Citrus Sinensis ID: 003485

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-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810------

MSDEGEKTCPLCAEEMDLTDQQLKPCKCGYEICVWCWHHIMDMAEKEETEGRCPACRSPYDKEKIVGMAAKCERLVAEISMERKMKSQKSKTKSSEGKKQQLSSVRVIQRNLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCSVYITYSKEEEAVRCIQSVHGFVLEGKSLKACFGTTKYCHAWLRNVPCTNPDCLYLHEVGSQEDSFTKDEIISAYTRSRVQQITGTTNNLQRRSGNVLPPPFDDYCHINSVSTAKPSVKNAANNTASISKDPIPNGSSARSVALPAAASWGMRASNQQSVATSACSNGPSKQRPDTVGGALAFSSAVANTPSVSTLHVDVVKRPTVHEDSQITDSKSKSDISKPSRQHFGSEPPTPNGEPASVSLSNQASCPTKYTDKSLNMPPNVIHSSDTTDHSCLSGPEKEENVTADVKMQGLCSDVSAMSIDRNATNEHSGVARASSALPDHGMMKLPRNQGLQPYNADLCREPLMSPETGKSITSKNDAFVSREPFDWRTDPTQAATDASPQEEEDVLSFDNQRLKDPEVVCRSNYLPKSANSLHVTNHSRSHSFQNSDALTASNLNSDPQFVDNSVNDGSHPHLSSSSLKSNGYPEKLARNTSGPGRAVENAFLLSNEGQRMPRELQGDANIDAAVDTGENSIISNILSMDFDTWDDPLALPQNLAKLLSEPEKEPSSLKMSSSWKGHNHNQSRFSFARQEESRSHTFDNERSFSGFIQQPKSHSFNQDFAGNRDPLLDKLGLRNGFHPSSFEESDNFSSNHAVFSPNKLSGEYHYSIN

ccccccccccccccccccccccccccccccEEEHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccEEEEcEEEEEccccccccHHHHcccccccccccEEEEEEEEcccccccccccccEEEEEEEccHHHHHHHHHHHccccccccEEEEEccccHHHHcccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc

ccccccccccccEcccccccccccccccccHEEHHHHHHHHHHHccccccccccccccccccccEEEEcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEccEEEEEccccccccHHHHccccHcccccEEEEEEEEccccccccccccccEEEEEEEccHHHHHHHHHHHccccccccEEEEEccccHHHHHHHccccccccccEEEcccccccccccHHHHHHHHHccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccHEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccHHHHHHHcccccccccccccHHHHHHHHccccccccccccccccccccccccEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc

msdegektcplcaeemdltdqqlkpckcgyeiCVWCWHHIMDMaekeetegrcpacrspydkeKIVGMAAKCERLVAEISMERKMksqksktkssegkkqqLSSVRVIQRNLVYIVglplnlgdedLLQRREYFGQYGKVLKVSMSRTAAGviqqfpnntcsvyITYSKEEEAVRCIQSVHGFvlegkslkacfgttkychawlrnvpctnpdclylhevgsqedsftkdeIISAYTRSRVQQITgttnnlqrrsgnvlpppfddychinsvstakpsvknaanntasiskdpipngssarsvalpaaaswgmrasnqqsvatsacsngpskqrpdtvggALAFSSavantpsvstlhvdvvkrptvhedsqitdsksksdiskpsrqhfgsepptpngepasvslsnqascptkytdkslnmppnvihssdttdhsclsgpekeenvtADVKMQGLCSdvsamsidrnatnehsgvarassalpdhgmmklprnqglqpynadlcreplmspetgksitskndafvsrepfdwrtdptqaatdaspqeeedvlsfdnqrlkdpevvcrsnylpksanslhvtnhsrshsfqnsdaltasnlnsdpqfvdnsvndgshphlsssslksngypeklarntsgpgraVENAFllsnegqrmprelqgdanidaavdtgensiISNIlsmdfdtwddplalPQNLAKLlsepekepsslkmssswkghnhnqsrfsfarqeesrshtfdnersfsgfiqqpkshsfnqdfagnrdplldklglrngfhpssfeesdnfssnhavfspnklsgeyhysin

msdegektcplcaeemdltdqqlkPCKCGYEICVWCWHHIMDMAEKEETEGRCPACRSPYDKEKIVGMAAKCERLVAEISMerkmksqksktkssegkkqqlssvrvIQRNLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAAgviqqfpnnTCSVYITYSKEEEAVRCIQSVHGFVLEGKSLKACFGTTKYCHAWLRNVPCTNPDCLYLHEVGSQEDSFTKDEIISAYTRSRVqqitgttnnlqrrsgnVLPPPFDDYCHINSVSTAKPSVKNAANNTasiskdpipngssARSVALPAAASWGMRASNQQSVATSACSNGPSKQRPDTVGGALAFSSAvantpsvstlhvdvvkrptvhedsqitdsksksdiskpsrqhfgsepptpngepasVSLSNQASCPTKYTDKSLNMPPNVIHSSDTTDHSCLSGPEKEENVTADVKMQGLCSDVSAMSIDRNATNEHSGVARASSALPDHGMMKLPRNQGLQPYNADLCREPLMSpetgksitskndaFVSREPFDWRTDPTqaatdaspqeeeDVLSFDNQRLKDPEVVCRSNYLPKSANSLHVTNHSRSHSFQNSDALTASNLNSDPQFVDNSVNDGSHPHLsssslksngyPEKLArntsgpgrAVENAFLLSNEGQRMPRELQGDANIDAAVDTGENSIISNILSMDFDTWDDPLALPQNLAKLLSEPEKEPSSLKMSSSWKGHNHNQSRFSFARQEESRSHTFDNERSFSGFIQQPKSHSFNQDFAGNRDPLLDKLGLRNGFHPSsfeesdnfssnhavfspnklsgeyhysin

MSDEGEKTCPLCAEEMDLTDQQLKPCKCGYEICVWCWHHIMDMAEKEETEGRCPACRSPYDKEKIVGMAAKCERLVAEISMERkmksqksktkssegkkqqLSSVRVIQRNLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCSVYITYSKEEEAVRCIQSVHGFVLEGKSLKACFGTTKYCHAWLRNVPCTNPDCLYLHEVGSQEDSFTKDEIISAYTRSRVQQITGTTNNLQRRSGNVLPPPFDDYCHINSVSTAKPSVKNAANNTASISKDPIPNGSSARSVALPAAASWGMRASNQQSVATSACSNGPSKQRPDTVGGALAFSSAVANTPSVSTLHVDVVKRPTVHEdsqitdsksksdiskpsRQHFGSEPPTPNGEPASVSLSNQASCPTKYTDKSLNMPPNVIHSSDTTDHSCLSGPEKEENVTADVKMQGLCSDVSAMSIDRNATNEHSGVARASSALPDHGMMKLPRNQGLQPYNADLCREPLMSPETGKSITSKNDAFVSREPFDWRTDPTQAATDASPQEEEDVLSFDNQRLKDPEVVCRSNYLPKSANSLHVTNHSRSHSFQNSDALTASNLNSDPQFVDNSVNDGshphlsssslksNGYPEKLARNTSGPGRAVENAFLLSNEGQRMPRELQGDANIDAAVDTGENSIISNILSMDFDTWDDPLALPQNLAKLLSEPEKEPSSLKMSSSWKGHNHNQSRFSFARQEESRSHTFDNERSFSGFIQQPKSHSFNQDFAGNRDPLLDKLGLRNGFHPssfeesdnfssnHAVFSPNKLSGEYHYSIN

**********LCAEEMDLTDQQLKPCKCGYEICVWCWHHIMDMA********CPACRSPYDKEKIVGMAAKCERLVA***************************VRVIQRNLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCSVYITYSKEEEAVRCIQSVHGFVLEGKSLKACFGTTKYCHAWLRNVPCTNPDCLYLHEVGSQEDSFTKDEIISAYTRSRVQQIT****************PFDDYCHIN***************************************************************************************HV************************************************************************************************************************************************************************************************************************************************************************************************************************AVDTGENSIISNILSMDFDTWDDPLALP*********************************************************************************************************************

****GEKTCPLCAEEMDLTDQQLKPCKCGYEICVWCWHHIMDM***********ACRSPYDKEKIVGMA*************************************VIQRNLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSM***************CSVYITYSKEEEAVRCIQSVHGFVLEGKSLKACFGTTKYCHAWLRNVPCTNPDCLYLHEVGSQEDSFT************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************

********CPLCAEEMDLTDQQLKPCKCGYEICVWCWHHIMDMAE********PACRSPYDKEKIVGMAAKCERLVAEISM**********************SVRVIQRNLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCSVYITYSKEEEAVRCIQSVHGFVLEGKSLKACFGTTKYCHAWLRNVPCTNPDCLYLHEVGSQEDSFTKDEIISAYTRSRVQQITGTTNNLQRRSGNVLPPPFDDYCHINSVSTAKPSVKNAANNTASISKDPIPNGSSARSVALPAAASW**************************VGGALAFSSAVANTPSVSTLHVDVVKRPTV*********************************************PTKYTDKSLNMPPNVIHSSDTTDHSCLSGPEKEENVTADVKMQGLCSDVSAMSIDRNATNEHSGVARASSALPDHGMMKLPRNQGLQPYNADLCREPLMSPETGKSITSKNDAFVSREPFDWRTD*****************SFDNQRLKDPEVVCRSNYLPKSANSLHVTNHSRSHSFQNSDALTASNLNSDPQFVDNSVNDG************NGYPEKLARNTSGPGRAVENAFLLSNEGQRMPRELQGDANIDAAVDTGENSIISNILSMDFDTWDDPLALPQNLAKLL*********************NQSRF***************ERSFSGFIQQPKSHSFNQDFAGNRDPLLDKLGLRNGFHPSS********SNHAVFSPNKLSGEYHYSIN

******KTCPLCAEEMDLTDQQLKPCKCGYEICVWCWHHIMDMAEKEETEGRCPACRSPYDKEKIVGMAAKCERLVAEISMERKMKSQKSKTKSSEGKKQQLSSVRVIQRNLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAA*****FPNNTCSVYITYSKEEEAVRCIQSVHGFVLEGKSLKACFGTTKYCHAWLRNVPCTNPDCLYLHEVGSQEDSFTKDEIISAYTRS*************************************************************************************************************************************************************************************************************************************************************************L************SITSKNDAFVSREPFDWRTDPTQAATD***QEEEDVLSFDNQRLKDPEVVCRSNYLPKSANSLHVTNHSRSHSFQNSDALTASNLNSDPQFVDNSVNDGSHPHLSSSSLKSNGYPEKLARNTSGPGRAVENAFL**************************NSIISNILSMDFDTWDDPLALPQNLAKLLSE***********************F****Q****SHT****RSFSGFIQQPKSHSFNQDFAGNRDPLLDKLGLRNGFHPSSF**SDNFSSNHAVF***K**********

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		816	2.2.26 [Sep-21-2011]
Q8BT14		575	CCR4-NOT transcription co	no	no	0.295	0.419	0.419	7e-55
O95628		575	CCR4-NOT transcription co	no	no	0.295	0.419	0.419	8e-55
P34909		587	General negative regulato	yes	no	0.290	0.403	0.393	1e-50
Q09818		489	Putative general negative	yes	no	0.274	0.458	0.411	1e-43

>sp\|Q8BT14\|CNOT4_MOUSE CCR4-NOT transcription complex subunit 4 OS=Mus musculus GN=Cnot4 PE=1 SV=2	Back alignment and function desciption

 Score =  216 bits (549), Expect = 7e-55,   Method: Compositional matrix adjust.
 Identities = 107/255 (41%), Positives = 159/255 (62%), Gaps = 14/255 (5%)

Query: 9   CPLCAEEMDLTDQQLKPCKCGYEICVWCWHHIMDMAEKEETEGRCPACRSPYDKEKIVGM 68
           CPLC E +++ D    PC CGY+IC +CWH I     + +  G CPACR PY ++  V  
Sbjct: 14  CPLCMEPLEIDDINFFPCTCGYQICRFCWHRI-----RTDENGLCPACRKPYPEDPAVYK 68

Query: 69  AAKCERLVAEISMERKMKSQKSKTKSSEGKKQQLSSVRVIQRNLVYIVGLPLNLGDEDLL 128
               E L   I  E+K K  + K K SE +K  L+SVRV+Q+NLV++VGL   L D ++L
Sbjct: 69  PLSQEEL-QRIKNEKKQKQNERKQKISENRKH-LASVRVVQKNLVFVVGLSQRLADPEVL 126

Query: 129 QRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCSVYITYSKEEEAVRCIQSVHGFVLEGK 188
           +R EYFG++GK+ KV ++ + +    Q P  + S Y+TY + E+A+R IQ V+  V++G+
Sbjct: 127 KRPEYFGKFGKIHKVVINNSTSYAGSQGP--SASAYVTYIRSEDALRAIQCVNNVVVDGR 184

Query: 189 SLKACFGTTKYCHAWLRNVPCTNPDCLYLHEVGSQEDSFTKDEIISA----YTRSRVQQI 244
           +LKA  GTTKYC  +L+N+ C  PDC+YLHE+G +  SFTK+E+ +     Y +  +Q++
Sbjct: 185 TLKASLGTTKYCSYFLKNMQCPKPDCMYLHELGDEAASFTKEEMQAGKHQEYEQKLLQEL 244

Query: 245 TGTTNN-LQRRSGNV 258
                N LQ  +G+V
Sbjct: 245 YKLNPNFLQLSTGSV 259

Has E3 ubiquitin ligase activity. The CCR4-NOT complex functions as general transcription regulation complex.
Mus musculus (taxid: 10090)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp\|O95628\|CNOT4_HUMAN CCR4-NOT transcription complex subunit 4 OS=Homo sapiens GN=CNOT4 PE=1 SV=3	Back alignment and function description

>sp\|P34909\|NOT4_YEAST General negative regulator of transcription subunit 4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=MOT2 PE=1 SV=1	Back alignment and function description

>sp\|Q09818\|YAC4_SCHPO Putative general negative regulator of transcription C16C9.04c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC16C9.04c 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		816
359478673		1024	PREDICTED: uncharacterized protein LOC10	0.962	0.766	0.598	0.0
297746185		1022	unnamed protein product [Vitis vinifera]	0.959	0.766	0.596	0.0
356542573		1022	PREDICTED: uncharacterized protein LOC10	0.954	0.762	0.569	0.0
356541279		1023	PREDICTED: uncharacterized protein LOC10	0.959	0.765	0.551	0.0
357472457		1223	CCR4-NOT transcription complex subunit [	0.958	0.639	0.508	0.0
356550179		1003	PREDICTED: uncharacterized protein LOC10	0.946	0.769	0.525	0.0
356557479		1045	PREDICTED: uncharacterized protein LOC10	0.955	0.746	0.531	0.0
357453719		1007	CCR4-NOT transcription complex subunit [	0.938	0.760	0.529	0.0
449461035		1092	PREDICTED: uncharacterized protein LOC10	0.941	0.703	0.508	0.0
297793573		1001	hypothetical protein ARALYDRAFT_358235 [	0.920	0.750	0.488	0.0

>gi\|359478673\|ref\|XP_002281895.2\| PREDICTED: uncharacterized protein LOC100267264 [Vitis vinifera]	Back alignment and taxonomy information

 Score =  961 bits (2484), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 491/821 (59%), Positives = 598/821 (72%), Gaps = 36/821 (4%)

Query: 1   MSDEGEKTCPLCAEEMDLTDQQLKPCKCGYEICVWCWHHIMDMAEKEETEGRCPACRSPY 60
           MSDEGEKTCPLCAEEMDLTDQQLKPCKCGYEICVWCWHHIM+MAEK+ETEGRCPACR PY
Sbjct: 1   MSDEGEKTCPLCAEEMDLTDQQLKPCKCGYEICVWCWHHIMNMAEKDETEGRCPACRVPY 60

Query: 61  DKEKIVGMAAKCERLVAEISMERKMKSQKSKTKSSEGKKQQLSSVRVIQRNLVYIVGLPL 120
           +KEKIVGMAA C+RLVAEI++ERKMKSQK+KTK SEG+KQ L SVRVIQRNLVYIVGLPL
Sbjct: 61  NKEKIVGMAADCKRLVAEINLERKMKSQKAKTKLSEGRKQ-LGSVRVIQRNLVYIVGLPL 119

Query: 121 NLGDEDLLQRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCSVYITYSKEEEAVRCIQSV 180
           NL DEDLLQR+EYFG YGKVLKVSMSRTAAGVIQQFPNNTCSVYITYSKEEEAVRCIQ+V
Sbjct: 120 NLADEDLLQRKEYFGLYGKVLKVSMSRTAAGVIQQFPNNTCSVYITYSKEEEAVRCIQTV 179

Query: 181 HGFVLEGKSLKACFGTTKYCHAWLRNVPCTNPDCLYLHEVGSQEDSFTKDEIISAYTRSR 240
           HGFVL+G+ L+ACFGTTKYCH WLRNVPC NPDCLYLHE+GSQEDSFTKDEIIS+YTR+R
Sbjct: 180 HGFVLDGRPLRACFGTTKYCHQWLRNVPCNNPDCLYLHEIGSQEDSFTKDEIISSYTRNR 239

Query: 241 VQQITGTTNNLQRRSGNVLPPPFDDYCHINSVSTAKPSVKNAANNTASISKDPIPNGSSA 300
           VQQITG TNNLQRRSGN+LPPP D+YC+ +S S  KP  KNA+NN+ SI+K   PN SS 
Sbjct: 240 VQQITGATNNLQRRSGNMLPPPADEYCNNSSASMGKPITKNASNNSVSIAKGSPPNSSSG 299

Query: 301 RSVALPAAASWGMRASNQQSVATS-ACSNGPSKQRPDTVGGALAFSSAVAN-----TPSV 354
           RS ALPAAASWGMR+SN Q++A+S +C NGP KQ+PD+  G++AFSSAV +     T   
Sbjct: 300 RSNALPAAASWGMRSSNSQTMASSLSCGNGPFKQKPDSFSGSVAFSSAVTSTTLPLTTQA 359

Query: 355 STLHVDVVKRPTVHEDSQITDSKSKSDISKPSRQHFGSEPP----TPNGEPASVSLSNQA 410
             LH +V K+PT++E++++ + K K +  +  +QH   +      TP+  PAS+ L  Q 
Sbjct: 360 VALHSEVGKKPTLNEENRLINPKGKLESLESMKQHISMDTSEGLITPDEAPASLPLGGQL 419

Query: 411 SCP--TKYTDKSLNMPPNVIHSSDTTDHSCLSGPEKEENVTADVKMQGLCSDVSAMSIDR 468
           SCP  +K  D+ +++ P V +SSD T     SG E+E NV  D  +  L SD+S+MSIDR
Sbjct: 420 SCPPTSKDNDRGISLSPKVTNSSDFTRQPNCSGSEREGNVATDGNLHNLLSDMSSMSIDR 479

Query: 469 NATNEHSGVARASSALPDHGMMKLPRNQGLQPYNADLCREPLMSPETGKSITSKNDAFVS 528
              +EH GV R++ +L D+G+ + P +QGLQ Y A+  +E L SP + K  T+ N   V 
Sbjct: 480 QLKSEHPGVLRSNCSLSDNGLTQTPGSQGLQQYYAEQFKESLTSPVSRKVSTTINGVCVP 539

Query: 529 REPFDWRTDP-TQAATDASPQEEEDVLSFDNQRLKDPEVVCRSNYLPKSANSLHVTNHSR 587
            E  DWR+D  TQ   +   + E+D+LSFDNQRLKD EVV  + YLP S++ LH +N  R
Sbjct: 540 DEQNDWRSDSQTQVVPNMCSEMEDDLLSFDNQRLKDSEVVSGTTYLPNSSHLLHHSNDLR 599

Query: 588 SHSFQNSDALTASNLNSDPQFVDNSVNDGSHPHLSSSSLKSNGYPEKLARNTSGPGRAVE 647
             S Q++D     + N+DP FV    ++GS  H   +S+ SNG+PEK   N++G  R   
Sbjct: 600 GKSSQHNDIHNGVSFNADPIFVGRKFSEGSLTHAPGASVISNGFPEKRVGNSAGLDR--- 656

Query: 648 NAFLLSNEGQRMPRELQGDANIDAAVDTGENSIISNILSMDFDTWDDPLALPQNLAKLLS 707
                              AN    +D GENSIISNILS+DFD WDD +  PQNLA+LL 
Sbjct: 657 -------------------ANASTTMDVGENSIISNILSLDFDAWDDSITSPQNLAQLLG 697

Query: 708 EPEKEPSSLKMSSSWKGHNHNQSRFSFARQEESRSHTFDNERSFSGFIQQPKSHSFNQDF 767
           E +K+ SSLK S SWK  N NQSRFSFARQEES++  FD E SFS   Q P++ SFNQ+F
Sbjct: 698 ENDKQHSSLKTSGSWKVQNSNQSRFSFARQEESKNQVFDIEPSFSNIGQVPRNCSFNQNF 757

Query: 768 AGNRDPLLDKLGLRNGFHPSSFEESDNFSSNHAVFSPNKLS 808
             +RDP LDKLG  + F  + F ESDNF+  H+V S NK+S
Sbjct: 758 VESRDPFLDKLGNGSLFSSNIFGESDNFAPGHSVISSNKIS 798

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|297746185\|emb\|CBI16241.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356542573\|ref\|XP_003539741.1\| PREDICTED: uncharacterized protein LOC100801880 [Glycine max]	Back alignment and taxonomy information

>gi\|356541279\|ref\|XP_003539106.1\| PREDICTED: uncharacterized protein LOC100813427 [Glycine max]	Back alignment and taxonomy information

>gi\|357472457\|ref\|XP_003606513.1\| CCR4-NOT transcription complex subunit [Medicago truncatula] gi\|355507568\|gb\|AES88710.1\| CCR4-NOT transcription complex subunit [Medicago truncatula]	Back alignment and taxonomy information

>gi\|356550179\|ref\|XP_003543466.1\| PREDICTED: uncharacterized protein LOC100805811 [Glycine max]	Back alignment and taxonomy information

>gi\|356557479\|ref\|XP_003547043.1\| PREDICTED: uncharacterized protein LOC100796804 [Glycine max]	Back alignment and taxonomy information

>gi\|357453719\|ref\|XP_003597140.1\| CCR4-NOT transcription complex subunit [Medicago truncatula] gi\|355486188\|gb\|AES67391.1\| CCR4-NOT transcription complex subunit [Medicago truncatula]	Back alignment and taxonomy information

>gi\|449461035\|ref\|XP_004148249.1\| PREDICTED: uncharacterized protein LOC101221790 [Cucumis sativus] gi\|449515295\|ref\|XP_004164685.1\| PREDICTED: uncharacterized protein LOC101225784 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|297793573\|ref\|XP_002864671.1\| hypothetical protein ARALYDRAFT_358235 [Arabidopsis lyrata subsp. lyrata] gi\|297310506\|gb\|EFH40930.1\| hypothetical protein ARALYDRAFT_358235 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

Prediction of Gene Ontology (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

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		816
COG5175		480	COG5175, MOT2, Transcriptional repressor [Transcri	8e-69
cd12438		98	cd12438, RRM_CNOT4, RNA recognition motif in Eukar	8e-52
cd00590		72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-12
pfam00076		70	pfam00076, RRM_1, RNA recognition motif	1e-09
smart00360		73	smart00360, RRM, RNA recognition motif	2e-09
pfam14259		69	pfam14259, RRM_6, RNA recognition motif (a	7e-08
cd12354		73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-07
pfam13893		56	pfam13893, RRM_5, RNA recognition motif	4e-07
cd12393		78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	5e-07
smart00361		70	smart00361, RRM_1, RNA recognition motif	1e-06
cd12232		89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	1e-05
cd12380		80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-05
cd12374		85	cd12374, RRM_UHM_SPF45_PUF60, RNA recognition moti	9e-05
cd12355		80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-04
cd12432		90	cd12432, RRM_ACINU, RNA recognition motif in apopt	3e-04
cd12246		78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	3e-04
cd12382		80	cd12382, RRM_RBMX_like, RNA recognition motif in h	3e-04
cd12377		78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-04
cd12417		74	cd12417, RRM_SAFB_like, RNA recognition motif in t	3e-04
cd12362		73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-04
cd12284		73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	4e-04
cd12282		91	cd12282, RRM2_TatSF1_like, RNA recognition motif 2	6e-04
pfam13923		45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	0.001
cd12653		84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	0.001
cd12565		76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	0.002
cd12305		75	cd12305, RRM_NELFE, RNA recognition motif in negat	0.002
cd12251		72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	0.002
COG0724		306	COG0724, COG0724, RNA-binding proteins (RRM domain	0.002
cd12375		77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.002

>gnl\|CDD\|227502 COG5175, MOT2, Transcriptional repressor [Transcription]	Back alignment and domain information

 Score =  235 bits (600), Expect = 8e-69
 Identities = 136/428 (31%), Positives = 211/428 (49%), Gaps = 37/428 (8%)

Query: 2   SDEGEKTCPLCAEEMDLTDQQLKPCKCGYEICVWCWHHIMDMAEKEETEGRCPACRSPYD 61
           S++ E  CPLC E MD+TD+   PC CGY+IC +C+++I     ++   GRCPACR  YD
Sbjct: 10  SEDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNI-----RQNLNGRCPACRRKYD 64

Query: 62  KEKIVGMAAKCERLVAEISM--ERKMKSQKSKTKSSEGKKQQLSSVRVIQRNLVYIVGLP 119
            E +  +    E L  E++   ERKM+ ++ K    + +K  LS++RV+Q+NLVY++G+P
Sbjct: 65  DENVRYVTLSPEELKMELARKEERKMREKERKEAEGQNRKH-LSNIRVVQKNLVYVIGIP 123

Query: 120 LNLGDED---LLQRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCSVYITYSKEEEAVRC 176
             + DE+   +L+R EYFGQYGK+ K+ +++  + +      +   VYITYS +E+A RC
Sbjct: 124 PKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSL--NSTASHAGVYITYSTKEDAARC 181

Query: 177 IQSVHGFVLEGKSLKACFGTTKYCHAWLRNVPCTNPDCLYLHEVGSQEDSFTKDEIISAY 236
           I  V G +L+G+ LKA +GTTKYC ++LRN  C NPDC+YLHE G ++DS TKDE+ +  
Sbjct: 182 IAEVDGSLLDGRVLKATYGTTKYCTSYLRNAVCPNPDCMYLHEPGPEKDSLTKDELCN-- 239

Query: 237 TRSRVQQITGTTNNLQRRSGNVLPPPFDDYCHINSVSTAKPSVKNAANNTASISKDPIPN 296
                   +   N  ++R          D   +N   T  P+   A     +      P+
Sbjct: 240 -SQHKLHGSEVRNKNKKRIHRSTSTARYDTDLLNFTGTPSPAAMEAQFKHKTSRVFKAPD 298

Query: 297 GSSARSVALPAAASWGMRASNQQSVATSACSNGPSKQRP--DTVGGALAFSSAVANTPSV 354
                 +            +N QS      SN  S   P  +   G    ++   NT + 
Sbjct: 299 KILFPPLD----------FTNTQSATPVTLSNSSSINLPTLNDSLGHHTETTTTTNTNAT 348

Query: 355 STLHVDVVKRPTVHEDSQITDSKSKSDISKPSRQHFGSEPPTPNGEPASVSLSNQASCPT 414
           S  H    K+    E+ +         +   +R H        N +   +S+ +      
Sbjct: 349 SHSHGSKKKQSLAAEEYK----DPYDALGNAARLH-----SLSNYQKRPISIKSDEETYK 399

Query: 415 KYTDKSLN 422
           K+  KS N
Sbjct: 400 KWDKKSDN 407

Length = 480

>gnl\|CDD\|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily	Back alignment and domain information

>gnl\|CDD\|215696 pfam00076, RRM_1, RNA recognition motif	Back alignment and domain information

>gnl\|CDD\|214636 smart00360, RRM, RNA recognition motif	Back alignment and domain information

>gnl\|CDD\|222631 pfam14259, RRM_6, RNA recognition motif (a	Back alignment and domain information

>gnl\|CDD\|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1	Back alignment and domain information

>gnl\|CDD\|206064 pfam13893, RRM_5, RNA recognition motif	Back alignment and domain information

>gnl\|CDD\|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins	Back alignment and domain information

>gnl\|CDD\|214637 smart00361, RRM_1, RNA recognition motif	Back alignment and domain information

>gnl\|CDD\|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins	Back alignment and domain information

>gnl\|CDD\|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins	Back alignment and domain information

>gnl\|CDD\|240878 cd12432, RRM_ACINU, RNA recognition motif in apoptotic chromatin condensation inducer in the nucleus (acinus) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family	Back alignment and domain information

>gnl\|CDD\|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family	Back alignment and domain information

>gnl\|CDD\|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family	Back alignment and domain information

>gnl\|CDD\|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins	Back alignment and domain information

>gnl\|CDD\|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins	Back alignment and domain information

>gnl\|CDD\|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins	Back alignment and domain information

>gnl\|CDD\|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger)	Back alignment and domain information

>gnl\|CDD\|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)	Back alignment and domain information

>gnl\|CDD\|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins	Back alignment and domain information

>gnl\|CDD\|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		816
COG5175		480	MOT2 Transcriptional repressor [Transcription]	100.0
KOG2068		327	consensus MOT2 transcription factor [Transcription	100.0
PF14570		48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	99.84
PLN03134		144	glycine-rich RNA-binding protein 4; Provisional	99.53
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.53
PF00076		70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.52
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.47
PF14259		70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.36
KOG0125		376	consensus Ataxin 2-binding protein (RRM superfamil	99.34
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	99.3
smart00362		72	RRM_2 RNA recognition motif.	99.29
KOG0114		124	consensus Predicted RNA-binding protein (RRM super	99.29
PLN03120		260	nucleic acid binding protein; Provisional	99.28
KOG0111		298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.26
COG0724		306	RNA-binding proteins (RRM domain) [General functio	99.25
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	99.24
TIGR01645		612	half-pint poly-U binding splicing factor, half-pin	99.24
cd00590		74	RRM RRM (RNA recognition motif), also known as RBD	99.24
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	99.24
KOG0122		270	consensus Translation initiation factor 3, subunit	99.22
KOG0107		195	consensus Alternative splicing factor SRp20/9G8 (R	99.21
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	99.21
smart00360		71	RRM RNA recognition motif.	99.21
TIGR01645		612	half-pint poly-U binding splicing factor, half-pin	99.2
KOG4206		221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.2
TIGR01642		509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.19
PLN03213		759	repressor of silencing 3; Provisional	99.18
KOG0148		321	consensus Apoptosis-promoting RNA-binding protein	99.17
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	99.17
PF13893		56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.16
KOG0149		247	consensus Predicted RNA-binding protein SEB4 (RRM	99.15
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.12
KOG0145		360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.11
KOG0148		321	consensus Apoptosis-promoting RNA-binding protein	99.11
KOG0126		219	consensus Predicted RNA-binding protein (RRM super	99.09
KOG4207		256	consensus Predicted splicing factor, SR protein su	99.08
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	99.08
smart00361		70	RRM_1 RNA recognition motif.	99.05
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.04
KOG0121		153	consensus Nuclear cap-binding protein complex, sub	99.04
PLN03121		243	nucleic acid binding protein; Provisional	99.01
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.98
KOG0131		203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.97
KOG0105		241	consensus Alternative splicing factor ASF/SF2 (RRM	98.95
KOG0117		506	consensus Heterogeneous nuclear ribonucleoprotein	98.94
KOG0108		435	consensus mRNA cleavage and polyadenylation factor	98.93
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.93
KOG0113		335	consensus U1 small nuclear ribonucleoprotein (RRM	98.77
KOG0130		170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.72
KOG0127		678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.69
TIGR01642		509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.69
KOG0127		678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.65
KOG0117		506	consensus Heterogeneous nuclear ribonucleoprotein	98.64
KOG0144		510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.64
KOG0147		549	consensus Transcriptional coactivator CAPER (RRM s	98.6
KOG0145		360	consensus RNA-binding protein ELAV/HU (RRM superfa	98.6
KOG0132		894	consensus RNA polymerase II C-terminal domain-bind	98.6
KOG0146		371	consensus RNA-binding protein ETR-3 (RRM superfami	98.53
KOG2068		327	consensus MOT2 transcription factor [Transcription	98.53
KOG0124		544	consensus Polypyrimidine tract-binding protein PUF	98.47
KOG4208		214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.42
KOG0533		243	consensus RRM motif-containing protein [RNA proces	98.38
KOG0144		510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.34
KOG0131		203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.34
KOG0123		369	consensus Polyadenylate-binding protein (RRM super	98.34
KOG4661		940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.32
KOG0151		877	consensus Predicted splicing regulator, contains R	98.28
KOG0109		346	consensus RNA-binding protein LARK, contains RRM a	98.28
KOG0153		377	consensus Predicted RNA-binding protein (RRM super	98.23
KOG0415		479	consensus Predicted peptidyl prolyl cis-trans isom	98.22
KOG0109		346	consensus RNA-binding protein LARK, contains RRM a	98.22
KOG0123		369	consensus Polyadenylate-binding protein (RRM super	98.2
KOG0110		725	consensus RNA-binding protein (RRM superfamily) [G	98.19
KOG1548		382	consensus Transcription elongation factor TAT-SF1	98.07
KOG0124		544	consensus Polypyrimidine tract-binding protein PUF	97.96
KOG4660		549	consensus Protein Mei2, essential for commitment t	97.89
KOG4205		311	consensus RNA-binding protein musashi/mRNA cleavag	97.85
KOG1548		382	consensus Transcription elongation factor TAT-SF1	97.79
KOG4205		311	consensus RNA-binding protein musashi/mRNA cleavag	97.77
KOG1995		351	consensus Conserved Zn-finger protein [General fun	97.75
KOG0106		216	consensus Alternative splicing factor SRp55/B52/SR	97.74
KOG0110		725	consensus RNA-binding protein (RRM superfamily) [G	97.69
KOG2202		260	consensus U2 snRNP splicing factor, small subunit,	97.69
KOG4454		267	consensus RNA binding protein (RRM superfamily) [G	97.62
KOG0147		549	consensus Transcriptional coactivator CAPER (RRM s	97.58
PF11608		90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.55
KOG0116		419	consensus RasGAP SH3 binding protein rasputin, con	97.52
KOG4209		231	consensus Splicing factor RNPS1, SR protein superf	97.51
KOG0146		371	consensus RNA-binding protein ETR-3 (RRM superfami	97.45
KOG4212		608	consensus RNA-binding protein hnRNP-M [RNA process	97.4
KOG4212		608	consensus RNA-binding protein hnRNP-M [RNA process	97.36
KOG1190		492	consensus Polypyrimidine tract-binding protein [RN	97.36
KOG1457		284	consensus RNA binding protein (contains RRM repeat	97.3
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	97.11
KOG0120		500	consensus Splicing factor U2AF, large subunit (RRM	97.04
PLN02189		1040	cellulose synthase	96.96
KOG1996		378	consensus mRNA splicing factor [RNA processing and	96.95
PF05172		100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.91
PF14605		53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.86
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	96.82
TIGR00570		309	cdk7 CDK-activating kinase assembly factor MAT1. A	96.8
PF08777		105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.67
KOG2314		698	consensus Translation initiation factor 3, subunit	96.61
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	96.56
KOG4211		510	consensus Splicing factor hnRNP-F and related RNA-	96.52
PLN02436		1094	cellulose synthase A	96.52
PF04059		97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	96.51
KOG0120		500	consensus Splicing factor U2AF, large subunit (RRM	96.44
PLN03208		193	E3 ubiquitin-protein ligase RMA2; Provisional	96.36
KOG4210		285	consensus Nuclear localization sequence binding pr	96.22
PHA02929		238	N1R/p28-like protein; Provisional	96.09
KOG0226		290	consensus RNA-binding proteins [General function p	95.95
KOG3152		278	consensus TBP-binding protein, activator of basal	95.93
KOG0106		216	consensus Alternative splicing factor SRp55/B52/SR	95.68
KOG1456		494	consensus Heterogeneous nuclear ribonucleoprotein	95.65
KOG1365		508	consensus RNA-binding protein Fusilli, contains RR	95.52
PLN02248		1135	cellulose synthase-like protein	95.41
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	95.35
KOG1190		492	consensus Polypyrimidine tract-binding protein [RN	95.21
PLN02195		977	cellulose synthase A	95.03
PF08952		146	DUF1866: Domain of unknown function (DUF1866) ; In	94.95
TIGR00599		397	rad18 DNA repair protein rad18. This family is bas	94.84
KOG2177		386	consensus Predicted E3 ubiquitin ligase [Posttrans	94.77
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	94.58
KOG4206		221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	94.55
PF14634		44	zf-RING_5: zinc-RING finger domain	94.41
KOG4307		944	consensus RNA binding protein RBM12/SWAN [General	94.29
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	94.29
PF05290		140	Baculo_IE-1: Baculovirus immediate-early protein (	94.17
PF14569		80	zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.	93.83
KOG0320		187	consensus Predicted E3 ubiquitin ligase [Posttrans	93.78
KOG1456		494	consensus Heterogeneous nuclear ribonucleoprotein	93.68
PF00097		41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	93.25
KOG4285		350	consensus Mitotic phosphoprotein [Cell cycle contr	93.18
KOG2416		718	consensus Acinus (induces apoptotic chromatin cond	93.16
KOG0112		975	consensus Large RNA-binding protein (RRM superfami	93.08
KOG0129		520	consensus Predicted RNA-binding protein (RRM super	93.08
PLN02915		1044	cellulose synthase A [UDP-forming], catalytic subu	92.89
KOG4211		510	consensus Splicing factor hnRNP-F and related RNA-	92.88
KOG1457		284	consensus RNA binding protein (contains RRM repeat	92.85
PLN02638		1079	cellulose synthase A (UDP-forming), catalytic subu	92.72
PHA02926		242	zinc finger-like protein; Provisional	92.38
KOG0129		520	consensus Predicted RNA-binding protein (RRM super	92.14
KOG0115		275	consensus RNA-binding protein p54nrb (RRM superfam	91.93
PLN02400		1085	cellulose synthase	91.26
PF15227		42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	91.13
PF10309		62	DUF2414: Protein of unknown function (DUF2414); In	91.0
KOG3002		299	consensus Zn finger protein [General function pred	90.83
KOG0317		293	consensus Predicted E3 ubiquitin ligase, integral	90.78
PF13445		43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	90.75
KOG1855		484	consensus Predicted RNA-binding protein [General f	90.71
COG5236		493	Uncharacterized conserved protein, contains RING Z	90.54
PF04641		260	Rtf2: Rtf2 RING-finger	90.22
PF04847		184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	89.78
PF08675		87	RNA_bind: RNA binding domain; InterPro: IPR014789	89.66
PF12861		85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	88.97
KOG1365		508	consensus RNA-binding protein Fusilli, contains RR	88.69
KOG2193		584	consensus IGF-II mRNA-binding protein IMP, contain	86.1
KOG4307		944	consensus RNA binding protein RBM12/SWAN [General	85.34
PF03467		176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	84.87
KOG2135		526	consensus Proteins containing the RNA recognition	84.65
COG5432		391	RAD18 RING-finger-containing E3 ubiquitin ligase [	84.4
KOG3800		300	consensus Predicted E3 ubiquitin ligase containing	83.99
PF10650		23	zf-C3H1: Putative zinc-finger domain; InterPro: IP	83.64
KOG0128		881	consensus RNA-binding protein SART3 (RRM superfami	83.17
KOG2857		157	consensus Predicted MYND Zn-finger protein/hormone	82.87
COG5574		271	PEX10 RING-finger-containing E3 ubiquitin ligase [	82.63
KOG0287		442	consensus Postreplication repair protein RAD18 [Re	82.4
PF11767		66	SET_assoc: Histone lysine methyltransferase SET as	82.34
KOG4676		479	consensus Splicing factor, arginine/serine-rich [R	81.74
PF04564		73	U-box: U-box domain; InterPro: IPR003613 Quality c	81.62
COG5243		491	HRD1 HRD ubiquitin ligase complex, ER membrane com	81.56
KOG2164		513	consensus Predicted E3 ubiquitin ligase [Posttrans	80.08

>COG5175 MOT2 Transcriptional repressor [Transcription]	Back alignment and domain information

Probab=100.00  E-value=7.6e-79  Score=637.48  Aligned_cols=229  Identities=46%  Similarity=0.955  Sum_probs=204.4

Q ss_pred             CccCCCCCCCcccCCCccCCCccccCCCchhhhhhHhHhHHhhhhcccCCCCCCCCCCCcccchhcccchhHHHHHHHHH
Q 003485            2 SDEGEKTCPLCAEEMDLTDQQLKPCKCGYEICVWCWHHIMDMAEKEETEGRCPACRSPYDKEKIVGMAAKCERLVAEISM   81 (816)
Q Consensus         2 sde~d~~CPLC~EelD~tD~~f~PC~CGYQIC~fC~h~I~~~~~K~~~~grCPACRr~Ydee~i~~~~~~~eel~~~~~~   81 (816)
                      |+|+|+.||||||+||+||++|+||+||||||+||||+|+     ++++||||||||-||++.+.|.++++||+.-++..
T Consensus        10 sedeed~cplcie~mditdknf~pc~cgy~ic~fc~~~ir-----q~lngrcpacrr~y~denv~~~~~s~ee~kmel~r   84 (480)
T COG5175          10 SEDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIR-----QNLNGRCPACRRKYDDENVRYVTLSPEELKMELAR   84 (480)
T ss_pred             cccccccCcccccccccccCCcccCCcccHHHHHHHHHHH-----hhccCCChHhhhhccccceeEEecCHHHHHHHHHh
Confidence            5667777999999999999999999999999999999995     57999999999999999999999999999777543


Q ss_pred             --HHHHhhhhcccCcccchhccCccccccccCEEEEeCCCCCCChHH---HHHHHhhhcCCcceeEEEEeecCCcccccc
Q 003485           82 --ERKMKSQKSKTKSSEGKKQQLSSVRVIQRNLVYIVGLPLNLGDED---LLQRREYFGQYGKVLKVSMSRTAAGVIQQF  156 (816)
Q Consensus        82 --~kk~K~qk~k~k~se~RK~~LanVRVIQrNLVYVvGLP~~IaeED---LLKk~EyFGQYGKI~KIvInrd~~g~~~q~  156 (816)
                        +||+++...|+.+-.+|| ||+++||||+|||||+||++.+++|+   +|+++|||||||+|.||+|++.....  ..
T Consensus        85 k~erk~rekerke~e~~nrk-hlsniRVvQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~--ns  161 (480)
T COG5175          85 KEERKMREKERKEAEGQNRK-HLSNIRVVQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSL--NS  161 (480)
T ss_pred             hhhhhccHHHHhhhhccccc-ccccceeeecceeEEecCCCCCCcccccccccchhhhhhccceeEEEeccccccc--cc
Confidence              444444444555567899 99999999999999999999999999   89999999999999999999876432  11


Q ss_pred             CCCceEEEEEeCCHHHHHHHHHHhcCCccCCeEEEEeecCCCccccccCCCCCCCCCCcccccCCCCCCCccHHHHHhhh
Q 003485          157 PNNTCSVYITYSKEEEAVRCIQSVHGFVLEGKSLKACFGTTKYCHAWLRNVPCTNPDCLYLHEVGSQEDSFTKDEIISAY  236 (816)
Q Consensus       157 ps~rgsAYVTFs~~EDA~rAIqaLNG~~LdGR~LRASfGTTKYCs~FLRg~~C~NpdCmYLHE~g~~~DsfTKeem~~~~  236 (816)
                      .....++||||.++|||++||+++||..+|||.|||+|||||||++||||++|+||+||||||.|++.|+|||+||....
T Consensus       162 t~~h~gvYITy~~kedAarcIa~vDgs~~DGr~lkatYGTTKYCtsYLRn~~CpNp~CMyLHEpg~e~Ds~tK~el~n~q  241 (480)
T COG5175         162 TASHAGVYITYSTKEDAARCIAEVDGSLLDGRVLKATYGTTKYCTSYLRNAVCPNPDCMYLHEPGPEKDSLTKDELCNSQ  241 (480)
T ss_pred             ccccceEEEEecchHHHHHHHHHhccccccCceEeeecCchHHHHHHHcCCCCCCCCeeeecCCCcccccccHHHHhhhh
Confidence            12346789999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             cc
Q 003485          237 TR  238 (816)
Q Consensus       237 ~~  238 (816)
                      +.
T Consensus       242 h~  243 (480)
T COG5175         242 HK  243 (480)
T ss_pred             hh
Confidence            43

>KOG2068 consensus MOT2 transcription factor [Transcription]	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

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

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

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

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

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

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

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

>smart00362 RRM_2 RNA recognition motif	Back alignment and domain information

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>PLN03120 nucleic acid binding protein; Provisional	Back alignment and domain information

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]	Back alignment and domain information

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

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family	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

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family	Back alignment and domain information

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

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

>smart00360 RRM RNA recognition motif	Back alignment and domain information

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family	Back alignment and domain information

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]	Back alignment and domain information

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor	Back alignment and domain information

>PLN03213 repressor of silencing 3; Provisional	Back alignment and domain information

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family	Back alignment and domain information

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

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]	Back alignment and domain information

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

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]	Back alignment and domain information

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

>smart00361 RRM_1 RNA recognition motif	Back alignment and domain information

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family	Back alignment and domain information

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>PLN03121 nucleic acid binding protein; Provisional	Back alignment and domain information

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family	Back alignment and domain information

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]	Back alignment and domain information

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]	Back alignment and domain information

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

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor	Back alignment and domain information

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]	Back alignment and domain information

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]	Back alignment and domain information

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG2068 consensus MOT2 transcription factor [Transcription]	Back alignment and domain information

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]	Back alignment and domain information

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]	Back alignment and domain information

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]	Back alignment and domain information

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]	Back alignment and domain information

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]	Back alignment and domain information

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]	Back alignment and domain information

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]	Back alignment and domain information

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]	Back alignment and domain information

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]	Back alignment and domain information

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]	Back alignment and domain information

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]	Back alignment and domain information

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]	Back alignment and domain information

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]	Back alignment and domain information

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]	Back alignment and domain information

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]	Back alignment and domain information

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes	Back alignment and domain information

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]	Back alignment and domain information

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]	Back alignment and domain information

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]	Back alignment and domain information

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]	Back alignment and domain information

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]	Back alignment and domain information

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]	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

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>PLN02189 cellulose synthase	Back alignment and domain information

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]	Back alignment and domain information

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []	Back alignment and domain information

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif	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

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

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation	Back alignment and domain information

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]	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

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]	Back alignment and domain information

>PLN02436 cellulose synthase A	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

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

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

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]	Back alignment and domain information

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

>KOG0226 consensus RNA-binding proteins [General function prediction only]	Back alignment and domain information

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]	Back alignment and domain information

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]	Back alignment and domain information

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]	Back alignment and domain information

>PLN02248 cellulose synthase-like protein	Back alignment and domain information

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

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]	Back alignment and domain information

>PLN02195 cellulose synthase A	Back alignment and domain information

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function	Back alignment and domain information

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

>KOG2177 consensus Predicted E3 ubiquitin ligase [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

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]	Back alignment and domain information

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

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]	Back alignment and domain information

>smart00184 RING Ring finger	Back alignment and domain information

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

>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A	Back alignment and domain information

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

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]	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

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]	Back alignment and domain information

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]	Back alignment and domain information

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit	Back alignment and domain information

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]	Back alignment and domain information

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]	Back alignment and domain information

>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit	Back alignment and domain information

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

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>PLN02400 cellulose synthase	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

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function	Back alignment and domain information

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

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

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]	Back alignment and domain information

>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]	Back alignment and domain information

>PF04641 Rtf2: Rtf2 RING-finger	Back alignment and domain information

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells	Back alignment and domain information

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)	Back alignment and domain information

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

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]	Back alignment and domain information

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]	Back alignment and domain information

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]	Back alignment and domain information

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons	Back alignment and domain information

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]	Back alignment and domain information

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

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

>PF10650 zf-C3H1: Putative zinc-finger domain; InterPro: IPR019607 This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger	Back alignment and domain information

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]	Back alignment and domain information

>COG5574 PEX10 RING-finger-containing 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

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes	Back alignment and domain information

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]	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

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

>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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		816
2cpi_A		111	Solution Structure Of The Rna Recognition Motif Of		1e-19
1ur6_B		52	Nmr Based Structural Model Of The Ubch5b-Cnot4 Comp		1e-10
1e4u_A		78	N-Terminal Ring Finger Domain Of Human Not-4 Length		4e-10

>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4 Length = 111

Back alignment and structure

Iteration: 1

Score = 95.1 bits (235), Expect = 1e-19, Method: Composition-based stats. Identities = 45/96 (46%), Positives = 69/96 (71%), Gaps = 2/96 (2%) Query: 105 VRVIQRNLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCSVY 164 VRV+Q+NLV++VGL L D ++L+R EYFG++GK+ KV ++ + + Q P + S Y Sbjct: 10 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGP--SASAY 67 Query: 165 ITYSKEEEAVRCIQSVHGFVLEGKSLKACFGTTKYC 200 +TY + E+A+R IQ V+ V++G++LKA GTTKYC Sbjct: 68 VTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYC 103

PyMOL of 2cpi

>pdb|1UR6|B Chain B, Nmr Based Structural Model Of The Ubch5b-Cnot4 Complex Length = 52

Back alignment and structure

>pdb|1E4U|A Chain A, N-Terminal Ring Finger Domain Of Human Not-4 Length = 78

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		816
2cpi_A		111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-35
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	1e-21
2e44_A		96	Insulin-like growth factor 2 mRNA binding protein	1e-10
3smz_A		284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-09
3smz_A		284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-05
3smz_A		284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-04
2a3j_A		127	U1 small nuclear ribonucleoprotein A; computationa	1e-08
1nu4_A		97	U1A RNA binding domain; RNA recognition motif, U1	1e-08
2la4_A		101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-08
1x5p_A		97	Negative elongation factor E; structure genomics,	2e-08
1s79_A		103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-08
1x4g_A		109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-08
2jvo_A		108	Nucleolar protein 3; nucleus, phosphorylation, rib	5e-08
2ghp_A		292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-07
2ghp_A		292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-05
2ghp_A		292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-04
1fje_B		175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-07
3s8s_A		110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-07
1x4e_A		85	RNA binding motif, single-stranded interacting pro	2e-07
2bz2_A		121	Negative elongation factor E; NELF E, RNA recognit	2e-07
2dgu_A		103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-07
2ywk_A		95	Putative RNA-binding protein 11; RRM-domain, struc	4e-07
2err_A		109	Ataxin-2-binding protein 1; protein-RNA complex, R	7e-07
3lqv_A		115	PRE-mRNA branch site protein P14; cysless mutant,	8e-07
2f3j_A		177	RNA and export factor binding protein 2; RRM domai	1e-06
2ytc_A		85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-06
2e5h_A		94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-06
3tyt_A		205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-06
3tyt_A		205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-04
2yh0_A		198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-06
2yh0_A		198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-04
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	2e-06
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	3e-04
2cpj_A		99	Non-POU domain-containing octamer-binding protein;	2e-06
3nmr_A		175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-06
3nmr_A		175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-05
1x5o_A		114	RNA binding motif, single-stranded interacting pro	3e-06
2cpd_A		99	Apobec-1 stimulating protein; RNA recognition moti	3e-06
2do4_A		100	Squamous cell carcinoma antigen recognized by T- c	3e-06
1qm9_A		198	Polypyrimidine tract-binding protein; ribonucleopr	4e-06
1qm9_A		198	Polypyrimidine tract-binding protein; ribonucleopr	4e-05
3pgw_A		282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04
3sde_A		261	Paraspeckle component 1; RRM, anti parallel right	8e-06
3egn_A		143	RNA-binding protein 40; RNA recognition motif (RRM	8e-06
2cq3_A		103	RNA-binding protein 9; RRM domain, structural geno	1e-05
2khc_A		118	Testis-specific RNP-type RNA binding protein; RRM,	1e-05
2cpx_A		115	Hypothetical protein FLJ11016; RRM domain, structu	1e-05
2cpz_A		115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-05
2kt5_A		124	RNA and export factor-binding protein 2; chaperone	1e-05
4a8x_A		88	RNA-binding protein with serine-rich domain 1; tra	1e-05
2cqc_A		95	Arginine/serine-rich splicing factor 10; RNA recog	2e-05
3ulh_A		107	THO complex subunit 4; nuclear protein, RNA bindin	2e-05
1rk8_A		165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-05
2do0_A		114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-05
1fxl_A		167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-05
1fxl_A		167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-04
2fy1_A		116	RNA-binding motif protein, Y chromosome, family 1	3e-05
2dnh_A		105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-05
3v4m_A		105	Splicing factor U2AF 65 kDa subunit; canonical RNA	3e-05
2adc_A		229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-05
2dgv_A		92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-05
2nlw_A		105	Eukaryotic translation initiation factor 3 subunit	3e-05
2dnp_A		90	RNA-binding protein 14; RRM domain, RBD, structura	4e-05
1wf1_A		110	RNA-binding protein RALY; structural genomics, RRM	4e-05
2xs2_A		102	Deleted in azoospermia-like; RNA binding protein-R	4e-05
2cpf_A		98	RNA binding motif protein 19; RNA recognition moti	4e-05
2dgt_A		92	RNA-binding protein 30; RRM domain, structural gen	4e-05
2cq0_A		103	Eukaryotic translation initiation factor 3 subunit	4e-05
1b7f_A		168	Protein (SXL-lethal protein), RNA (5'-R(PGPUP*UP	5e-05
1b7f_A		168	Protein (SXL-lethal protein), RNA (5'-R(PGPUP*UP	5e-04
2cq2_A		114	Hypothetical protein LOC91801; RRM domain, structu	5e-05
2hvz_A		101	Splicing factor, arginine/serine-rich 7; RRM, RNA	6e-05
1why_A		97	Hypothetical protein riken cDNA 1810017N16; RNA re	8e-05
2g4b_A		172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	8e-05
2g4b_A		172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	9e-05
2krb_A		81	Eukaryotic translation initiation factor 3 subunit	9e-05
2kxn_B		129	Transformer-2 protein homolog beta; SR protein, RR	1e-04
4f25_A		115	Polyadenylate-binding protein 1; RRM fold, transla	1e-04
2dnq_A		90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-04
3ue2_A		118	Poly(U)-binding-splicing factor PUF60; RNA recogni	1e-04
1oo0_B		110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-04
1x5s_A		102	Cold-inducible RNA-binding protein; structure geno	2e-04
2dnm_A		103	SRP46 splicing factor; RRM domain, RBD, structural	2e-04
3d2w_A		89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-04
1wf0_A		88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-04
1wg1_A		88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-04
1x4a_A		109	Splicing factor, arginine/serine-rich 1 (splicing	2e-04
1whw_A		99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-04
2kvi_A		96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-04
1h2v_Z		156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-04
1u6f_A		139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-04
3mdf_A		85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-04
2e5g_A		94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-04
1weo_A		93	Cellulose synthase, catalytic subunit (IRX3); stru	4e-04
2dit_A		112	HIV TAT specific factor 1 variant; structural geno	4e-04
1wex_A		104	Hypothetical protein (riken cDNA 2810036L13); stru	5e-04
2dnz_A		95	Probable RNA-binding protein 23; RNA recognition m	5e-04
2xnq_A		97	Nuclear polyadenylated RNA-binding protein 3; tran	5e-04
1p27_B		106	RNA-binding protein 8A; nuclear protein, mRNA spli	6e-04
2x1f_A		96	MRNA 3'-END-processing protein RNA15; transcriptio	6e-04
1x4h_A		111	RNA-binding protein 28; structural genomics, RRM d	6e-04
2ku7_A		140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	6e-04
2i2y_A		150	Fusion protein consists of immunoglobin G- binding	7e-04
1fjc_A		96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	8e-04
3r27_A		100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	8e-04
2jrs_A		108	RNA-binding protein 39; RNA binding motif of RBM39	8e-04
2voo_A		193	Lupus LA protein; RNA-binding protein, RNA recogni	8e-04
2cpe_A		113	RNA-binding protein EWS; RNA recognition motif, RR	9e-04
3ns6_A		100	Eukaryotic translation initiation factor 3 subuni;	9e-04

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111	Back alignment and structure

 Score =  128 bits (322), Expect = 5e-35
 Identities = 46/103 (44%), Positives = 71/103 (68%), Gaps = 2/103 (1%)

Query: 98  KKQQLSSVRVIQRNLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAAGVIQQFP 157
                +SVRV+Q+NLV++VGL   L D ++L+R EYFG++GK+ KV ++ + +    Q P
Sbjct: 3   SGSSGASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGP 62

Query: 158 NNTCSVYITYSKEEEAVRCIQSVHGFVLEGKSLKACFGTTKYC 200
             + S Y+TY + E+A+R IQ V+  V++G++LKA  GTTKYC
Sbjct: 63  --SASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYC 103

PyMOL of 2cpi

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

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96	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: 3h2u_B 3h2v_E Length = 284	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: 3h2u_B 3h2v_E Length = 284	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: 3h2u_B 3h2v_E Length = 284	Back alignment and structure

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127	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* ... Length = 97	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} Length = 101	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 Length = 97	Back alignment and structure

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103	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 Length = 109	Back alignment and structure

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108	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 Length = 292	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 Length = 292	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 Length = 292	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 Length = 175	Back alignment and structure

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110	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 Length = 85	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 Length = 103	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} Length = 95	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 Length = 109	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} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115	Back alignment and structure

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177	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} Length = 85	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} Length = 94	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 Length = 205	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 Length = 205	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 Length = 198	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 Length = 198	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 Length = 216	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 Length = 216	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 Length = 99	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 Length = 175	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 Length = 175	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 Length = 114	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 Length = 99	Back alignment and structure

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100	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 Length = 198	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 Length = 198	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 Length = 282	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

>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

>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 Length = 261	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} Length = 143	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 Length = 103	Back alignment and structure

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118	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 Length = 115	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 Length = 115	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} Length = 124	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} Length = 88	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 Length = 95	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 Length = 107	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 Length = 165	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} Length = 114	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 Length = 167	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 Length = 167	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} Length = 116	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 Length = 105	Back alignment and structure

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105	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 Length = 229	Back alignment and structure

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92	Back alignment and structure

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105	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} Length = 90	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 Length = 110	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 Length = 102	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 Length = 98	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} Length = 92	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 Length = 103	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 Length = 168	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 Length = 168	Back alignment and structure

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114	Back alignment and structure

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101	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 Length = 97	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 Length = 172	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 Length = 172	Back alignment and structure

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81	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 Length = 129	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 Length = 115	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} Length = 90	Back alignment and structure

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} PDB: 3us5_A 2dny_A Length = 118	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* Length = 110	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 Length = 102	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} Length = 103	Back alignment and structure

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89	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 Length = 88	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 Length = 88	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 Length = 109	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 Length = 99	Back alignment and structure

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96	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 Length = 156	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 Length = 139	Back alignment and structure

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85	Back alignment and structure

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94	Back alignment and structure

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1 Length = 93	Back alignment and structure

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112	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 Length = 104	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} Length = 95	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 Length = 97	Back alignment and structure

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106	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 Length = 96	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 Length = 111	Back alignment and structure

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140	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 Length = 150	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 Length = 96	Back alignment and structure

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100	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} Length = 108	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 Length = 193	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 Length = 113	Back alignment and structure

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

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		816
d2cpia1		89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	8e-15
d1ur6b_		52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	1e-10
d1no8a_		78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	4e-09
d1cvja1		80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	8e-09
d1b7fa2		85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-08
d2cpea1		101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	5e-08
d1b7fa1		82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-07
d1rk8a_		88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-07
d2cpja1		86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-07
d1g25a_		65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	2e-07
d1h2vz_		93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-07
d1o0pa_		104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-07
d1x5ta1		83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-07
d1cvja2		89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	6e-07
d2cqca1		83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-06
d2f9da1		114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-06
d1x5ua1		93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-06
d1wf2a_		98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-06
d1fxla2		85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	4e-06
d2cqba1		89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-06
d1x4ga1		96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	5e-06
d1nu4a_		91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	5e-06
d2cqia1		90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-06
d2u2fa_		85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	9e-06
d1whwa_		99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	9e-06
d2cpha1		94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-05
d1x4ea1		72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-05
d1uawa_		77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-05
d2cq0a1		90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-05
d1fxla1		82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-05
d1vyxa_		60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	4e-05
d1x4aa1		95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	7e-05
d2dita1		99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	8e-05
d1x0fa1		75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-04
d2cpza1		102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-04
d2ghpa3		86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	3e-04
d1chca_		68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	4e-04
d1u2fa_		90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.001
d1x4ba1		103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	0.001
d2cpxa1		102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	0.002
d2baya1		56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	0.002
d1x5oa1		101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	0.002
d1jm7a_		103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	0.002
d2disa1		96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	0.002
d1jm7b_		97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	0.002
d1iyma_		55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	0.003
d3dplr1		88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	0.004
d1wima_		94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	0.004

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.3 bits (166), Expect = 8e-15
 Identities = 40/90 (44%), Positives = 65/90 (72%), Gaps = 2/90 (2%)

Query: 103 SSVRVIQRNLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCS 162
           +SVRV+Q+NLV++VGL   L D ++L+R EYFG++GK+ KV ++ + +    Q P  + S
Sbjct: 1   ASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGP--SAS 58

Query: 163 VYITYSKEEEAVRCIQSVHGFVLEGKSLKA 192
            Y+TY + E+A+R IQ V+  V++G++LKA
Sbjct: 59  AYVTYIRSEDALRAIQCVNNVVVDGRTLKA 88

PyMOL of d2cpia1

>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

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78	Back information, alignment and structure

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80	Back information, alignment and structure

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85	Back information, alignment and structure

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101	Back information, alignment and structure

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82	Back information, alignment and structure

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88	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]} Length = 86	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

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93	Back information, alignment and structure

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104	Back information, alignment and structure

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83	Back information, alignment and structure

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89	Back information, alignment and structure

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83	Back information, alignment and structure

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114	Back information, alignment and structure

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93	Back information, alignment and structure

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98	Back information, alignment and structure

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85	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]} Length = 89	Back information, alignment and structure

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96	Back information, alignment and structure

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91	Back information, alignment and structure

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

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85	Back information, alignment and structure

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99	Back information, alignment and structure

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94	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]} Length = 72	Back information, alignment and structure

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77	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]} Length = 90	Back information, alignment and structure

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82	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]} Length = 60	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]} Length = 95	Back information, alignment and structure

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99	Back information, alignment and structure

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75	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]} Length = 102	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]} 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

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90	Back information, alignment and structure

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103	Back information, alignment and structure

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102	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]} Length = 56	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]} Length = 101	Back information, alignment and structure

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103	Back information, alignment and structure

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96	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

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55	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]} Length = 88	Back information, alignment and structure

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]} Length = 94	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		816
d2cpia1		89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.84
d1rk8a_		88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.6
d1u6fa1		139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.57
d2cq0a1		90	Eukaryotic translation initiation factor 3 subunit	99.57
d2cqba1		89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.56
d2cq3a1		93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.55
d1whwa_		99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.54
d1fxla1		82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.54
d1x5ua1		93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.54
d1b7fa1		82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.53
d1h2vz_		93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.53
d2cpza1		102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.53
d2ghpa3		86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.53
d2cqia1		90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.52
d1cvja1		80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.51
d1no8a_		78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.51
d1b7fa2		85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.51
d1p1ta_		104	Cleavage stimulation factor, 64 kda subunit {Human	99.51
d1fxla2		85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.51
d2f9da1		114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.5
d2cpha1		94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.5
d1x5sa1		90	Cold-inducible RNA-binding protein {Human (Homo sa	99.5
d2cpja1		86	Non-POU domain-containing octamer-binding protein,	99.5
d1cvja2		89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.5
d2cpfa1		85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.49
d2u2fa_		85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.49
d2cpea1		101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.48
d1x4ha1		98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.48
d1x4ba1		103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.48
d1whxa_		111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.47
d2cqda1		103	RNA-binding region containing protein 1 {Human (Ho	99.47
d1x4ga1		96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.47
d1x5ta1		83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.47
d2cqca1		83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.47
d1nu4a_		91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.47
d2adca1		109	Polypyrimidine tract-binding protein {Human (Homo	99.45
d2cq4a1		101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.45
d2cqga1		90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.44
d1x4aa1		95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.43
d2cpxa1		102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.43
d2ghpa1		81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.43
d1x5oa1		101	RNA-binding motif, single-stranded-interacting pro	99.42
d1l3ka1		84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.41
d2bz2a1		79	Negative elongation factor E, NELF-E {Human (Homo	99.41
d1wf2a_		98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.41
d1wi6a1		75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.39
d1uawa_		77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.39
d2adca2		88	Polypyrimidine tract-binding protein {Human (Homo	99.39
d2adba1		108	Polypyrimidine tract-binding protein {Human (Homo	99.37
d1fjca_		96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.36
d1hd0a_		75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.36
d2cpda1		86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.36
d3begb1		87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.36
d1wg1a_		88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.36
d1x4ea1		72	RNA-binding motif, single-stranded-interacting pro	99.35
d2cqha1		80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.35
d1zh5a2		85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.35
d1fjeb1		91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.35
d2b0ga1		83	Splicesomal U1A protein {Drosophila melanogaster [	99.34
d2msta_		75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.34
d1l3ka2		79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.34
d1wexa_		104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.34
d1u1qa_		183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.34
d2ghpa2		75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.34
d1weza_		102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.33
d2disa1		96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.32
d1wi8a_		104	Eukaryotic translation initiation factor 4B {Human	99.32
d1whya_		97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.32
d1x4fa1		99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.31
d2cqpa1		86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.31
d1wf0a_		88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.3
d1wg4a_		98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.29
d1wg5a_		104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.28
d1weya_		104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.28
d2cq1a1		88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.26
d2cpya1		103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.26
d1x0fa1		75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.26
d2dita1		99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.22
d1x4da1		89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.21
d1wela1		112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.15
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	99.13
d1owxa_		113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.07
d1o0pa_		104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.02
d1u2fa_		90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.98
d1u1qa_		183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.96
d1wwha1		81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.96
d2cq2a1		101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	98.94
d1ur6b_		52	Not-4 N-terminal RING finger domain {Human (Homo s	98.55
d1g25a_		65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	97.6
d1jm7b_		97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	97.48
d1vyxa_		60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	97.42
d1v87a_		114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	97.29
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	97.16
d1chca_		68	Immediate early protein, IEEHV {Equine herpesvirus	96.82
d1jm7a_		103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	96.79
d1fbva4		79	CBL {Human (Homo sapiens) [TaxId: 9606]}	96.51
d1ufwa_		95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.07
d1rmda2		86	V(D)J recombination activating protein 1 (RAG1), d	95.81
d3dplr1		88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	95.77
d1wima_		94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	95.67
d1weoa_		93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	95.5
d1bora_		56	Acute promyelocytic leukaemia proto-oncoprotein PM	95.5
d2dgxa1		73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	95.48
d1uw4a_		91	RNA processing protein UPF3x, RRM domain {Human (H	95.12
d1wgma_		98	Ubiquitin conjugation factor E4A {Human (Homo sapi	94.52
d1t1ha_		78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	94.43
d2c2la2		80	STIP1 homology and U box-containing protein 1, STU	94.37
d2baya1		56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	92.96
d1whva_		100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	91.41

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=8.3e-21  Score=155.01  Aligned_cols=89  Identities=43%  Similarity=0.764  Sum_probs=80.2

Q ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEECCHHHHHHHHHHHCC
Q ss_conf             66564446779995899999937887778631478542699994227864344689960899993999999999999559
Q 003485          103 SSVRVIQRNLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCSVYITYSKEEEAVRCIQSVHG  182 (816)
Q Consensus       103 anVRVIQKNLVYVvGLP~~IAeEDLLk~~EyFGQYGKI~KIvIsrd~~g~~~q~p~~rgsAYVTFs~~EDA~kAIqaLDG  182 (816)
                      ++|||+|+|+|||.|||+++++|+|++..|+|++||+|.+|.|.+++.+..  .+..+|+|||+|.+.++|.+||+.|||
T Consensus         1 ~~~Rviq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~--~~~~~g~aFV~f~~~~~A~~Ai~~lng   78 (89)
T d2cpia1           1 ASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAG--SQGPSASAYVTYIRSEDALRAIQCVNN   78 (89)
T ss_dssp             SCCCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCS--SSCCCEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCEEEEECCEEEEECCCCCCCHHHHHHHHHHHCCCCCCEEEEEEECCCCCC--CCCCCEEEEEECCCCHHHHHHHHHHCC
T ss_conf             965598268899979897638789998898763558825877720267687--777653799851541229999998589


Q ss_pred             CCCCCEEEEEE
Q ss_conf             83399089996
Q 003485          183 FVLEGKSLKAC  193 (816)
Q Consensus       183 s~LdGRvLRAS  193 (816)
                      ..++||+||||
T Consensus        79 ~~~~gr~lkvS   89 (89)
T d2cpia1          79 VVVDGRTLKAS   89 (89)
T ss_dssp             EEETTEEEEEE
T ss_pred             CEECCEEEEEC
T ss_conf             99999788879

PyMOL of d2cpia1

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

>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

>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

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

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {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

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}	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

>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

>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

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {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

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}	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

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {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

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {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

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {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

>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

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

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

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

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {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

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {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

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {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

>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

>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

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {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

>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

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {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

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {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

>d1uawa_ d.58.7.1 (A:) Musashi-1 {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

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {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

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}	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

>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

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

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {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

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}	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

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

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

>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

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {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

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {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

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	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

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {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

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

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {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

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {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

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {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

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

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {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

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}	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

>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

>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

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

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

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {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

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {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

>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

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

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	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

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {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

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]}	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

>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

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure