNHPITIEE--AGFCTVSSTATR--SRANPNPKFSERRGLVHLFRGTSQS 56
             MF+LRVHSVD   PI++EE  +GF   S  A        P+ K ++R+GL+HL+R +S S
Sbjct:     1 MFILRVHSVDSERPISVEEEESGFTYASKRAQPPLKLIQPSLKLTDRKGLIHLYRKSSHS 60

Query:    57 YQQNPNSRSTCIFVVAVPNYLSSDEFVRFCGSHIDHVEELIFIRNDAMEDRYSVLIKLVD 116
                NP+SRST +F+VAVPNYLSS +F+RFC S I  V +++FIRND MEDRYSVLI   D
Sbjct:    61 SLPNPSSRSTTLFIVAVPNYLSSLDFIRFCDSRISQVSDILFIRNDGMEDRYSVLITFSD 120

Query:   117 QLTADEFYSNLNGKRFSPAEAEVCHMLFMLSVEYTELAEIASTPPAGFTELPTCPICLER 176
             Q  AD FY+NLNGK+F+P+EAEVCH+L+++SVE+TE  E+A+  P GFTELPTCPICLER
Sbjct:   121 QSEADGFYNNLNGKKFAPSEAEVCHILYVMSVEHTEFDEVAAEAPTGFTELPTCPICLER 180

Query:   177 LDPDTSGILSTICDHSFQCSCTAKWTVLSCQVCRFCHQQDERPTCSVCGTVENLWVCLIC 236
             LDPDTSGI+ST+CDHSFQCSCT+KWT LSCQVCR C QQDE   CS+CG  EN+W CL+C
Sbjct:   181 LDPDTSGIVSTLCDHSFQCSCTSKWTYLSCQVCRLCQQQDEILNCSICGKTENVWACLVC 240

Query:   237 GFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYVGDNYVHRLNQSKADGKLVEMNSP 296
             GFVGCGRYKEGH++RHWK+T H YSLDLRTQQIWDYVGD+YVHRLN SK DGK VEM++ 
Sbjct:   241 GFVGCGRYKEGHSIRHWKETHHCYSLDLRTQQIWDYVGDSYVHRLNHSKIDGKSVEMSTS 300

Query:   297 CMSHEAHCGTCECSEDSGISGALFNSKVEAIVDEYNRLLATQLETQRQYYESLLAEAKSK 356
             C+SH+  CG CECSED+GISGA+FNSKV++IV EYN LLA+QL+ QRQYYESL+ EA+SK
Sbjct:   301 CLSHQGDCGLCECSEDTGISGAIFNSKVDSIVIEYNDLLASQLKGQRQYYESLIVEARSK 360

Query:   357 RESLIPETVEKAVASKMQDIQNELDICEEAKKAVADVN 394
             +ES I E VE+ V + MQ++QN+++ CEE K  + +VN
Sbjct:   361 QESSIAEAVEQIVVNTMQELQNKIEKCEEEKSGITEVN 398

GO:0003824 "catalytic activity" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000151 "ubiquitin ligase complex" evidence=IC

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

GO:0010029 "regulation of seed germination" evidence=IMP

GO:0046982 "protein heterodimerization activity" evidence=IDA

TAIR\|locus:2057469 BRIZ2 "AT2G26000" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0270200 DDB_G0270200 "BRCA1-associated protein" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

MGI\|MGI:1919649 Brap "BRCA1 associated protein" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|F1PGI5 BRAP "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-040718-168 brap "BRCA1 associated protein" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NJH4 BRAP "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NR06 BRAP "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|A6H716 BRAP "BRAP protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|J3KNN7 BRAP "BRCA1-associated protein" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	AT2G42160	zinc finger (ubiquitin-hydrolase) domain-containing protein; zinc finger (ubiquitin-hydrolase) domain-containing protein; FUNCTIONS IN- protein binding, catalytic activity, zinc ion binding; EXPRESSED IN- 22 plant structures; EXPRESSED DURING- 13 growth stages; CONTAINS InterPro DOMAIN/s- BRCA1-associated 2 (InterPro-IPR011422), Zinc finger, UBP-type (InterPro-IPR001607), Zinc finger, RING-type (InterPro-IPR001841); BEST Arabidopsis thaliana protein match is- zinc finger (C3HC4-type RING finger) family protein (TAIR-AT2G26000.2); Has 920 Blast hits to 905 proteins in 150 species- Archa [...] (488 aa)
		(Arabidopsis thaliana)
Predicted Functional Partners:
	AT2G26000	zinc finger (C3HC4-type RING finger) family protein; zinc finger (C3HC4-type RING finger) famil [...] (479 aa)		•	•	•	0.880
	AT3G45555	zinc finger (C3HC4-type RING finger) family protein; zinc finger (C3HC4-type RING finger) famil [...] (213 aa)			•		0.718
	AT5G37270	zinc finger (C3HC4-type RING finger) family protein; zinc finger (C3HC4-type RING finger) famil [...] (208 aa)			•		0.716
	AT2G34000	zinc finger protein-related; zinc finger protein-related; FUNCTIONS IN- protein binding, zinc i [...] (151 aa)			•		0.716
	AT1G50440	zinc finger (C3HC4-type RING finger) family protein; zinc finger (C3HC4-type RING finger) famil [...] (250 aa)			•		0.716
	UBC30	UBC30 (ubiquitin-conjugating enzyme 30); ubiquitin-protein ligase; ubiquitin-conjugating enzyme [...] (148 aa)	•				0.548
	AT5G47600	heat shock protein-related; heat shock protein-related; FUNCTIONS IN- molecular_function unknow [...] (131 aa)	•				0.548
	CYP705A18	CYP705A18; electron carrier/ heme binding / iron ion binding / monooxygenase/ oxygen binding; m [...] (386 aa)	•				0.548
	HDG3	HDG3 (HOMEODOMAIN GLABROUS 3); DNA binding / transcription factor; Encodes a homeobox-leucine z [...] (725 aa)	•				0.548
	BAS1	BAS1 (PHYB ACTIVATION TAGGED SUPPRESSOR 1); oxygen binding / steroid hydroxylase; Encodes a mem [...] (520 aa)	•				0.548

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		423
cd12437		82	cd12437, RRM_BRAP2_like, RNA recognition motif in	1e-28
pfam07576		110	pfam07576, BRAP2, BRCA1-associated protein 2	5e-28
pfam02148		63	pfam02148, zf-UBP, Zn-finger in ubiquitin-hydrolas	2e-23
smart00290		50	smart00290, ZnF_UBP, Ubiquitin Carboxyl-terminal H	9e-20
cd12717		82	cd12717, RRM_ETP1, RNA recognition motif in yeast	2e-16
cd12718		84	cd12718, RRM_BRAP2, RNA recognition motif in BRCA1	5e-16
COG5207		749	COG5207, UBP14, Isopeptidase T [Posttranslational	9e-09

>gnl\|CDD\|240883 cd12437, RRM_BRAP2_like, RNA recognition motif in BRCA1-associated protein (BRAP2) and similar proteins	Back alignment and domain information

 Score =  106 bits (268), Expect = 1e-28
 Identities = 36/82 (43%), Positives = 55/82 (67%)

Query: 68  IFVVAVPNYLSSDEFVRFCGSHIDHVEELIFIRNDAMEDRYSVLIKLVDQLTADEFYSNL 127
           + ++AVP+Y++S +   FCGS I  + ++  +RN+   +RY VLIK   Q  AD FY++ 
Sbjct: 1   LCILAVPSYMTSADLCTFCGSFIQQISDMRILRNEGRGNRYMVLIKFRSQEDADSFYNDF 60

Query: 128 NGKRFSPAEAEVCHMLFMLSVE 149
           NGK F+  E EVCH++F+ SVE
Sbjct: 61  NGKPFNSLEPEVCHLVFVKSVE 82

This subfamily corresponds to the RRM domain of BRAP2, also termed impedes mitogenic signal propagation (IMP), or ring finger protein 52, or renal carcinoma antigen NY-REN-63, a novel cytoplasmic protein interacting with the two functional nuclear localisation signal (NLS) motifs of BRCA1, a nuclear protein linked to breast cancer. It also binds to the SV40 large T antigen NLS motif and the bipartite NLS motif found in mitosin. BRAP2 may serve as a cytoplasmic retention protein and play a role in the regulation of nuclear protein transport. The family also includes RING finger protein ETP1 and its homologs found in fungi. ETP1, also termed BRAP2 homolog, or ethanol tolerance protein 1, is the yeast homolog of BRCA1-associated protein (BRAP2) found in vertebrates. It may be involved in ethanol and salt-induced transcriptional activation of the NHA1 promoter and heat shock protein genes (HSP12 and HSP26), and participate in ethanol-induced turnover of the low-affinity hexose transporter Hxt3p. Members in this family contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C3HC4-type ring finger domain and a UBP-type zinc finger. . Length = 82

>gnl\|CDD\|191791 pfam07576, BRAP2, BRCA1-associated protein 2	Back alignment and domain information

>gnl\|CDD\|216903 pfam02148, zf-UBP, Zn-finger in ubiquitin-hydrolases and other protein	Back alignment and domain information

>gnl\|CDD\|197632 smart00290, ZnF_UBP, Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger	Back alignment and domain information

>gnl\|CDD\|241161 cd12717, RRM_ETP1, RNA recognition motif in yeast RING finger protein ETP1 and similar proteins	Back alignment and domain information

>gnl\|CDD\|241162 cd12718, RRM_BRAP2, RNA recognition motif in BRCA1-associated protein (BRAP2)	Back alignment and domain information

>gnl\|CDD\|227532 COG5207, UBP14, Isopeptidase T [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		423
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	100.0
PF07576		110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	99.97
PF02148		63	zf-UBP: Zn-finger in ubiquitin-hydrolases and othe	99.7
KOG0944		763	consensus Ubiquitin-specific protease UBP14 [Postt	99.38
COG5207		749	UBP14 Isopeptidase T [Posttranslational modificati	99.27
smart00290		50	ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like	99.15
cd02669		440	Peptidase_C19M A subfamily of Peptidase C19. Pepti	98.97
KOG1873		877	consensus Ubiquitin-specific protease [Posttransla	98.77
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	98.76
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.6
KOG4628		348	consensus Predicted E3 ubiquitin ligase [Posttrans	98.45
PF12678		73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	98.33
PHA02929		238	N1R/p28-like protein; Provisional	98.25
PF15227		42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.24
COG5540		374	RING-finger-containing ubiquitin ligase [Posttrans	98.11
PLN03208		193	E3 ubiquitin-protein ligase RMA2; Provisional	98.08
KOG0317		293	consensus Predicted E3 ubiquitin ligase, integral	97.93
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	97.93
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	97.93
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	97.89
PF14634		44	zf-RING_5: zinc-RING finger domain	97.84
PHA02926		242	zinc finger-like protein; Provisional	97.82
PF00097		41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	97.73
KOG0823		230	consensus Predicted E3 ubiquitin ligase [Posttrans	97.69
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	97.68
TIGR00599		397	rad18 DNA repair protein rad18. This family is bas	97.62
KOG0320		187	consensus Predicted E3 ubiquitin ligase [Posttrans	97.62
KOG2177		386	consensus Predicted E3 ubiquitin ligase [Posttrans	97.46
PF12861		85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	97.42
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	97.39
PF13445		43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	97.37
PF14835		65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.28
KOG2164		513	consensus Predicted E3 ubiquitin ligase [Posttrans	97.25
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	97.1
PF14259		70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	97.06
COG5243		491	HRD1 HRD ubiquitin ligase complex, ER membrane com	96.96
TIGR00570		309	cdk7 CDK-activating kinase assembly factor MAT1. A	96.83
COG5574		271	PEX10 RING-finger-containing E3 ubiquitin ligase [	96.79
COG5432		391	RAD18 RING-finger-containing E3 ubiquitin ligase [	96.76
PF00076		70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	96.66
COG5194		88	APC11 Component of SCF ubiquitin ligase and anapha	96.58
smart00744		49	RINGv The RING-variant domain is a C4HC3 zinc-fing	96.57
KOG0828		636	consensus Predicted E3 ubiquitin ligase [Posttrans	96.43
KOG0287		442	consensus Postreplication repair protein RAD18 [Re	96.4
cd00590		74	RRM RRM (RNA recognition motif), also known as RBD	96.38
KOG1734		328	consensus Predicted RING-containing E3 ubiquitin l	96.18
PF04564		73	U-box: U-box domain; InterPro: IPR003613 Quality c	95.93
smart00362		72	RRM_2 RNA recognition motif.	95.92
KOG0827		465	consensus Predicted E3 ubiquitin ligase [Posttrans	95.81
KOG0825		1134	consensus PHD Zn-finger protein [General function	95.75
PF11793		70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	95.67
KOG0978		698	consensus E3 ubiquitin ligase involved in syntaxin	95.62
KOG1493		84	consensus Anaphase-promoting complex (APC), subuni	95.08
smart00360		71	RRM RNA recognition motif.	95.01
COG5219		1525	Uncharacterized conserved protein, contains RING Z	94.89
KOG1039		344	consensus Predicted E3 ubiquitin ligase [Posttrans	94.44
PF04059		97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	94.41
KOG0311		381	consensus Predicted E3 ubiquitin ligase [Posttrans	94.28
KOG0824		324	consensus Predicted E3 ubiquitin ligase [Posttrans	94.11
KOG0297		391	consensus TNF receptor-associated factor [Signal t	93.88
KOG2930		114	consensus SCF ubiquitin ligase, Rbx1 component [Po	93.43
PF11789		57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	93.1
KOG1645		463	consensus RING-finger-containing E3 ubiquitin liga	92.93
PLN03134		144	glycine-rich RNA-binding protein 4; Provisional	92.55
PF05883		134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	92.25
PF10367		109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	91.85
KOG1941		518	consensus Acetylcholine receptor-associated protei	91.04
KOG1785		563	consensus Tyrosine kinase negative regulator CBL [	88.38
PRK10884		206	SH3 domain-containing protein; Provisional	88.33
KOG3970		299	consensus Predicted E3 ubiquitin ligase [Posttrans	88.02
KOG4445		368	consensus Uncharacterized conserved protein, conta	87.64
KOG2879		298	consensus Predicted E3 ubiquitin ligase [Posttrans	87.61
KOG4159		398	consensus Predicted E3 ubiquitin ligase [Posttrans	87.31
PF14570		48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	86.71
KOG4739		233	consensus Uncharacterized protein involved in syna	86.64
COG5152		259	Uncharacterized conserved protein, contains RING a	85.79
KOG1940		276	consensus Zn-finger protein [General function pred	85.5
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	85.35
KOG1952		950	consensus Transcription factor NF-X1, contains NFX	85.33
PF07800		162	DUF1644: Protein of unknown function (DUF1644); In	84.41
PRK08476		141	F0F1 ATP synthase subunit B'; Validated	84.27
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	84.17
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	84.02
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	83.15
PF09731		582	Mitofilin: Mitochondrial inner membrane protein; I	83.0
KOG2660		331	consensus Locus-specific chromosome binding protei	82.77
KOG2932		389	consensus E3 ubiquitin ligase involved in ubiquiti	81.88
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	81.31
PF12906		47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	81.13
PF00038		312	Filament: Intermediate filament protein; InterPro:	80.76
PF13893		56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	80.73
KOG2114		933	consensus Vacuolar assembly/sorting protein PEP5/V	80.66

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]	Back alignment and domain information

Probab=100.00  E-value=1.8e-108  Score=830.08  Aligned_cols=401  Identities=44%  Similarity=0.794  Sum_probs=352.4

Q ss_pred             CeEEEEee---cCCCCcccc-cccceeeecCcc---cccccCCCCceeeeeeEEEEccCCCCCcCCCCCCCccEEEEEec
Q 014500            1 MFVLRVHS---VDDNHPITI-EEAGFCTVSSTA---TRSRANPNPKFSERRGLVHLFRGTSQSYQQNPNSRSTCIFVVAV   73 (423)
Q Consensus         1 ~~~~~~~~---~~~~~~~~~-~~~~~~~~~~~~---~~~f~sgnp~v~~~~G~vhl~r~~~~~~~~~~~~~~~~lcilaV   73 (423)
                      |++.++++   +++..+++. .+.-++.-.|..   ++-|+||||.|++|+|||||||.++.++.+.+.. ++|||||||
T Consensus         4 v~~e~~~~~~~~~ssr~i~~r~~d~g~~~~s~~~~~~~~~~sgnp~ve~t~GiiHLyk~n~~~s~~~~~~-~~mLcilaV   82 (493)
T KOG0804|consen    4 VIIESLVSEPLVDSSREISGRSEDSGFTSASERLPSQIKYSSGNPSVEETHGIIHLYKKNSHSSLKNASS-STMLCILAV   82 (493)
T ss_pred             chhhhcccCcccccccccCCcccccccchhhhccCCcccccCCCCceeeeceeEEEEecCcccccccCCC-CcEEEEEec
Confidence            46778887   899998888 333366666655   3349999999999999999999998888766543 899999999


Q ss_pred             CCCCCHHHHHHHhcccccceeEEEEeecCCCCCceEEEEEeCChhhHHHHHhhhCCCcCCCCCcCceEEEEEEEEEEeec
Q 014500           74 PNYLSSDEFVRFCGSHIDHVEELIFIRNDAMEDRYSVLIKLVDQLTADEFYSNLNGKRFSPAEAEVCHMLFMLSVEYTEL  153 (423)
Q Consensus        74 P~~ms~~d~l~F~~~~~~~I~~iriir~~~~p~~ymvLikF~~q~~AdeF~~~~ng~~Fnsle~e~C~v~~v~~v~~~~~  153 (423)
                      |+|||++||++|++++..+|++||||| |++||||||||||++|.+|+.||.+|||++||++|||+||++||.+|+++.+
T Consensus        83 P~~mt~~Dll~F~~~~~~~I~~irivR-d~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~le~e~Chll~V~~ve~~~s  161 (493)
T KOG0804|consen   83 PAYMTSHDLLRFCASFIKQISDIRIVR-DGMPNRYMVLIKFRDQADADTFYEEFNGKQFNSLEPEVCHLLYVDRVEVTES  161 (493)
T ss_pred             cccccHHHHHHHHHHHhhhhheeEEee-cCCCceEEEEEEeccchhHHHHHHHcCCCcCCCCCccceeEEEEEEEEEEec
Confidence            999999999999999999999999999 7899999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCCCCCCCCCCcccccccCCCCCcceeecCCCccchhhhhcccccCcccccccccC--CCCCCcCCCCCCCcee
Q 014500          154 AEIASTPPAGFTELPTCPICLERLDPDTSGILSTICDHSFQCSCTAKWTVLSCQVCRFCHQQ--DERPTCSVCGTVENLW  231 (423)
Q Consensus       154 ~~~~~~~~~~l~ElptCpICLE~ld~~~~gi~t~~C~H~Fh~~Cl~kW~~~~CPvCR~~~~~--~~~~~C~~C~~~~~lW  231 (423)
                      .+++++|+.+++|+|||||||||||++++||++++|+|+||+.|+.+|.+++||||||+++|  .+...|.+|+..++||
T Consensus       162 ~d~as~~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~~scpvcR~~q~p~~ve~~~c~~c~~~~~Lw  241 (493)
T KOG0804|consen  162 EDGASEPPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWDSSCPVCRYCQSPSVVESSLCLACGCTEDLW  241 (493)
T ss_pred             ccCCCCCCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhcccCcChhhhhhcCcchhhhhhhhhhcccccEE
Confidence            99999999999999999999999999999999999999999999999999999999999863  2467899999999999


Q ss_pred             eecccCcccccCCcchhhhhhhhcCCCceeeeCCCceEEEccCCccccccccccccCCeeeecCCCCCC-CCCCCCCcCC
Q 014500          232 VCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYVGDNYVHRLNQSKADGKLVEMNSPCMSH-EAHCGTCECS  310 (423)
Q Consensus       232 iCL~CG~vgCgRy~~~HA~~H~e~t~H~lal~l~t~rVwcY~cd~yVHrl~q~k~dgklvel~~~~~~~-~~~~~~~~~~  310 (423)
                      +||+||++|||||..+||++||++|+|+|+|+|+|+|||||++|+||||++|+++|||+|++...+..+ .+.|++++..
T Consensus       242 icliCg~vgcgrY~eghA~rHweet~H~yalel~tqrVWDYAGDnYVhRl~~~~~dGklve~~~~~~~~~~~~~~~~~~~  321 (493)
T KOG0804|consen  242 ICLICGNVGCGRYKEGHARRHWEETGHCYALELETQRVWDYAGDNYVHRLPQSKTDGKLVESSTEGDDSRKDDCDSLELE  321 (493)
T ss_pred             EEEEccceecccccchhHHHHHHhhcceEEEeecceeeeecccchhhhhccccCCCCceEEeccccccccccCcceEEee
Confidence            999999999999999999999999999999999999999999999999999999999999998887553 3445554433


Q ss_pred             CCCCcchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 014500          311 EDSGISGALFNSKVEAIVDEYNRLLATQLETQRQYYESLLAEAKS-KRESLIPETVEKAVASKMQDIQNELDICEEAKKA  389 (423)
Q Consensus       311 ~~~~~~~~~~~~K~e~i~~EY~~lL~sQLe~Qr~yyE~~l~~~~~-~~~~~i~~~~~k~~~~k~~~lq~kl~~~~~E~~~  389 (423)
                      ... +.....+++..-....|+.+..+|||+||+|||.++.++.+ +.+..+.++.+|.+..|++++|.|++|+.+|+++
T Consensus       322 ~s~-ll~sqleSqr~y~e~~~~e~~qsqlen~k~~~e~~~~e~~~l~~~~~~~e~~kk~~e~k~~q~q~k~~k~~kel~~  400 (493)
T KOG0804|consen  322 YSP-LLTSQLESQRKYYEQIMSEYEQSQLENQKQYYELLITEADSLKQESSDLEAEKKIVERKLQQLQTKLKKCQKELKE  400 (493)
T ss_pred             cch-hhhhhhhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            222 22222333333344455555558888888888888888887 7778888888899999999999999999999999


Q ss_pred             HHHHhhhhccCCcEE
Q 014500          390 VADVNPLTTHFRSVI  404 (423)
Q Consensus       390 l~~ln~~L~~~~~~~  404 (423)
                      ++++|++|.+|+.|.
T Consensus       401 ~~E~n~~l~knq~vw  415 (493)
T KOG0804|consen  401 EREENKKLIKNQDVW  415 (493)
T ss_pred             HHHHHHHHHhhHHHH
Confidence            999999999998763

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []	Back alignment and domain information

>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule	Back alignment and domain information

>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger	Back alignment and domain information

>cd02669 Peptidase_C19M A subfamily of Peptidase C19	Back alignment and domain information

>KOG1873 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>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	Back alignment and domain information

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]	Back alignment and domain information

>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>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	Back alignment and domain information

>PHA02929 N1R/p28-like protein; Provisional	Back alignment and domain information

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

>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional	Back alignment and domain information

>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>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	Back alignment and domain information

>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)

Back alignment and domain information

>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	Back alignment and domain information

>PF14634 zf-RING_5: zinc-RING finger domain	Back alignment and domain information

>PHA02926 zinc finger-like protein; Provisional	Back alignment and domain information

>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	Back alignment and domain information

>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>smart00184 RING Ring finger	Back alignment and domain information

>TIGR00599 rad18 DNA repair protein rad18	Back alignment and domain information

>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger	Back alignment and domain information

>smart00504 Ubox Modified RING finger domain	Back alignment and domain information

>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A	Back alignment and domain information

>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B	Back alignment and domain information

>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF14259 RRM_6: RNA recognition motif (a	Back alignment and domain information

>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1	Back alignment and domain information

>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]	Back alignment and domain information

>PF00076 RRM_1: RNA recognition motif	Back alignment and domain information

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

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

>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]	Back alignment and domain information

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability	Back alignment and domain information

>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

>smart00362 RRM_2 RNA recognition motif	Back alignment and domain information

>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0825 consensus PHD Zn-finger protein [General function prediction only]	Back alignment and domain information

>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A	Back alignment and domain information

>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

>smart00360 RRM RNA recognition motif	Back alignment and domain information

>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]	Back alignment and domain information

>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2	Back alignment and domain information

>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]	Back alignment and domain information

>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PLN03134 glycine-rich RNA-binding protein 4; Provisional	Back alignment and domain information

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

>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	Back alignment and domain information

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]	Back alignment and domain information

>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]	Back alignment and domain information

>PRK10884 SH3 domain-containing protein; Provisional	Back alignment and domain information

>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]	Back alignment and domain information

>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

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

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

>KOG1940 consensus Zn-finger protein [General function prediction only]	Back alignment and domain information

>TIGR01659 sex-lethal sex-lethal family splicing factor	Back alignment and domain information

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

>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	Back alignment and domain information

>PRK08476 F0F1 ATP synthase subunit B'; Validated	Back alignment and domain information

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor	Back alignment and domain information

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family	Back alignment and domain information

>TIGR01622 SF-CC1 splicing factor, CC1-like family	Back alignment and domain information

>PF09731 Mitofilin: Mitochondrial inner membrane protein; InterPro: IPR019133 Mitofilin controls mitochondrial cristae morphology	Back alignment and domain information

>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]	Back alignment and domain information

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

>TIGR01622 SF-CC1 splicing factor, CC1-like family	Back alignment and domain information

>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A	Back alignment and domain information

>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope	Back alignment and domain information

>PF13893 RRM_5: RNA recognition motif	Back alignment and domain information

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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		423
3c5k_A		109	Crystal Structure Of Human Hdac6 Zinc Finger Domain		2e-06
3gv4_A		107	Crystal Structure Of Human Hdac6 Zinc Finger Domain		2e-06
2uzg_A		97	Zf-Ubp Domain Of Vdu1 Length = 97		5e-04

>pdb|3C5K|A Chain A, Crystal Structure Of Human Hdac6 Zinc Finger Domain Length = 109

Back alignment and structure

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 24/59 (40%), Positives = 30/59 (50%)
Query: 221 CSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYVGDNYVH 279
           C  CGT++  WVCL C  V CGRY  GH ++H  ++ H   L       W Y    YVH
Sbjct: 27  CGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVH 85

PyMOL of 3c5k

>pdb|3GV4|A Chain A, Crystal Structure Of Human Hdac6 Zinc Finger Domain And Ubiquitin C-Terminal Peptide Rlrgg Length = 107

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		423
2i50_A		126	Ubiquitin carboxyl-terminal hydrolase 16; alpha/be	2e-27
3c5k_A		109	HD6, histone deacetylase 6; HDAC6, zinc finger, ac	3e-25
2uzg_A		97	Ubiquitin carboxyl-terminal hydrolase 33; UBL conj	1e-20
2g45_A		129	Ubiquitin carboxyl-terminal hydrolase 5; zinc fing	1e-19
2ida_A		102	Hypothetical protein; zinc binding protein, struct	5e-17
3ihp_A		854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	8e-11
3mhs_A		476	Ubiquitin carboxyl-terminal hydrolase 8; multi-pro	9e-09
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	3e-04
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	4e-04
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	7e-04

>2i50_A Ubiquitin carboxyl-terminal hydrolase 16; alpha/beta zinc-finger, ring-finger, ZNF-UBP, metalloprotein, ubiquitin-binding protein, USP; NMR {Homo sapiens} Length = 126	Back alignment and structure

 Score =  105 bits (262), Expect = 2e-27
 Identities = 30/127 (23%), Positives = 50/127 (39%), Gaps = 11/127 (8%)

Query: 183 GILSTICDHSFQCSCTAKWTVL----SCQVCRFCHQQ--DERPTCSVCGTVENLWVCLIC 236
           G    +C H  +                 +C+ C      +           ++W+CL C
Sbjct: 1   GSHMPVCRHIRKGLEQGNLKKALVNVEWNICQDCKTDNKVKDKAEEETEEKPSVWLCLKC 60

Query: 237 GFVGCGRY-KEGHAVRHW---KDTQHWYSLDLRTQQIWDYVGDNYVHRLNQSKADGKLVE 292
           G  GCGR  +E HA++H+   +   H   L L    +W YV DN V   + ++  G++V+
Sbjct: 61  GHQGCGRNSQEQHALKHYLTPRSEPHCLVLSLDNWSVWCYVCDNEVQYCSSNQ-LGQVVD 119

Query: 293 MNSPCMS 299
                 S
Sbjct: 120 YVRKQAS 126

PyMOL of 2i50

>3c5k_A HD6, histone deacetylase 6; HDAC6, zinc finger, actin-binding, chromatin regulator, cytoplasm, hydrolase, metal-binding, nucleus, phosphoprotein; 1.55A {Homo sapiens} PDB: 3gv4_A 3phd_A Length = 109	Back alignment and structure

>2g45_A Ubiquitin carboxyl-terminal hydrolase 5; zinc finger, hydrolase; 1.99A {Homo sapiens} SCOP: g.44.1.5 PDB: 2g43_A 2l80_A Length = 129	Back alignment and structure

>2ida_A Hypothetical protein; zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Rhodopseudomonas palustris} SCOP: g.44.1.5 Length = 102	Back alignment and structure

>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol protease, UBL conjugation pathway, metal-binding, zinc-finger,structural genomics; 2.80A {Homo sapiens} Length = 854	Back alignment and structure

>3mhs_A Ubiquitin carboxyl-terminal hydrolase 8; multi-protein complex, hydrolase-transcription regulator-Pro binding complex, acetylation, cytoplasm; 1.89A {Saccharomyces cerevisiae} PDB: 3mhh_A 3m99_A Length = 476	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

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

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

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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		423
2i50_A		126	Ubiquitin carboxyl-terminal hydrolase 16; alpha/be	99.85
2g45_A		129	Ubiquitin carboxyl-terminal hydrolase 5; zinc fing	99.85
3c5k_A		109	HD6, histone deacetylase 6; HDAC6, zinc finger, ac	99.8
2uzg_A		97	Ubiquitin carboxyl-terminal hydrolase 33; UBL conj	99.74
3ihp_A		854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	99.73
2ida_A		102	Hypothetical protein; zinc binding protein, struct	99.71
3mhs_A		476	Ubiquitin carboxyl-terminal hydrolase 8; multi-pro	99.29
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.85
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	98.78
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	98.78
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	98.72
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	98.7
2ect_A		78	Ring finger protein 126; metal binding protein, st	98.7
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	98.69
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	98.68
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	98.67
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	98.65
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	98.65
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	98.63
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	98.61
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	98.61
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	98.6
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	98.6
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	98.6
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	98.59
4ayc_A		138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	98.58
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	98.57
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	98.57
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	98.55
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	98.55
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	98.53
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	98.52
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	98.51
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	98.51
1t1h_A		78	Gspef-atpub14, armadillo repeat containing protein	98.5
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	98.49
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	98.47
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	98.47
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	98.46
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	98.45
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	98.43
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	98.42
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	98.39
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.39
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	98.38
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	98.37
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	98.36
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	98.36
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	98.28
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.27
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	98.25
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	98.23
1z6u_A		150	NP95-like ring finger protein isoform B; structura	98.22
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	98.21
4ic3_A		74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.21
2kr4_A		85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.16
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	98.13
2kre_A		100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.1
1wgm_A		98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.1
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.05
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	98.04
2yu4_A		94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.02
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	97.91
2ecg_A		75	Baculoviral IAP repeat-containing protein 4; BIRC4	97.86
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	97.85
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	97.78
2yho_A		79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	97.75
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	97.71
3t6p_A		345	Baculoviral IAP repeat-containing protein 2; ring,	97.69
2f42_A		179	STIP1 homology and U-box containing protein 1; cha	97.65
2vje_B		63	MDM4 protein; proto-oncogene, phosphorylation, alt	97.55
2ea5_A		68	Cell growth regulator with ring finger domain prot	97.52
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	97.51
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	97.31
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	97.24
1vyx_A		60	ORF K3, K3RING; zinc-binding protein, ring domain,	97.19
2dgw_A		91	Probable RNA-binding protein 19; RRM domain, struc	96.87
2bay_A		61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	96.64
3bs9_A		87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	96.48
3vk6_A		101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	96.43
2dgv_A		92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	96.36
2dng_A		103	Eukaryotic translation initiation factor 4H; RRM d	96.32
2cq3_A		103	RNA-binding protein 9; RRM domain, structural geno	96.29
2dnh_A		105	Bruno-like 5, RNA binding protein; RRM domain, RBD	96.29
2ywk_A		95	Putative RNA-binding protein 11; RRM-domain, struc	96.17
2dnz_A		95	Probable RNA-binding protein 23; RNA recognition m	96.17
2d9p_A		103	Polyadenylate-binding protein 3; RRM domain, struc	96.12
2cqc_A		95	Arginine/serine-rich splicing factor 10; RNA recog	96.09
2jrs_A		108	RNA-binding protein 39; RNA binding motif of RBM39	96.06
2do4_A		100	Squamous cell carcinoma antigen recognized by T- c	96.05
2dgo_A		115	Cytotoxic granule-associated RNA binding protein 1	96.02
2fy1_A		116	RNA-binding motif protein, Y chromosome, family 1	96.0
1oo0_B		110	CG8781-PA, drosophila Y14; RNA recognition motif,	95.99
1wi8_A		104	EIF-4B, eukaryotic translation initiation factor 4	95.97
1p27_B		106	RNA-binding protein 8A; nuclear protein, mRNA spli	95.96
2e5h_A		94	Zinc finger CCHC-type and RNA-binding motif- conta	95.9
2la6_A		99	RNA-binding protein FUS; structural genomics, nort	95.84
2dnm_A		103	SRP46 splicing factor; RRM domain, RBD, structural	95.83
2do0_A		114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	95.82
2cqi_A		103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	95.81
2cph_A		107	RNA binding motif protein 19; RNA recognition moti	95.77
1x4e_A		85	RNA binding motif, single-stranded interacting pro	95.76
3mdf_A		85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	95.71
1x5o_A		114	RNA binding motif, single-stranded interacting pro	95.7
2dhg_A		104	TRNA selenocysteine associated protein (SECP43); R	95.69
3ulh_A		107	THO complex subunit 4; nuclear protein, RNA bindin	95.66
3md1_A		83	Nuclear and cytoplasmic polyadenylated RNA-bindin	95.64
2ytc_A		85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	95.56
2cq0_A		103	Eukaryotic translation initiation factor 3 subunit	95.55
1whw_A		99	Hypothetical protein riken cDNA 1200009A02; RNA re	95.53
3lqv_A		115	PRE-mRNA branch site protein P14; cysless mutant,	95.53
1x5s_A		102	Cold-inducible RNA-binding protein; structure geno	95.53
2cpz_A		115	CUG triplet repeat RNA-binding protein 1; RRM doma	95.46
2err_A		109	Ataxin-2-binding protein 1; protein-RNA complex, R	95.42
2x1f_A		96	MRNA 3'-END-processing protein RNA15; transcriptio	95.32
1x5u_A		105	Splicing factor 3B subunit 4 (spliceosome associat	95.32
2dgs_A		99	DAZ-associated protein 1; RRM domain, structural g	95.24
2kt5_A		124	RNA and export factor-binding protein 2; chaperone	95.24
2div_A		99	TRNA selenocysteine associated protein; structural	95.21
3nmr_A		175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	95.21
2cpj_A		99	Non-POU domain-containing octamer-binding protein;	95.2
3ex7_B		126	RNA-binding protein 8A; protein-RNA complex, mRNA	95.2
2dgt_A		92	RNA-binding protein 30; RRM domain, structural gen	95.17
2dgp_A		106	Bruno-like 4, RNA binding protein; RRM domain, str	95.16
2krb_A		81	Eukaryotic translation initiation factor 3 subunit	95.11
1x5t_A		96	Splicing factor 3B subunit 4; structure genomics,	95.11
2kxn_B		129	Transformer-2 protein homolog beta; SR protein, RR	95.08
2fc9_A		101	NCL protein; structure genomics, RRM_1 domain, str	95.07
4a8x_A		88	RNA-binding protein with serine-rich domain 1; tra	95.07
4fxv_A		99	ELAV-like protein 1; RNA recognition motif, putati	95.05
1fxl_A		167	Paraneoplastic encephalomyelitis antigen HUD; prot	95.03
2dnp_A		90	RNA-binding protein 14; RRM domain, RBD, structura	95.02
3md3_A		166	Nuclear and cytoplasmic polyadenylated RNA-bindin	95.0
2ku7_A		140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	95.0
2j76_E		100	EIF-4B, EIF4B, eukaryotic translation initiation f	94.96
1p1t_A		104	Cleavage stimulation factor, 64 kDa subunit; RNA r	94.91
2cqb_A		102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	94.9
3nmr_A		175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	94.88
2khc_A		118	Testis-specific RNP-type RNA binding protein; RRM,	94.86
2cpe_A		113	RNA-binding protein EWS; RNA recognition motif, RR	94.8
2xs2_A		102	Deleted in azoospermia-like; RNA binding protein-R	94.76
1rk8_A		165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	94.61
1x4a_A		109	Splicing factor, arginine/serine-rich 1 (splicing	94.61
2cqd_A		116	RNA-binding region containing protein 1; RNA recog	94.57
2cpf_A		98	RNA binding motif protein 19; RNA recognition moti	94.49
2hzc_A		87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	94.48
2la4_A		101	Nuclear and cytoplasmic polyadenylated RNA-bindin	94.47
2fc8_A		102	NCL protein; structure genomics, RRM_1 domain, str	94.36
2dis_A		109	Unnamed protein product; structural genomics, RRM	94.32
3ucg_A		89	Polyadenylate-binding protein 2; ferredoxin-like,	94.31
1b7f_A		168	Protein (SXL-lethal protein), RNA (5'-R(PGPUP*UP	94.28
2cpy_A		114	RNA-binding protein 12; RRM domain, structural gen	94.28
3md3_A		166	Nuclear and cytoplasmic polyadenylated RNA-bindin	94.25
1h2v_Z		156	20 kDa nuclear CAP binding protein; CAP-binding-co	94.25
1x4g_A		109	Nucleolysin TIAR; structural genomics, RRM domain,	94.23
2dh8_A		105	DAZ-associated protein 1; RRM domain, structural g	94.23
2dgu_A		103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	94.18
1u6f_A		139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	94.11
4f25_A		115	Polyadenylate-binding protein 1; RRM fold, transla	94.08
2jwn_A		124	Embryonic polyadenylate-binding protein 2-B; epabp	94.06
1x4h_A		111	RNA-binding protein 28; structural genomics, RRM d	94.04
2lmi_A		107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	93.94
1fxl_A		167	Paraneoplastic encephalomyelitis antigen HUD; prot	93.86
2e44_A		96	Insulin-like growth factor 2 mRNA binding protein	93.82
1why_A		97	Hypothetical protein riken cDNA 1810017N16; RNA re	93.82
2db1_A		118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	93.82
3nw0_A		238	Non-structural maintenance of chromosomes element	93.82
2dnq_A		90	RNA-binding protein 4B; RRM domain,RBD, structural	93.77
2mss_A		75	Protein (musashi1); RNA-binding domain, RNA bindin	93.77
2g4b_A		172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	93.74
1wg1_A		88	KIAA1579 protein, homolog EXC-7; RBD, structural g	93.72
2dgx_A		96	KIAA0430 protein; RRM domain, structural genomics,	93.72
2cpd_A		99	Apobec-1 stimulating protein; RNA recognition moti	93.69
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	93.67
2cpi_A		111	CCR4-NOT transcription complex subunit 4; RNA reco	93.65
1b7f_A		168	Protein (SXL-lethal protein), RNA (5'-R(PGPUP*UP	93.64
2kn4_A		158	Immunoglobulin G-binding protein G, splicing FACT	93.63
1nu4_A		97	U1A RNA binding domain; RNA recognition motif, U1	93.58
2cq4_A		114	RNA binding motif protein 23; RRM domain, structur	93.56
1s79_A		103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	93.52
2dnn_A		109	RNA-binding protein 12; RRM domain, RBD, structura	93.46
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	93.43
2hvz_A		101	Splicing factor, arginine/serine-rich 7; RRM, RNA	93.42
1wg5_A		104	Heterogeneous nuclear ribonucleoprotein H; structu	93.39
1x4c_A		108	Splicing factor, arginine/serine-rich 1; structura	93.39
3s7r_A		87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	93.29
2cqg_A		103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	93.22
1l3k_A		196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	93.19
2lea_A		135	Serine/arginine-rich splicing factor 2; SR protein	93.14
3ns6_A		100	Eukaryotic translation initiation factor 3 subuni;	93.12
2ek1_A		95	RNA-binding protein 12; RNA recognition motif, dim	93.11
2f3j_A		177	RNA and export factor binding protein 2; RRM domai	93.06
2cqp_A		98	RNA-binding protein 12; RNA recognition motif, RRM	93.05
2ki2_A		90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	92.92
3p5t_L		90	Cleavage and polyadenylation specificity factor S;	92.81
3s8s_A		110	Histone-lysine N-methyltransferase SETD1A; chromat	92.79
2nlw_A		105	Eukaryotic translation initiation factor 3 subunit	92.7
1wez_A		102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	92.63
2lxi_A		91	RNA-binding protein 10; NMR {Homo sapiens}	92.54
3beg_B		115	Splicing factor, arginine/serine-rich 1; kinase, S	92.47
3s9g_A		104	Protein hexim1; cyclin T-binding domain (TBD), cyc	92.43
2yh0_A		198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	92.37
2e5j_A		97	Methenyltetrahydrofolate synthetase domain contain	92.35
2i2y_A		150	Fusion protein consists of immunoglobin G- binding	92.21
2cpx_A		115	Hypothetical protein FLJ11016; RRM domain, structu	92.2
1fjc_A		96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	92.17
2hgm_A		126	HNRPF protein, heterogeneous nuclear ribonucleopro	92.1
3n9u_C		156	Cleavage and polyadenylation specificity factor S;	92.1
1wf1_A		110	RNA-binding protein RALY; structural genomics, RRM	92.1
2hgl_A		136	HNRPF protein, heterogeneous nuclear ribonucleopro	92.06
2jvo_A		108	Nucleolar protein 3; nucleus, phosphorylation, rib	92.05
1qm9_A		198	Polypyrimidine tract-binding protein; ribonucleopr	91.99
1uaw_A		77	Mouse-musashi-1; RNP-type structure, RNA binding p	91.79
2adc_A		229	Polypyrimidine tract-binding protein 1; RBD, RRM,	91.65
2xnq_A		97	Nuclear polyadenylated RNA-binding protein 3; tran	91.47
3smz_A		284	Protein raver-1, ribonucleoprotein PTB-binding 1;	91.41
1x4b_A		116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	91.27
2lkz_A		95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	91.25
1wel_A		124	RNA-binding protein 12; structural genomics, NPPSF	90.93
1qm9_A		198	Polypyrimidine tract-binding protein; ribonucleopr	90.85
3egn_A		143	RNA-binding protein 40; RNA recognition motif (RRM	90.76
2cqh_A		93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	90.6
1whx_A		111	Hypothetical protein riken cDNA 1200009A02; RNA re	90.59
3q2s_C		229	Cleavage and polyadenylation specificity factor S;	90.58
1l3k_A		196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	90.57
4f02_A		213	Polyadenylate-binding protein 1; mRNA, eukaryotic	90.49
3r27_A		100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	90.35
2ghp_A		292	U4/U6 snRNA-associated splicing factor PRP24; RNA	90.34
2adc_A		229	Polypyrimidine tract-binding protein 1; RBD, RRM,	90.27
2cjk_A		167	Nuclear polyadenylated RNA-binding protein 4; HRP1	89.81
2jun_A		101	Midline-1; B-BOX, TRIM, ring finger, alternative s	89.67
3smz_A		284	Protein raver-1, ribonucleoprotein PTB-binding 1;	89.6
2kvi_A		96	Nuclear polyadenylated RNA-binding protein 3; RNA-	89.5
4f02_A		213	Polyadenylate-binding protein 1; mRNA, eukaryotic	89.04
1wex_A		104	Hypothetical protein (riken cDNA 2810036L13); stru	89.0
1iqt_A		75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	88.88
1uw4_A		91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	88.83
2ghp_A		292	U4/U6 snRNA-associated splicing factor PRP24; RNA	88.62
2cjk_A		167	Nuclear polyadenylated RNA-binding protein 4; HRP1	88.44
3sde_A		261	Paraspeckle component 1; RRM, anti parallel right	88.37
1fje_B		175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	88.33
2rs2_A		109	Musashi-1, RNA-binding protein musashi homolog 1;	88.21
3sde_A		261	Paraspeckle component 1; RRM, anti parallel right	88.03
2g4b_A		172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	87.74
2e5g_A		94	U6 snRNA-specific terminal uridylyltransferase 1;	87.52
1fj7_A		101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	87.18
2voo_A		193	Lupus LA protein; RNA-binding protein, RNA recogni	87.13
2dha_A		123	FLJ20171 protein; RRM domain, structural genomics,	86.94
2cq1_A		101	PTB-like protein L; RRM domain, structural genomic	86.84
2jvr_A		111	Nucleolar protein 3; RNA recognition motif, nucleu	86.57
3trt_A		77	Vimentin; cytoskeleton, intermediate filament, alp	86.46
2dnl_A		114	Cytoplasmic polyadenylation element binding protei	86.19
1sjr_A		164	Polypyrimidine tract-binding protein 1; extended b	85.95
3pgw_A		282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	85.8
2e5i_A		124	Heterogeneous nuclear ribonucleoprotein L-like; RR	85.47
3pgw_A		282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	85.36
2m2b_A		131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	85.27
2a3j_A		127	U1 small nuclear ribonucleoprotein A; computationa	84.83
2lcw_A		116	RNA-binding protein FUS; RRM, nucleic acid binding	84.93
1x4d_A		102	Matrin 3; structural genomics, RRM domain, NPPSFA,	84.44
1wf0_A		88	TDP-43, TAR DNA-binding protein-43; structural gen	84.22
2hgn_A		139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	83.87
3ghg_A		562	Fibrinogen alpha chain; triple-stranded coiled coi	83.1
3pgw_S		437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	82.8
3tyt_A		205	Heterogeneous nuclear ribonucleoprotein L; ferredo	82.77
2pe8_A		105	Splicing factor 45; RRM, protein binding; 2.00A {H	82.29
2yh0_A		198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	82.16
1x5p_A		97	Negative elongation factor E; structure genomics,	81.43
2l08_A		97	Regulator of nonsense transcripts 3A; NESG, nonsen	80.84

>2i50_A Ubiquitin carboxyl-terminal hydrolase 16; alpha/beta zinc-finger, ring-finger, ZNF-UBP, metalloprotein, ubiquitin-binding protein, USP; NMR {Homo sapiens}	Back alignment and structure

Probab=99.85  E-value=1.3e-22  Score=177.61  Aligned_cols=108  Identities=28%  Similarity=0.520  Sum_probs=90.8

Q ss_pred             eeecCCCccchhhhhccc-------ccCcccccccccCCCCCCcCCCCCCCceeeecccCcccccCC-cchhhhhhhhc-
Q 014500          185 LSTICDHSFQCSCTAKWT-------VLSCQVCRFCHQQDERPTCSVCGTVENLWVCLICGFVGCGRY-KEGHAVRHWKD-  255 (423)
Q Consensus       185 ~t~~C~H~Fh~~Cl~kW~-------~~~CPvCR~~~~~~~~~~C~~C~~~~~lWiCL~CG~vgCgRy-~~~HA~~H~e~-  255 (423)
                      ++..|.|.++..++.+|.       ...|+.|+... ......+.+|....++|+||+||++||||| .++||.+||++ 
T Consensus         3 ~~~~C~H~~~~~~l~~~~~~~~~~~~~~C~~C~~~~-~~~~~~~~~~~~~~~Lw~CL~CG~vgCgr~~~~~Ha~~H~~~~   81 (126)
T 2i50_A            3 HMPVCRHIRKGLEQGNLKKALVNVEWNICQDCKTDN-KVKDKAEEETEEKPSVWLCLKCGHQGCGRNSQEQHALKHYLTP   81 (126)
T ss_dssp             --CCCSCHHHHCCHHHHHHHHSSCCSSSCHHHHTCT-TSSCSSCTTTCCCCCEEEETTTCCEEECTTSSSCHHHHHHHSC
T ss_pred             CCCCCcChhhccccccccccccCCCCCcCccccccc-cccccccccccccccceeeeeCCccccCCCCcchHHHHHHhCc
Confidence            467899999998887775       25699998854 223445678999999999999999999998 67999999999 


Q ss_pred             --CCCceeeeCCCceEEEccCCccccccccccccCCeeeec
Q 014500          256 --TQHWYSLDLRTQQIWDYVGDNYVHRLNQSKADGKLVEMN  294 (423)
Q Consensus       256 --t~H~lal~l~t~rVwcY~cd~yVHrl~q~k~dgklvel~  294 (423)
                        ++||++++++|.+||||.||+||+ ..+.+.++++|++.
T Consensus        82 ~~t~H~l~~~l~t~~vwCY~cd~~V~-~~~~~~l~~~v~~~  121 (126)
T 2i50_A           82 RSEPHCLVLSLDNWSVWCYVCDNEVQ-YCSSNQLGQVVDYV  121 (126)
T ss_dssp             CSSCCCEEEETTTCCEEETTTTEEEC-CCTTSHHHHHHHHH
T ss_pred             CCCCCcEEEECCCCeEEeCCCCcEEE-cCcchhHHHHHHHH
Confidence              899999999999999999999998 56777788888763

PyMOL of 2i50

>2g45_A Ubiquitin carboxyl-terminal hydrolase 5; zinc finger, hydrolase; 1.99A {Homo sapiens} SCOP: g.44.1.5 PDB: 2g43_A 2l80_A	Back alignment and structure

>3c5k_A HD6, histone deacetylase 6; HDAC6, zinc finger, actin-binding, chromatin regulator, cytoplasm, hydrolase, metal-binding, nucleus, phosphoprotein; 1.55A {Homo sapiens} PDB: 3gv4_A 3phd_A	Back alignment and structure

>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol protease, UBL conjugation pathway, metal-binding, zinc-finger,structural genomics; 2.80A {Homo sapiens}	Back alignment and structure

>2ida_A Hypothetical protein; zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Rhodopseudomonas palustris} SCOP: g.44.1.5	Back alignment and structure

>3mhs_A Ubiquitin carboxyl-terminal hydrolase 8; multi-protein complex, hydrolase-transcription regulator-Pro binding complex, acetylation, cytoplasm; 1.89A {Saccharomyces cerevisiae} PDB: 3mhh_A 4fjc_A 4fk5_A 4fip_A 3m99_A	Back alignment and structure

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

>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	Back alignment and structure

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

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

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

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

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

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

>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}	Back alignment and structure

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

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

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

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

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

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

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

>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	Back alignment and structure

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>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	Back alignment and structure

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

>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}	Back alignment and structure

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

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

>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}	Back alignment and structure

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

>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	Back alignment and structure

>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	Back alignment and structure

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

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

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

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

>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	Back alignment and structure

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

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

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

>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	Back alignment and structure

>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	Back alignment and structure

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

>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	Back alignment and structure

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

>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*	Back alignment and structure

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

>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}	Back alignment and structure

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

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

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

>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*	Back alignment and structure

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

>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}	Back alignment and structure

>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	Back alignment and structure

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

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

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>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	Back alignment and structure

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}	Back alignment and structure

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

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A	Back alignment and structure

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}	Back alignment and structure

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A	Back alignment and structure

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}	Back alignment and structure

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}	Back alignment and structure

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A	Back alignment and structure

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}	Back alignment and structure

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*	Back alignment and structure

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}	Back alignment and structure

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*	Back alignment and structure

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A	Back alignment and structure

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0	Back alignment and structure

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B	Back alignment and structure

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A	Back alignment and structure

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B	Back alignment and structure

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}	Back alignment and structure

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A	Back alignment and structure

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*	Back alignment and structure

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A	Back alignment and structure

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}	Back alignment and structure

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A	Back alignment and structure

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}	Back alignment and structure

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}	Back alignment and structure

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A	Back alignment and structure

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}	Back alignment and structure

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}	Back alignment and structure

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}	Back alignment and structure

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A	Back alignment and structure

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}	Back alignment and structure

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A	Back alignment and structure

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A	Back alignment and structure

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A	Back alignment and structure

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}	Back alignment and structure

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A	Back alignment and structure

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(PGPUPUPGPUPUPUPUPUPUPUPU)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A	Back alignment and structure

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}	Back alignment and structure

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X	Back alignment and structure

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A	Back alignment and structure

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1	Back alignment and structure

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A	Back alignment and structure

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}	Back alignment and structure

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}	Back alignment and structure

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A	Back alignment and structure

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}	Back alignment and structure

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

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A	Back alignment and structure

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A	Back alignment and structure

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A	Back alignment and structure

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A	Back alignment and structure

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(PGPUPUPGPUPUPUPUPUPUPUPU)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A	Back alignment and structure

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}	Back alignment and structure

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...	Back alignment and structure

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A	Back alignment and structure

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}	Back alignment and structure

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A	Back alignment and structure

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A	Back alignment and structure

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A	Back alignment and structure

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A	Back alignment and structure

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A	Back alignment and structure

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}	Back alignment and structure

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}	Back alignment and structure

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C	Back alignment and structure

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}	Back alignment and structure

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}	Back alignment and structure

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}	Back alignment and structure

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A	Back alignment and structure

>3s9g_A Protein hexim1; cyclin T-binding domain (TBD), cyclin T1/P-TEFB/7SK snRNA, N transcription; 2.10A {Homo sapiens} PDB: 2gd7_A	Back alignment and structure

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A	Back alignment and structure

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A	Back alignment and structure

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1	Back alignment and structure

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A	Back alignment and structure

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}	Back alignment and structure

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A	Back alignment and structure

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A	Back alignment and structure

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A	Back alignment and structure

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1	Back alignment and structure

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A	Back alignment and structure

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A	Back alignment and structure

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E	Back alignment and structure

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}	Back alignment and structure

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1	Back alignment and structure

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}	Back alignment and structure

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C	Back alignment and structure

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A	Back alignment and structure

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*	Back alignment and structure

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}	Back alignment and structure

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A	Back alignment and structure

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A	Back alignment and structure

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C	Back alignment and structure

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

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E	Back alignment and structure

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}	Back alignment and structure

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*	Back alignment and structure

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A	Back alignment and structure

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4	Back alignment and structure

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A	Back alignment and structure

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C	Back alignment and structure

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B	Back alignment and structure

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A	Back alignment and structure

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}	Back alignment and structure

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B	Back alignment and structure

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A	Back alignment and structure

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1	Back alignment and structure

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A	Back alignment and structure

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A	Back alignment and structure

>3trt_A Vimentin; cytoskeleton, intermediate filament, alpha-helix, structural protein; 2.30A {Homo sapiens} PDB: 3klt_A*	Back alignment and structure

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A	Back alignment and structure

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A	Back alignment and structure

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}	Back alignment and structure

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A	Back alignment and structure

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}	Back alignment and structure

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}	Back alignment and structure

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}	Back alignment and structure

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A	Back alignment and structure

>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A* 2a45_G*	Back alignment and structure

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*	Back alignment and structure

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A	Back alignment and structure

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A	Back alignment and structure

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A	Back alignment and structure

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		423
d2uzga1		95	g.44.1.5 (A:36-130) Ubiquitin carboxyl-terminal hy	2e-19
d2g45a1		113	g.44.1.5 (A:173-285) Ubiquitin carboxyl-terminal h	2e-17
d2idaa1		102	g.44.1.5 (A:1-102) Hypothetical protein RPA1320 {R	2e-14
d1iyma_		55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	1e-04
d1ur6b_		52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	1e-04
d1g25a_		65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	0.002
d1rmda2		86	g.44.1.1 (A:1-86) V(D)J recombination activating p	0.003
d1chca_		68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	0.004
d1jm7b_		97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	0.004
d1fbva4		79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	0.004

>d2uzga1 g.44.1.5 (A:36-130) Ubiquitin carboxyl-terminal hydrolase 33, UBP33 {Human (Homo sapiens) [TaxId: 9606]} Length = 95	Back information, alignment and structure


class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Zf-UBP
domain: Ubiquitin carboxyl-terminal hydrolase 33, UBP33
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 80.4 bits (198), Expect = 2e-19
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 3/77 (3%)

Query: 206 CQVCRFCHQQDERPTCSVCG-TVENLWVCL--ICGFVGCGRYKEGHAVRHWKDTQHWYSL 262
            ++ +    Q    TC  C     NLW CL   C +VGCG  +  H+  H ++T+H+ ++
Sbjct: 11  GEITKEDLIQKSLGTCQDCKVQGPNLWACLENRCSYVGCGESQVDHSTIHSQETKHYLTV 70

Query: 263 DLRTQQIWDYVGDNYVH 279
           +L T ++W Y     V 
Sbjct: 71  NLTTLRVWCYACSKEVF 87

PyMOL of d2uzga1

>d2g45a1 g.44.1.5 (A:173-285) Ubiquitin carboxyl-terminal hydrolase 5, UBP5 {Human (Homo sapiens) [TaxId: 9606]} Length = 113	Back information, alignment and structure

>d2idaa1 g.44.1.5 (A:1-102) Hypothetical protein RPA1320 {Rhodopseudomonas palustris [TaxId: 1076]} Length = 102	Back information, alignment and structure

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55	Back information, alignment and structure

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52	Back information, alignment and structure

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 65	Back information, alignment and structure

>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	Back information, alignment and structure

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68	Back information, alignment and structure

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97	Back information, alignment and structure

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79	Back information, alignment and structure

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		423
d2g45a1		113	Ubiquitin carboxyl-terminal hydrolase 5, UBP5 {Hum	99.74
d2uzga1		95	Ubiquitin carboxyl-terminal hydrolase 33, UBP33 {H	99.74
d2idaa1		102	Hypothetical protein RPA1320 {Rhodopseudomonas pal	99.64
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	98.97
d1ur6b_		52	Not-4 N-terminal RING finger domain {Human (Homo s	98.82
d1chca_		68	Immediate early protein, IEEHV {Equine herpesvirus	98.73
d1g25a_		65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	98.65
d1jm7b_		97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.59
d1bora_		56	Acute promyelocytic leukaemia proto-oncoprotein PM	98.57
d1fbva4		79	CBL {Human (Homo sapiens) [TaxId: 9606]}	98.57
d3dplr1		88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	98.5
d1rmda2		86	V(D)J recombination activating protein 1 (RAG1), d	98.45
d1jm7a_		103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	98.44
d1v87a_		114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	98.42
d2c2la2		80	STIP1 homology and U box-containing protein 1, STU	98.23
d2baya1		56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	98.2
d1t1ha_		78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.18
d1vyxa_		60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.17
d1wgma_		98	Ubiquitin conjugation factor E4A {Human (Homo sapi	97.43
d1wima_		94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	97.14
d2cqca1		83	Arginine/serine-rich splicing factor 10 {Human (Ho	96.23
d1fxla2		85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	96.17
d1fxla1		82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	96.12
d1rk8a_		88	RNA-binding protein 8 {Fruit fly (Drosophila melan	96.1
d1b7fa2		85	Sex-lethal protein {Drosophila melanogaster [TaxId	96.07
d1x5oa1		101	RNA-binding motif, single-stranded-interacting pro	96.06
d1b7fa1		82	Sex-lethal protein {Drosophila melanogaster [TaxId	95.96
d2ghpa2		75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	95.88
d2b0ga1		83	Splicesomal U1A protein {Drosophila melanogaster [	95.8
d2cqpa1		86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	95.71
d2f9da1		114	Pre-mRNA branch site protein p14 {Human (Homo sapi	95.61
d1wi8a_		104	Eukaryotic translation initiation factor 4B {Human	95.58
d1cvja1		80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	95.55
d2cqia1		90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	95.5
d2cq3a1		93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	95.48
d1zh5a2		85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	95.31
d1wg4a_		98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	95.28
d2cpxa1		102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	95.25
d1x5ua1		93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	95.1
d1h2vz_		93	CBP20, 20KDa nuclear cap-binding protein {Human (H	95.01
d2u2fa_		85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	95.01
d1wg5a_		104	Heterogeneous nuclear ribonucleoprotein H' {Human	94.99
d1no8a_		78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	94.96
d2adca1		109	Polypyrimidine tract-binding protein {Human (Homo	94.93
d1whya_		97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	94.92
d1wexa_		104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	94.85
d1p1ta_		104	Cleavage stimulation factor, 64 kda subunit {Human	94.7
d2ghpa1		81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	94.69
d1x4ga1		96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	94.64
d2disa1		96	Hypothetical protein FLJ20273 {Human (Homo sapiens	94.39
d1weza_		102	Heterogeneous nuclear ribonucleoprotein H' {Human	94.26
d1x4aa1		95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	94.22
d2cpja1		86	Non-POU domain-containing octamer-binding protein,	94.18
d2cpea1		101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	94.18
d2cq0a1		90	Eukaryotic translation initiation factor 3 subunit	94.15
d2cpha1		94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	94.14
d1cvja2		89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	94.12
d2cpfa1		85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	94.11
d2adca2		88	Polypyrimidine tract-binding protein {Human (Homo	94.03
d1nu4a_		91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	93.98
d2cpza1		102	CUG triplet repeat RNA-binding protein 1 {Human (H	93.97
d1whxa_		111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	93.68
d1x4ea1		72	RNA-binding motif, single-stranded-interacting pro	93.66
d2bz2a1		79	Negative elongation factor E, NELF-E {Human (Homo	93.63
d2cqba1		89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	93.59
d1fjca_		96	Nucleolin {Golden hamster (Mesocricetus auratus) [	93.55
d1whwa_		99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	93.53
d2cq1a1		88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	93.49
d1x5ta1		83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	93.39
d1x5sa1		90	Cold-inducible RNA-binding protein {Human (Homo sa	93.22
d2cpia1		89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	92.94
d2ghpa3		86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	92.93
d1u6fa1		139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	92.44
d1l3ka1		84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	92.19
d3begb1		87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	91.97
d1uawa_		77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	91.88
d2cqga1		90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	91.88
d1wi6a1		75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	91.42
d2msta_		75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	91.42
d2cpya1		103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	91.4
d2cq4a1		101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	91.3
d1x4ha1		98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	91.16
d1wela1		112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	91.01
d1wg1a_		88	Probable RNA-binding protein KIAA1579 {Human (Homo	90.08
d1x4fa1		99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	89.29
d2cpda1		86	APOBEC1 stimulating protein {Human (Homo sapiens)	89.02
d1x4ba1		103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	88.83
d2cqda1		103	RNA-binding region containing protein 1 {Human (Ho	88.81
d1l3ka2		79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	88.71
d1u1qa_		183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	88.16
d1fjeb1		91	Nucleolin {Golden hamster (Mesocricetus auratus) [	87.43
d1hd0a_		75	Heterogeneous nuclear ribonucleoprotein d0 {Human	87.14
d1uw4a_		91	RNA processing protein UPF3x, RRM domain {Human (H	86.71
d1wf2a_		98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	84.37
d2adba1		108	Polypyrimidine tract-binding protein {Human (Homo	84.22
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_		104	U2	83.93
d1x0fa1		75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	83.83

>d2g45a1 g.44.1.5 (A:173-285) Ubiquitin carboxyl-terminal hydrolase 5, UBP5 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Zf-UBP
domain: Ubiquitin carboxyl-terminal hydrolase 5, UBP5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=4.6e-19  Score=150.34  Aligned_cols=65  Identities=34%  Similarity=0.571  Sum_probs=60.1

Q ss_pred             CCCCCCcCCCCCCCceeeecccCcccccCCc------chhhhhhhhcCCCceeeeCCC-----ceEEEccCCcccc
Q 014500          215 QDERPTCSVCGTVENLWVCLICGFVGCGRYK------EGHAVRHWKDTQHWYSLDLRT-----QQIWDYVGDNYVH  279 (423)
Q Consensus       215 ~~~~~~C~~C~~~~~lWiCL~CG~vgCgRy~------~~HA~~H~e~t~H~lal~l~t-----~rVwcY~cd~yVH  279 (423)
                      +++.++|.+|+...++|+||+||++|||||.      ++||++||++++|++++++.|     .+||||.||+||+
T Consensus        21 ~p~~~~C~~C~~~~~lWlCL~CG~vgCgR~~~~~~~~~~HA~~H~~~t~H~l~v~l~t~~~~~~~vwCY~cd~~V~   96 (113)
T d2g45a1          21 PPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLGTITPDGADVYSYDEDDMVL   96 (113)
T ss_dssp             CCCBCCCSSSSCCSSEEEETTTCCEEECCBCTTSCBCCSHHHHHHHHHCCCEEEETTCCBTTBCCEEETTTTEEEE
T ss_pred             CCCCCcccCCCCcCCEEEEecCCCCccCcccccCCCCChHHHHHHHhcCCCEEEEecCCCCCCceEEEecCCCEEE
Confidence            4677899999999999999999999999985      789999999999999999976     5799999999995

PyMOL of d2g45a1

>d2uzga1 g.44.1.5 (A:36-130) Ubiquitin carboxyl-terminal hydrolase 33, UBP33 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2idaa1 g.44.1.5 (A:1-102) Hypothetical protein RPA1320 {Rhodopseudomonas palustris [TaxId: 1076]}	Back information, alignment and structure

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}	Back information, alignment and structure

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}	Back information, alignment and structure

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}	Back information, alignment and structure

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}	Back information, alignment and structure

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}	Back information, alignment and structure

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}	Back information, alignment and structure

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure