Citrus Sinensis ID: 009947

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--

MSRYLFMVSLMQQLNQELEQDEARGFRHQVGSPVTNSPPGTWAQFGSPVERNPLHAFSKSPGLGTLSPINSNPLHAFSKSTGLATPTPVNSNHLPGLASILPPHLSNTGKIAPIGKDQGRANQTNHMFSNSASLQGAAYQHSQSFPEQKLSASPGPKSPFGESNSNSSGVGTLSGPQFLWGSPPPYSERSSSSAWPTSSVGHPFSSSGQGQGFPYGSRHGSFIGSHHQHHVGSAPSGVSLDRNFGFFPESPETSFTNPVPLGGMGLSRNNAGYMMNVGGRVGVGLPLNVTDNGSPSLRMMSFPRHGPLFFGNGSYSGLGTTSNEAFTERGRTRRVENCGSQVDSKKQYQLDLDKIISGEDTRTTLMIKNIPNKYTSKMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMVSPSHIISFYEAFNGKKWEKFNSEKVASLAYARIQGQAALVTHFQNSSLMNEDKRCRPIVFHSEGQETSDQEALLSSNLNIFIRQPDGSYSGDSLESLNGYPDEKPEKI

cccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccHHHHHHcccccEEEEEEcccccccHHHHHHHHHHHccccccEEEEcccccccccEEEEEEEcccHHHHHHHHHHHccccccccccccEEEEEEEEcccHHHHHHHHccccccccccccccEEEEccccccccccccccccccccccccccccccccccccccccccccccc

ccHHHHHHHHHHHccHHHHHHccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcHHHHHccccccEEEEEEcccccccHHHHHHHHHHHccccEEEEEEEEcccccccEEEEEEEcccHHHHHHHHHHHccccccccccHHHEEEEEHHHccHHHHHHHHccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccc

MSRYLFMVSLMQQLNQELEQDEArgfrhqvgspvtnsppgtwaqfgspvernplhafskspglgtlspinsnplhafskstglatptpvnsnhlpglasilpphlsntgkiapigkdqgranqtnhmfsnsaslqgaayqhsqsfpeqklsaspgpkspfgesnsnssgvgtlsgpqflwgspppyserssssawptssvghpfsssgqgqgfpygsrhgsfigshhqhhvgsapsgvsldrnfgffpespetsftnpvplggmglsrnnagymmnvggrvgvglplnvtdngspslrmmsfprhgplffgngsysglgttsneaftergrtrrvencgsqvdskkqyqldldkiisgedtrtTLMIKNIPNKYTSKMLLAAIDEnhrgtydflylpidfknkcnvGYAFINMVSPSHIISFYEAfngkkwekfNSEKVASLAYARIQGQAALVTHFqnsslmnedkrcrpivfhsegqetsdQEALLSSNlnifirqpdgsysgdsleslngypdekpeki

MSRYLFMVSLMQQLNQELEQDEARGFRHQVGSPVTNSPPGTWAQFGSPVERNPLHAFSKSPGLGTLSPINSNPLHAFSKSTGLATPTPVNSNHLPGLASILPPHLSNTGKIAPIGKDQGRANQTNHMFSNSASLQGAAYQHSQSFPEQKLSASPGPKSPFGESNSNSSGVGTLSGPQFLWGSPPPYSERSSSSAWPTSSVGHPFSSSGQGQGFPYGSRHGSFIGSHHQHHVGSAPSGVSLDRNFGFFPESPETSFTNPVPLGGMGLSRNNAGYMMNVGGRVGVGLPLNVTDNGSPSLRMMSFPRHGPLFFGNGSYSGLGTTSNeaftergrtrrvencgsqvdskkqyqldldkiisgedtrttlmiknipnkYTSKMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMVSPSHIISFYEAFNGKKWEKFNSEKVASLAYARIQGQAALVTHFQNSSLMNEDKRCRPIVFHSEGQETSDQEALLSSNLNIFIRQPdgsysgdsleslngypdekpeki

MSRYLFMVSLMQQLNQELEQDEARGFRHQVGSPVTNSPPGTWAQFGSPVERNPLHAFSKSPGLGTLSPINSNPLHAFSKSTGLATPTPVNSNHLPGLASILPPHLSNTGKIAPIGKDQGRANQTNHMFSNSASLQGAAYQHSQSFPEQKLSASPGPKSPFGESNSNSSGVGTLSGPQFLWGspppyserssssawpTSSVGHPFSSSGQGQGFPYGSRHGSFIGSHHQHHVGSAPSGVSLDRNFGFFPESPETSFTNPVPLGGMGLSRNNAGYMMNVGGRVGVGLPLNVTDNGSPSLRMMSFPRHGPLFFGNGSYSGLGTTSNEAFTERGRTRRVENCGSQVDSKKQYQLDLDKIISGEDTRTTLMIKNIPNKYTSKMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMVSPSHIISFYEAFNGKKWEKFNSEKVASLAYARIQGQAALVTHFQNSSLMNEDKRCRPIVFHSEGQETSDQEALLSSNLNIFIRQPDGSYSGDSLESLNGYPDEKPEKI

****LFMV***************************************************************************************************************************************************************************************************************************************************************MGLSRNNAGYMMNVGGRVGVGLPLNVT*************RHGPLFFGNGSY********************************YQLDLDKIISGEDTRTTLMIKNIPNKYTSKMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMVSPSHIISFYEAFNGKKWEKFNSEKVASLAYARIQGQAALVTHFQNSSLM****RCRPIVF******************NIFI**************************

*SRYLFMVSLM*************************************************************************************************************************************************************************************************************************************************************************************************************************************************QLDLDKIISGEDTRTTLMIKNIPNKYTSKMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMVSPSHIISFYEAFNGKKWEKFNSEKVASLAYARIQGQAALVTHFQNSSLMNEDKRCRPIVFHS**********************************************

MSRYLFMVSLMQQLNQELEQDEARGFRHQVGSPVTNSPPGTWAQFGSPVERNPLHAFSKSPGLGTLSPINSNPLHAFSKSTGLATPTPVNSNHLPGLASILPPHLSNTGKIAPIGKDQGRANQTNHMFSNSAS*************************************GTLSGPQFLWGS***************************GQGFPYGSRHGSFIGSHHQHHVGSAPSGVSLDRNFGFFPESPETSFTNPVPLGGMGLSRNNAGYMMNVGGRVGVGLPLNVTDNGSPSLRMMSFPRHGPLFFGNGSYSGLGTTSNEAFTER****************KQYQLDLDKIISGEDTRTTLMIKNIPNKYTSKMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMVSPSHIISFYEAFNGKKWEKFNSEKVASLAYARIQGQAALVTHFQNSSLMNEDKRCRPIVFHSEGQETSDQEALLSSNLNIFIRQPDGSYSGDSLESLNGYPDEKPEKI

*SRYLFMVSLMQQLNQELEQDEARGFRHQVGSPVTNSPPGTWAQFGSPVERNPLHAFSKSPGLGTLSPINSNPLHAFSKSTGLATPTPVNSNHLPGLASILPPHLSNTGKIAPIGKDQGRANQTNHMFSNSASLQGAAYQHSQSFPEQKLSASPGPKSPFGESNSNSSGVGTLSGPQFLWGSPPPYSERSSSSAWPTSSVGHPFSSSGQGQGFPYGSRHGSFIGSHHQHHVGSAPSGVSLDRNFGFFPESPETSFTNPVPLGGMGLSRNNAGYMMNVGGRVGVGLPLNVTDNGSPSLRMMSFPRHGPLFFGNGSYSGLGT************************KKQYQLDLDKIISGEDTRTTLMIKNIPNKYTSKMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMVSPSHIISFYEAFNGKKWEKFNSEKVASLAYARIQGQAALVTHFQNSSLMNEDKRCRPIVFHSE*********************************************

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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		522	2.2.26 [Sep-21-2011]
Q6ZI17		848	Protein MEI2-like 2 OS=Or	yes	no	0.865	0.533	0.525	1e-137
Q8VWF5		800	Protein MEI2-like 5 OS=Ar	yes	no	0.860	0.561	0.496	1e-107
Q9SVV9		759	Protein MEI2-like 3 OS=Ar	no	no	0.741	0.509	0.476	2e-98
Q6EQX3		811	Protein MEI2-like 5 OS=Or	no	no	0.829	0.533	0.434	4e-96
Q9SJG8		843	Protein MEI2-like 2 OS=Ar	no	no	0.856	0.530	0.419	3e-88
Q64M78		1001	Protein MEI2-like 4 OS=Or	no	no	0.854	0.445	0.398	2e-75
Q9LYN7		907	Protein MEI2-like 4 OS=Ar	no	no	0.538	0.309	0.517	9e-70
Q75M35		955	Protein MEI2-like 3 OS=Or	no	no	0.454	0.248	0.531	3e-68
Q8W4I9		915	Protein MEI2-like 1 OS=Ar	no	no	0.538	0.307	0.505	6e-68
P08965		750	Meiosis protein mei2 OS=S	yes	no	0.247	0.172	0.550	1e-36

>sp\|Q6ZI17\|OML2_ORYSJ Protein MEI2-like 2 OS=Oryza sativa subsp. japonica GN=ML2 PE=2 SV=1	Back alignment and function desciption

 Score =  488 bits (1256), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 268/510 (52%), Positives = 328/510 (64%), Gaps = 58/510 (11%)

Query: 9   SLMQQLNQELEQDEARGFRH-QVGSPVTNSPPGTWAQFGSPVERNPLHAFSKSPGLGTLS 67
           +LMQQL  +++QDE R +R   VGSP+ +SPPG WAQ+ SP + N L AF+ SP    +S
Sbjct: 361 NLMQQLGHDIDQDEPRSYRIPHVGSPIASSPPGAWAQYSSPTDNNLLQAFNASPTGNGMS 420

Query: 68  PINSNPLHAFSKSTGLATPTPVNSNHLPGLASILPPHL-SNTGKIAPIGKDQGRANQTNH 126
           PI                               +PP L SN  KIAPIGKD   + + + 
Sbjct: 421 PIG------------------------------MPPSLISNAVKIAPIGKDSNWS-KYDK 449

Query: 127 MFSNSASLQGAAYQHSQSFPEQKLSASPGPKSPFGESNSNSSGVGTLSGPQFLWGSPPPY 186
           +FSN+    GAA+QHS S+ + K             S   SS  GTL+GP+FLWGSP PY
Sbjct: 450 VFSNNNQPHGAAFQHSHSYQDHK-------------SEHMSSSPGTLTGPEFLWGSPKPY 496

Query: 187 SERSSSSAWPTSSVGH--PFSSSGQGQGFPYGSRHGSFIGSH---HQHHVGSAPSGVSLD 241
           SE + S  W   ++GH  P ++  QGQG  YG R  S  GS    H HHVGSAPSG   +
Sbjct: 497 SEHAQSPIWRPPAIGHAIPSNTRSQGQGLLYGGRQASLFGSQDQLHHHHVGSAPSGAPFE 556

Query: 242 RNFGFFPESPETSFTNPVP---LGGMGLSRNNAGYMMNVGGRVGV----GLPLNVTDNGS 294
            +FGF PESPETS+ N V    +G +G  RN  G M+N+  R  V     L  N++DN S
Sbjct: 557 SHFGFLPESPETSYMNQVRFGNIGNIGSGRNGTGLMLNMAARASVNPVSALSGNMSDNNS 616

Query: 295 PSLRMMSFPRHGPLFFGNGSYSGLGTTSNEAFTERGRTRRVENCGSQVDSKKQYQLDLDK 354
            S R +  PR G  F+GN +Y G G+   +   ERGR RRV++   Q DSKKQYQLDL+K
Sbjct: 617 SSFRPILSPRLGQSFYGNPTYQGPGSFGLDNSIERGRNRRVDSSVFQADSKKQYQLDLEK 676

Query: 355 IISGEDTRTTLMIKNIPNKYTSKMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMV 414
           I  G+DTRTTLMIKNIPNKYTSKMLLAAIDE H+GTYDF YLPIDFKNKCNVGYAFINM+
Sbjct: 677 IRKGDDTRTTLMIKNIPNKYTSKMLLAAIDEFHKGTYDFFYLPIDFKNKCNVGYAFINMI 736

Query: 415 SPSHIISFYEAFNGKKWEKFNSEKVASLAYARIQGQAALVTHFQNSSLMNEDKRCRPIVF 474
           SP HI+SFY+AFNGKKWEKFNSEKVASLAYARIQG+ AL++HFQNSSLMNEDKRCRPI+F
Sbjct: 737 SPVHIVSFYQAFNGKKWEKFNSEKVASLAYARIQGRTALISHFQNSSLMNEDKRCRPILF 796

Query: 475 HSEGQETSDQEALLSSNLNIFIRQPDGSYS 504
           HS G +  +QE    + + I +   DG+ +
Sbjct: 797 HSNGPDAGNQEPFPINGICIHMPLEDGAIA 826

Probable RNA-binding protein that may play a role in growth regulation.
Oryza sativa subsp. japonica (taxid: 39947)

>sp\|Q8VWF5\|AML5_ARATH Protein MEI2-like 5 OS=Arabidopsis thaliana GN=ML5 PE=1 SV=1	Back alignment and function description

>sp\|Q9SVV9\|AML3_ARATH Protein MEI2-like 3 OS=Arabidopsis thaliana GN=ML3 PE=2 SV=2	Back alignment and function description

>sp\|Q6EQX3\|OML5_ORYSJ Protein MEI2-like 5 OS=Oryza sativa subsp. japonica GN=ML5 PE=2 SV=1	Back alignment and function description

>sp\|Q9SJG8\|AML2_ARATH Protein MEI2-like 2 OS=Arabidopsis thaliana GN=ML2 PE=2 SV=2	Back alignment and function description

>sp\|Q64M78\|OML4_ORYSJ Protein MEI2-like 4 OS=Oryza sativa subsp. japonica GN=ML4 PE=2 SV=1	Back alignment and function description

>sp\|Q9LYN7\|AML4_ARATH Protein MEI2-like 4 OS=Arabidopsis thaliana GN=ML4 PE=1 SV=1	Back alignment and function description

>sp\|Q75M35\|OML3_ORYSJ Protein MEI2-like 3 OS=Oryza sativa subsp. japonica GN=ML3 PE=2 SV=2	Back alignment and function description

>sp\|Q8W4I9\|AML1_ARATH Protein MEI2-like 1 OS=Arabidopsis thaliana GN=ML1 PE=1 SV=1	Back alignment and function description

>sp\|P08965\|MEI2_SCHPO Meiosis protein mei2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=mei2 PE=1 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		522
359485142		842	PREDICTED: protein MEI2-like 2-like [Vit	0.927	0.574	0.766	0.0
224082554		741	predicted protein [Populus trichocarpa]	0.942	0.663	0.739	0.0
449481207		846	PREDICTED: protein MEI2-like 2-like [Cuc	0.931	0.574	0.702	0.0
449444985		846	PREDICTED: protein MEI2-like 2-like [Cuc	0.931	0.574	0.700	0.0
224066573		763	predicted protein [Populus trichocarpa]	0.835	0.571	0.724	0.0
356567420		857	PREDICTED: protein MEI2-like 2-like [Gly	0.936	0.570	0.691	0.0
356526987		856	PREDICTED: protein MEI2-like 2-like [Gly	0.932	0.568	0.677	0.0
255586946		779	RNA-binding protein, putative [Ricinus c	0.856	0.573	0.701	0.0
47834689		856	AML1 [Medicago truncatula]	0.932	0.568	0.661	0.0
225463378		860	PREDICTED: protein MEI2-like 2-like [Vit	0.934	0.567	0.633	0.0

>gi\|359485142\|ref\|XP_002279792.2\| PREDICTED: protein MEI2-like 2-like [Vitis vinifera]	Back alignment and taxonomy information

 Score =  786 bits (2029), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 390/509 (76%), Positives = 419/509 (82%), Gaps = 25/509 (4%)

Query: 9   SLMQQLNQELEQDEARGFRHQVGSPVTNSPPGTWAQFGSPVERNPLHAFSKSPGLGTLSP 68
           +LMQQL+QELEQDEAR FRH VGSPVTNSPPG WA F                     SP
Sbjct: 351 NLMQQLSQELEQDEARSFRHHVGSPVTNSPPGNWAAF---------------------SP 389

Query: 69  INSNPLHAFSKSTGLATPTPVNSNHLPGLASILPPHLSNTGKIAPIGKDQGRANQTNHMF 128
           +  NPL A+S S GL   +P+NSNHLPGLASILPPH+SN+ KIAPIGKDQGR N  N +F
Sbjct: 390 VEHNPLQAYSHSPGLGNISPINSNHLPGLASILPPHISNSVKIAPIGKDQGRVNHVNQVF 449

Query: 129 SNSASLQGAAYQHSQSFPEQKLSASPGPKSPFGESNSNSSGVGTLSGPQFLWGSPPPYSE 188
           +N+   QGAAYQ S S PEQKLSASPGP S  GESNSNSSG+GTLSGPQFLWGSP PYSE
Sbjct: 450 TNAKPTQGAAYQISHSVPEQKLSASPGPISSLGESNSNSSGIGTLSGPQFLWGSPTPYSE 509

Query: 189 RSSSSAWPTSSVGHPFSSSGQGQGFPYGSRHGSFIGSHHQHHVGSAPSGVSLDRNFGFFP 248
           R +SSAWPTSSVGHPF SSGQGQGFPY ++HGSF+GSH  HHVGSAPSGV LDR+FG+FP
Sbjct: 510 RPNSSAWPTSSVGHPFVSSGQGQGFPYSNQHGSFLGSHQHHHVGSAPSGVPLDRHFGYFP 569

Query: 249 ESPETSFTNPVPLGGMGLSRNNAGYMMNVGGRV----GVGLPLNVTDNGSPSLRMMSFPR 304
           ESPETSF +PV  GGMGLSR+N  + MNVG R     GV LP N+T+NG PS RM+S PR
Sbjct: 570 ESPETSFMSPVTFGGMGLSRSNGNFAMNVGARAAINTGVALPGNMTENGLPSFRMLSLPR 629

Query: 305 HGPLFFGNGSYSGLGTTSNEAFTERGRTRRVENCGSQVDSKKQYQLDLDKIISGEDTRTT 364
           HGP F GNG+Y   G TSNE   ERGRTRRVEN G+Q+DSKKQYQLDLDKIISGEDTRTT
Sbjct: 630 HGPPFLGNGTYPVSGVTSNEVLAERGRTRRVENSGNQIDSKKQYQLDLDKIISGEDTRTT 689

Query: 365 LMIKNIPNKYTSKMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMVSPSHIISFYE 424
           LMIKNIPNKYTSKMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMVSPSHII FYE
Sbjct: 690 LMIKNIPNKYTSKMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMVSPSHIIPFYE 749

Query: 425 AFNGKKWEKFNSEKVASLAYARIQGQAALVTHFQNSSLMNEDKRCRPIVFHSEGQETSDQ 484
           AFNGKKWEKFNSEKVASLAYARIQG+AALVTHFQNSSLMNEDKRCRPI+FHSEGQET DQ
Sbjct: 750 AFNGKKWEKFNSEKVASLAYARIQGKAALVTHFQNSSLMNEDKRCRPILFHSEGQETVDQ 809

Query: 485 EALLSSNLNIFIRQPDGSYSGDSLESLNG 513
           E   S NLNI IRQPDGSYSGDSLES  G
Sbjct: 810 EPFASGNLNICIRQPDGSYSGDSLESPKG 838

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224082554\|ref\|XP_002306739.1\| predicted protein [Populus trichocarpa] gi\|222856188\|gb\|EEE93735.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449481207\|ref\|XP_004156114.1\| PREDICTED: protein MEI2-like 2-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449444985\|ref\|XP_004140254.1\| PREDICTED: protein MEI2-like 2-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|224066573\|ref\|XP_002302143.1\| predicted protein [Populus trichocarpa] gi\|222843869\|gb\|EEE81416.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356567420\|ref\|XP_003551918.1\| PREDICTED: protein MEI2-like 2-like [Glycine max]	Back alignment and taxonomy information

>gi\|356526987\|ref\|XP_003532096.1\| PREDICTED: protein MEI2-like 2-like [Glycine max]	Back alignment and taxonomy information

>gi\|255586946\|ref\|XP_002534073.1\| RNA-binding protein, putative [Ricinus communis] gi\|223525900\|gb\|EEF28317.1\| RNA-binding protein, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|47834689\|gb\|AAT38998.1\| AML1 [Medicago truncatula]	Back alignment and taxonomy information

>gi\|225463378\|ref\|XP_002271605.1\| PREDICTED: protein MEI2-like 2-like [Vitis vinifera]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		522
TAIR\|locus:2013583		800	ML5 "MEI2-like protein 5" [Ara	0.789	0.515	0.489	1.3e-98
TAIR\|locus:2117706		759	ML3 "MEI2-like 3" [Arabidopsis	0.421	0.289	0.610	6.4e-85
TAIR\|locus:2045605		843	ML2 "MEI2-like 2" [Arabidopsis	0.835	0.517	0.423	8.2e-83
TAIR\|locus:2156166		915	ML1 "MEI2-like protein 1" [Ara	0.553	0.315	0.501	2e-71
TAIR\|locus:2182885		907	ML4 "MEI2-like 4" [Arabidopsis	0.536	0.308	0.518	2.1e-68
POMBASE\|SPAC27D7.03c		750	mei2 "RNA-binding protein invo	0.272	0.189	0.514	1.1e-36
GENEDB_PFALCIPARUM\|PFF1125c		427	PFF1125c "RNA-binding protein	0.279	0.341	0.4	1.3e-25
UNIPROTKB\|C6KT70		427	PFF1125c "RNA-binding protein	0.279	0.341	0.4	1.3e-25
TAIR\|locus:2090350		615	TEL1 "terminal EAR1-like 1" [A	0.204	0.173	0.434	1.1e-24
TAIR\|locus:2008530		527	TEL2 "terminal EAR1-like 2" [A	0.220	0.218	0.446	2.7e-20

TAIR\|locus:2013583 ML5 "MEI2-like protein 5" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 979 (349.7 bits), Expect = 1.3e-98, P = 1.3e-98
 Identities = 211/431 (48%), Positives = 272/431 (63%)

Query:    67 SPINSNPLHAFSKSTGLATPTPVNSNHLPGLASILPPHLSNTGKIAPIGKDQGRANQTNH 126
             SP+  +PL +    + +   +P  + HL GLAS L      + K+APIG+ Q  +N    
Sbjct:   370 SPVEGSPLQSVLSRSPVFGLSPTRNGHLSGLASALNSQ-GPSSKLAPIGRGQIGSNG--- 425

Query:   127 MFSNSASLQGAAYQHSQSFPEQKLSAS-PGPKSPFGESNSNSSGVGTLSGPQFLWGXXXX 185
              F  S+ L          F E K+     G  SP G   SN  G+ TLSG +FLWG    
Sbjct:   426 -FQQSSHL----------FQEPKMDNKYTGNLSPSGPLISNGGGIETLSGSEFLWGSPNA 474

Query:   186 XXXXXXXXXXXTSSVGHPFSSSGQGQGFPYGSRHGSFIGSHHQHHVGSAPSGVSLDRNFG 245
                        TSS G+P  S+   +  P+  +H +   SHH  HVGSAPSGV L+++FG
Sbjct:   475 RSEPSSSSVWSTSSTGNPLFSTRVDRSVPFPHQHQNQSRSHHHFHVGSAPSGVPLEKHFG 534

Query:   246 FFPESPETS-FTNPVPLGGM-GLSRNNAGYMMNVGGRVGVGLPLNVTDNGSPSLRMMSFP 303
             F PES + + F N V L GM G+  N   +   +    G+    ++ +NG  S RMMS P
Sbjct:   535 FVPESSKDALFMNTVGLQGMSGMGLNGGSFSSKMANN-GIINSGSMAENGFSSYRMMSSP 593

Query:   304 RHGPLFFGNGSYSGLGTTSNEAFTERGRTRRVENCGSQVDSKKQYQLDLDKIISGEDTRT 363
             R  P+F  +G   G   +  ++  E GR RRVEN  +QV+S+KQ+QLDL+KI++GED+RT
Sbjct:   594 RFSPMFLSSGLNPGRFASGFDSLYENGRPRRVENNSNQVESRKQFQLDLEKILNGEDSRT 653

Query:   364 TLMIKNIPNKYTSKMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMVSPSHIISFY 423
             TLMIKNIPNKYTSKMLLAAIDE ++GTY+FLYLPIDFKNKCNVGYAFINM++P  II FY
Sbjct:   654 TLMIKNIPNKYTSKMLLAAIDEKNQGTYNFLYLPIDFKNKCNVGYAFINMLNPELIIPFY 713

Query:   424 EAFNGKKWEKFNSEKVASLAYARIQGQAALVTHFQNSSLMNEDKRCRPIVFHSEGQETSD 483
             EAFNGKKWEKFNSEKVASLAYARIQG++AL+ HFQNSSLMNED RCRPI+F +     S 
Sbjct:   714 EAFNGKKWEKFNSEKVASLAYARIQGKSALIAHFQNSSLMNEDMRCRPIIFDTPNNPESV 773

Query:   484 QEALLSSNLNI 494
             ++ +   + N+
Sbjct:   774 EQVVDEESKNM 784

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0045836 "positive regulation of meiosis" evidence=IMP

GO:0045927 "positive regulation of growth" evidence=IMP

GO:0006635 "fatty acid beta-oxidation" evidence=RCA

GO:0016558 "protein import into peroxisome matrix" evidence=RCA

TAIR\|locus:2117706 ML3 "MEI2-like 3" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2045605 ML2 "MEI2-like 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2156166 ML1 "MEI2-like protein 1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2182885 ML4 "MEI2-like 4" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

POMBASE\|SPAC27D7.03c mei2 "RNA-binding protein involved in meiosis Mei2" [Schizosaccharomyces pombe (taxid:4896)]	Back alignment and assigned GO terms

GENEDB_PFALCIPARUM\|PFF1125c PFF1125c "RNA-binding protein mei2 homologue, putative" [Plasmodium falciparum (taxid:5833)]	Back alignment and assigned GO terms

UNIPROTKB\|C6KT70 PFF1125c "RNA-binding protein mei2 homologue, putative" [Plasmodium falciparum 3D7 (taxid:36329)]	Back alignment and assigned GO terms

TAIR\|locus:2090350 TEL1 "terminal EAR1-like 1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2008530 TEL2 "terminal EAR1-like 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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		522
pfam04059		97	pfam04059, RRM_2, RNA recognition motif 2	1e-64
cd12531		86	cd12531, RRM3_MEI2_like, RNA recognition motif 3 i	8e-64
cd12277		86	cd12277, RRM3_MEI2_EAR1_like, RNA recognition moti	2e-44
cd12530		101	cd12530, RRM3_EAR1_like, RNA recognition motif 3 i	3e-39
cd12532		90	cd12532, RRM3_MEI2_fungi, RNA recognition motif 3	6e-38
cd12455		88	cd12455, RRM_like_Smg4_UPF3, RNA recognition motif	6e-04
smart00360		73	smart00360, RRM, RNA recognition motif	7e-04

>gnl\|CDD\|112856 pfam04059, RRM_2, RNA recognition motif 2	Back alignment and domain information

 Score =  204 bits (521), Expect = 1e-64
 Identities = 82/97 (84%), Positives = 88/97 (90%)

Query: 362 RTTLMIKNIPNKYTSKMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMVSPSHIIS 421
           RTTLMIKNIPNKYT KMLLAAIDE ++GTYDFLYLPIDFKNKCNVGYAFINM+ P  II 
Sbjct: 1   RTTLMIKNIPNKYTQKMLLAAIDEKNKGTYDFLYLPIDFKNKCNVGYAFINMIEPQSIIP 60

Query: 422 FYEAFNGKKWEKFNSEKVASLAYARIQGQAALVTHFQ 458
           F +AFNGKKWEKFNSEKVASLAYARIQG+ AL+ HFQ
Sbjct: 61  FGKAFNGKKWEKFNSEKVASLAYARIQGKDALIAHFQ 97

Length = 97

>gnl\|CDD\|240975 cd12531, RRM3_MEI2_like, RNA recognition motif 3 in plant Mei2-like proteins	Back alignment and domain information

>gnl\|CDD\|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in Mei2-like proteins and terminal EAR1-like proteins	Back alignment and domain information

>gnl\|CDD\|240974 cd12530, RRM3_EAR1_like, RNA recognition motif 3 in terminal EAR1-like proteins	Back alignment and domain information

>gnl\|CDD\|240976 cd12532, RRM3_MEI2_fungi, RNA recognition motif 3 in fungal Mei2-like proteins	Back alignment and domain information

>gnl\|CDD\|240901 cd12455, RRM_like_Smg4_UPF3, RNA recognition motif-like Smg4_UPF3 domain in yeast up-frameshift suppressor 3 (Upf3p), Caenorhabditis elegans SMG-4, their human orthologs Upf3A and Upf3B, and similar proteins	Back alignment and domain information

 Score = 38.4 bits (90), Expect = 6e-04
 Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 7/87 (8%)

Query: 365 LMIKNIPNKYTSKMLLAAIDENHRGTYDFLY-----LPIDFKNKCNVGYAFINMVSPSHI 419
           ++I+ +P   T +  L  +    + T D+ Y        DFK       A+IN  +P  +
Sbjct: 2   VVIRRLPPSLTEEEFLEQVSPLIKPTVDWYYFVGGKSSKDFKPPIY-SRAYINFKNPEDL 60

Query: 420 ISFYEAFNGKKWE-KFNSEKVASLAYA 445
           + F   F+G  +     +E  A + YA
Sbjct: 61  LEFARRFDGHVFVDSKGNEYKAIVEYA 87

This subfamily corresponds to the RRM-like Smg4_UPF3 domain found in yeast up-frameshift suppressor 3 (Upf3p), Caenorhabditis elegans SMG-4, their human orthologs Upf3A and Upf3B, and similar proteins. Upf3p, also termed nonsense-mediated mRNA decay protein 3, or Sua6p, a surveillance factor encoded by UPF3 gene from Saccharomyces cerevisiae. It is required for nonsense-mediated mRNA decay (NMD) in yeast. Upf3p is primarily cytoplasmic but accumulates inside the nucleus. Its nuclear import is mediated by the Srp1p (importin-alpha)/beta heterodimer while its nuclear export is mediated by a leucine-rich nuclear export sequence (NES-A), but not the Crm1p exportin. C. elegans SMG-4 is a nuclear shuttling protein that shuttles between the cytoplasm and nucleus through nuclear import and export signals similar to that of the yeast Upf3p. It is regulated by phosphorylation. Human orthologs of yeast Upf3p and C. elegans SMG-4 include Upf3A and Upf3B, which derive from two genes, UPF3A and X-linked UPF3B, respectively. Both, Upf3A (Up-frameshift suppressor 3 homolog A, also termed regulator of nonsense transcripts 3A, or nonsense mRNA reducing factor 3A) and Upf3B (Up-frameshift suppressor 3 homolog B on chromosome X, also termed regulator of nonsense transcripts 3B, or nonsense mRNA reducing factor 3B), are nucleocytoplasmic shuttling proteins. They associate selectively with spliced beta-globin mRNA in vivo, and tethering of any human Upf protein to the 3'UTR of beta-globin mRNA prevents NMD. The function of the Upf proteins in identifying and targeting nonsense mRNAs for rapid decay is conserved among eukaryotes. Besides, all Upf proteins in this family contain a conserved Smg4_UPF3 domain with some similarity to an RNA recognition motif (RRM), indicating that they may be RNA binding proteins. . Length = 88

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		522
KOG4660		549	consensus Protein Mei2, essential for commitment t	100.0
PF04059		97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	100.0
KOG0145		360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.25
PLN03134		144	glycine-rich RNA-binding protein 4; Provisional	99.1
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.09
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	98.95
KOG0122		270	consensus Translation initiation factor 3, subunit	98.9
PF00076		70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	98.85
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	98.82
smart00362		72	RRM_2 RNA recognition motif.	98.74
PF03467		176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	98.7
smart00360		71	RRM RNA recognition motif.	98.7
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	98.67
cd00590		74	RRM RRM (RNA recognition motif), also known as RBD	98.66
COG0724		306	RNA-binding proteins (RRM domain) [General functio	98.63
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	98.63
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	98.62
PF14259		70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	98.62
TIGR01642		509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.59
KOG4207		256	consensus Predicted splicing factor, SR protein su	98.49
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	98.44
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	98.39
TIGR01645		612	half-pint poly-U binding splicing factor, half-pin	98.38
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.3
TIGR01645		612	half-pint poly-U binding splicing factor, half-pin	98.26
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.13
PLN03120		260	nucleic acid binding protein; Provisional	98.1
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.01
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	97.93
smart00361		70	RRM_1 RNA recognition motif.	97.93
KOG0117		506	consensus Heterogeneous nuclear ribonucleoprotein	97.77
KOG0117		506	consensus Heterogeneous nuclear ribonucleoprotein	97.75
KOG0108		435	consensus mRNA cleavage and polyadenylation factor	97.62
KOG0113		335	consensus U1 small nuclear ribonucleoprotein (RRM	97.62
KOG0125		376	consensus Ataxin 2-binding protein (RRM superfamil	97.61
PLN03213		759	repressor of silencing 3; Provisional	97.48
KOG0127		678	consensus Nucleolar protein fibrillarin NOP77 (RRM	97.42
PLN03121		243	nucleic acid binding protein; Provisional	97.41
PF13893		56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	97.37
TIGR01642		509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	97.24
KOG0107		195	consensus Alternative splicing factor SRp20/9G8 (R	97.23
KOG0147		549	consensus Transcriptional coactivator CAPER (RRM s	97.21
KOG4212		608	consensus RNA-binding protein hnRNP-M [RNA process	97.17
KOG0131		203	consensus Splicing factor 3b, subunit 4 [RNA proce	97.16
KOG1295		376	consensus Nonsense-mediated decay protein Upf3 [RN	97.12
KOG0123		369	consensus Polyadenylate-binding protein (RRM super	97.11
KOG4208		214	consensus Nucleolar RNA-binding protein NIFK [Gene	97.09
KOG4206		221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	96.99
KOG4212		608	consensus RNA-binding protein hnRNP-M [RNA process	96.96
KOG0144		510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	96.92
KOG0132		894	consensus RNA polymerase II C-terminal domain-bind	96.88
KOG0145		360	consensus RNA-binding protein ELAV/HU (RRM superfa	96.79
KOG0148		321	consensus Apoptosis-promoting RNA-binding protein	96.77
KOG0144		510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	96.69
KOG0148		321	consensus Apoptosis-promoting RNA-binding protein	96.67
KOG0127		678	consensus Nucleolar protein fibrillarin NOP77 (RRM	96.65
KOG0149		247	consensus Predicted RNA-binding protein SEB4 (RRM	96.53
KOG0123		369	consensus Polyadenylate-binding protein (RRM super	96.5
KOG0105		241	consensus Alternative splicing factor ASF/SF2 (RRM	96.46
PF07576		110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.42
KOG0110		725	consensus RNA-binding protein (RRM superfamily) [G	96.15
KOG0114		124	consensus Predicted RNA-binding protein (RRM super	96.1
KOG0121		153	consensus Nuclear cap-binding protein complex, sub	96.03
KOG0111		298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	95.96
KOG4660		549	consensus Protein Mei2, essential for commitment t	95.49
KOG0533		243	consensus RRM motif-containing protein [RNA proces	95.22
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	94.95
KOG0120		500	consensus Splicing factor U2AF, large subunit (RRM	94.95
KOG0110		725	consensus RNA-binding protein (RRM superfamily) [G	94.62
KOG0130		170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	94.57
KOG0146		371	consensus RNA-binding protein ETR-3 (RRM superfami	93.76
KOG0126		219	consensus Predicted RNA-binding protein (RRM super	93.18
KOG2314		698	consensus Translation initiation factor 3, subunit	92.8
KOG0131		203	consensus Splicing factor 3b, subunit 4 [RNA proce	92.58
KOG0109		346	consensus RNA-binding protein LARK, contains RRM a	92.04
KOG0109		346	consensus RNA-binding protein LARK, contains RRM a	92.0
KOG0415		479	consensus Predicted peptidyl prolyl cis-trans isom	90.8
KOG0226		290	consensus RNA-binding proteins [General function p	90.09
KOG0106		216	consensus Alternative splicing factor SRp55/B52/SR	89.51
KOG1457		284	consensus RNA binding protein (contains RRM repeat	87.24
KOG0124		544	consensus Polypyrimidine tract-binding protein PUF	86.31
KOG0153		377	consensus Predicted RNA-binding protein (RRM super	84.66
KOG4205		311	consensus RNA-binding protein musashi/mRNA cleavag	84.15
KOG0116		419	consensus RasGAP SH3 binding protein rasputin, con	84.15
KOG4205		311	consensus RNA-binding protein musashi/mRNA cleavag	83.97
KOG2416		718	consensus Acinus (induces apoptotic chromatin cond	82.84
KOG0151		877	consensus Predicted splicing regulator, contains R	82.19
PF11608		90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	80.32

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

Probab=100.00  E-value=3.9e-62  Score=513.67  Aligned_cols=368  Identities=46%  Similarity=0.657  Sum_probs=278.4

Q ss_pred             HHHHHHHhhchhhhhhhhcccccccCCCCCCCCCCCCCccCCCCCCCCCcccccCCCCCCCCCCCCCCccccccccCCCC
Q 009947            6 FMVSLMQQLNQELEQDEARGFRHQVGSPVTNSPPGTWAQFGSPVERNPLHAFSKSPGLGTLSPINSNPLHAFSKSTGLAT   85 (522)
Q Consensus         6 ~~r~lm~q~~~eleqde~~~~~~~~gsp~~nsppg~w~~~~sp~~~~~l~~~s~s~~~g~~~~~~~~~~~~~~~~~~~~~   85 (522)
                      +||.+|.|.+        ..|..|+++|++|+|||+|.               .++.+|.|+|+                
T Consensus       148 ~~~~~~~~~~--------~~~~~~~~~p~a~s~pgg~~---------------~~~~~g~l~P~----------------  188 (549)
T KOG4660|consen  148 ARRAMGLQSG--------TSFLNHFGSPLANSPPGGWP---------------RGQLFGMLSPT----------------  188 (549)
T ss_pred             ccccchhccc--------chhhhhccchhhcCCCCCCc---------------CCcceeeeccc----------------
Confidence            3555555554        67888999999999999997               44556668887                


Q ss_pred             CCCCCCCCCCCCcccCCCCCCCCCcccccCCCccccccccccccccccccCCcccCCCCcccccCCCCCCCCCCCCCCCC
Q 009947           86 PTPVNSNHLPGLASILPPHLSNTGKIAPIGKDQGRANQTNHMFSNSASLQGAAYQHSQSFPEQKLSASPGPKSPFGESNS  165 (522)
Q Consensus        86 ~~~~~~~~~~g~~s~~p~~~s~~~~~~~ig~~~~~~~~~~~~f~~~~~~~~~~~~~~hS~pe~~~~~~~g~~s~~g~s~s  165 (522)
                          .+       +|++.++++.-.-.+. ...++..|  |.|.+  +    ...-+|.++|...          |..++
T Consensus       189 ----~s-------~~~~~~~~~~~~~~~~-~~~~~~~h--q~~~~--~----~~~~s~a~~~~~~----------G~~~s  238 (549)
T KOG4660|consen  189 ----RS-------SILLEHISSVDGSSPG-RETPLLNH--QRFVE--F----ADNRSYAFSEPRG----------GFLIS  238 (549)
T ss_pred             ----hh-------hhhhhcchhccCcccc-ccccchhh--hhhhh--h----ccccchhhcccCC----------ceecC
Confidence                22       2444444333333233 66666666  44432  1    1124457777722          77788


Q ss_pred             CCCCCCCCCCCccccCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCcccccC
Q 009947          166 NSSGVGTLSGPQFLWGSPPPYSERSSSSAWPTSSVGHPFSSSGQGQGFPYGSRHGSFIGSHHQHHVGSAPSGVSLDRNFG  245 (522)
Q Consensus       166 ~~~~~~~l~g~~~~W~~~~~~~~~~~~~~w~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~hhvgSap~~~p~~r~~~  245 (522)
                      +..++.|++|+               .++|      +++.         ...+.......++|||||+||+.        
T Consensus       239 ~~~~v~t~S~~---------------~g~~------n~~~---------~~r~~~~~~~~~~~~hi~~~Ps~--------  280 (549)
T KOG4660|consen  239 NSSGVITFSGP---------------GGVW------NPFP---------SRRQRQNSSSSHYEHHIGSAPSM--------  280 (549)
T ss_pred             CCCceEEecCC---------------Cccc------CCcc---------ccccccccCcccccCccCCCccc--------
Confidence            88899999998               3455      2222         11122333446789999999991        


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCcccccC--CCccc-CCCCCcCCCCCCCCcCCCCCCCCCcccCCCCC-CCCCCC
Q 009947          246 FFPESPETSFTNPVPLGGMGLSRNNAGYMMNVG--GRVGV-GLPLNVTDNGSPSLRMMSFPRHGPLFFGNGSY-SGLGTT  321 (522)
Q Consensus       246 ~~~~sp~~s~~~~~~~g~~g~~~~~g~~~~~~~--~~~~~-~~~~~~~~~~~~~~~~~s~~~~~~~~f~~g~~-~~~~~~  321 (522)
                                .|...-+++++.+-.|++.++..  +..|+ ...++.+|..+++++|.+.++... .|. ++. .....+
T Consensus       281 ----------~~l~~~~~~~f~~~s~~~~~~~~~~~n~g~~~~t~~~~e~~s~n~~~e~~~rv~~-~f~-~~~~~~~~~~  348 (549)
T KOG4660|consen  281 ----------HHLLSRISVGFNGGSGALEMNSNGQANQGFLTKTGNVTEFNSKNVGMESSPRVPK-NFE-GRRSYTSQND  348 (549)
T ss_pred             ----------ccccccCccccCCCCCCccccccccCCCCccccCcccccccCCCccccccCCCCc-ccc-cccccccccc
Confidence                      12223344455555555533322  33443 577899999999999999999987 786 332 222223


Q ss_pred             CCcccccccccccccCCCCccCCCcccccCchhhccCCCccceEEEecCCCccCHHHHHHHHhhcCCCcCceEeecccCC
Q 009947          322 SNEAFTERGRTRRVENCGSQVDSKKQYQLDLDKIISGEDTRTTLMIKNIPNKYTSKMLLAAIDENHRGTYDFLYLPIDFK  401 (522)
Q Consensus       322 ~~~~~~er~r~~r~~~~~~q~~~~~q~~ldl~rI~~G~D~RTTLMIRNIPNKyTq~mLl~iIDe~~~G~YDFlYLPiDFk  401 (522)
                      ......+..|.||......+.. ++++.+|+++|++|++.|||+||||||||||++||++. ||..+|+|||+||||||+
T Consensus       349 ~~~~~~~~~~~~Rtt~~i~ni~-n~~~~~dl~~Ildge~~rtt~~iknipNK~T~~ml~~~-d~~~~gtYDFlYLPiDF~  426 (549)
T KOG4660|consen  349 YPVELILNYRDRRTTVMIKNIP-NKYGQLDLLRILDGECPRTTLMIKNIPNKYTSKMLLAA-DEKNKGTYDFLYLPIDFK  426 (549)
T ss_pred             cccccccccccchhhhhhhccc-cchhHHHHHHHHhCcCchhhhHhhccCchhhHHhhhhh-hccccCccceEEeccccc
Confidence            3334445888888777655555 88999999999999999999999999999999999999 999999999999999999


Q ss_pred             CCcceeEEEEeccChhhHHHHHHHhcCCccccCCCccEEEEEeecccChHHHHHhhccCCccCCCCCccceEEecCCCCC
Q 009947          402 NKCNVGYAFINMVSPSHIISFYEAFNGKKWEKFNSEKVASLAYARIQGQAALVTHFQNSSLMNEDKRCRPIVFHSEGQET  481 (522)
Q Consensus       402 nkcNvGYAFVNF~spe~a~~F~~~FnGkkW~~fnS~KVc~VsYAriQGk~ALi~hFrNSsVm~e~~~~RPilF~s~Gp~~  481 (522)
                      |+||||||||||+++++|++|+++|||++|++|+++|+|+|+|||||||++|++|||||++|||++.|+|++|++  |+.
T Consensus       427 nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYArIQGk~~Li~hFqnS~lm~E~e~y~Pvvf~p--p~d  504 (549)
T KOG4660|consen  427 NKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYARIQGKEALIEHFQNSSLMCEDEAYRPVVFSP--PED  504 (549)
T ss_pred             cccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhhhhchHHHHHHhhcccccccchhcCceEecC--ccc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999998  899


Q ss_pred             CCccccCCCCcceeec
Q 009947          482 SDQEALLSSNLNIFIR  497 (522)
Q Consensus       482 G~~Epfp~~~~~~~~~  497 (522)
                      |.+|++|... ++..+
T Consensus       505 g~~~~~p~~~-~~~a~  519 (549)
T KOG4660|consen  505 GREEPEPVKL-NQDAG  519 (549)
T ss_pred             ccccCccccc-cccCC
Confidence            9999999886 65533

>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

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

>TIGR01659 sex-lethal sex-lethal family splicing factor	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

>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

>smart00362 RRM_2 RNA recognition motif	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

>smart00360 RRM RNA recognition motif	Back alignment and domain information

>TIGR01659 sex-lethal sex-lethal family splicing factor	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

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

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

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

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

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

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

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

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

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

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

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

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

>PLN03120 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

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

>smart00361 RRM_1 RNA recognition motif	Back alignment and domain information

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (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

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

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

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

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

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

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

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

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

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

>KOG4212 consensus RNA-binding protein hnRNP-M [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

>KOG1295 consensus Nonsense-mediated decay protein Upf3 [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

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

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [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

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (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

>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

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (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

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

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [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

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

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

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

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]	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

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]	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

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

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

>KOG0120 consensus Splicing factor U2AF, large subunit (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

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

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

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]	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

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

>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

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

>KOG0226 consensus RNA-binding proteins [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

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

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

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]	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

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

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

>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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		522
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05

>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

 Score = 49.1 bits (116), Expect = 3e-06
 Identities = 35/216 (16%), Positives = 71/216 (32%), Gaps = 47/216 (21%)

Query: 324 EAFTERGRTRRVENCGSQVDSKKQYQLDLDKII--SGEDTRTTLMIKNIPNKYTSKMLLA 381
           +AF +    + V++    + SK+    ++D II      + T  +   + +K   +M+  
Sbjct: 27  DAFVDNFDCKDVQDMPKSILSKE----EIDHIIMSKDAVSGTLRLFWTLLSK-QEEMVQK 81

Query: 382 AIDENHRGTYDFLYLPIDFKNKCNVGYAFINMVSPSHIISFYEAFNGKKW------EKFN 435
            ++E  R  Y FL  PI  K +            PS +   Y     + +       K+N
Sbjct: 82  FVEEVLRINYKFLMSPI--KTEQR---------QPSMMTRMYIEQRDRLYNDNQVFAKYN 130

Query: 436 ---SEKVASL--AYARIQGQAALVTH----FQNSSLMNEDKRCRPIVFHSE--------- 477
               +    L  A   ++    ++         + +  +   C       +         
Sbjct: 131 VSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALD--VCLSYKVQCKMDFKIFWLN 188

Query: 478 -GQETSDQEALLSSNLNIFIRQPDGSYSGDSLESLN 512
                S +  L    L   + Q D +++  S  S N
Sbjct: 189 LKNCNSPETVLE--MLQKLLYQIDPNWTSRSDHSSN 222

PyMOL of 1vt4

>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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		522
4fxv_A		99	ELAV-like protein 1; RNA recognition motif, putati	99.44
2lkz_A		95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.38
3mdf_A		85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.35
2e5h_A		94	Zinc finger CCHC-type and RNA-binding motif- conta	99.33
1whw_A		99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.33
2div_A		99	TRNA selenocysteine associated protein; structural	99.33
3bs9_A		87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.33
2cpz_A		115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.32
2dnz_A		95	Probable RNA-binding protein 23; RNA recognition m	99.31
2cqb_A		102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.31
2cqc_A		95	Arginine/serine-rich splicing factor 10; RNA recog	99.31
1x5t_A		96	Splicing factor 3B subunit 4; structure genomics,	99.3
1x5s_A		102	Cold-inducible RNA-binding protein; structure geno	99.3
3md1_A		83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.3
1p27_B		106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.28
2dnm_A		103	SRP46 splicing factor; RRM domain, RBD, structural	99.28
1u6f_A		139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.28
2dgo_A		115	Cytotoxic granule-associated RNA binding protein 1	99.27
2cqp_A		98	RNA-binding protein 12; RNA recognition motif, RRM	99.27
2cpf_A		98	RNA binding motif protein 19; RNA recognition moti	99.27
1uw4_A		91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	99.26
1p1t_A		104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.26
2x1f_A		96	MRNA 3'-END-processing protein RNA15; transcriptio	99.26
2khc_A		118	Testis-specific RNP-type RNA binding protein; RRM,	99.26
2cq0_A		103	Eukaryotic translation initiation factor 3 subunit	99.26
2ywk_A		95	Putative RNA-binding protein 11; RRM-domain, struc	99.25
1x5u_A		105	Splicing factor 3B subunit 4 (spliceosome associat	99.25
2jrs_A		108	RNA-binding protein 39; RNA binding motif of RBM39	99.25
2dgp_A		106	Bruno-like 4, RNA binding protein; RRM domain, str	99.25
2do4_A		100	Squamous cell carcinoma antigen recognized by T- c	99.24
2lxi_A		91	RNA-binding protein 10; NMR {Homo sapiens}	99.24
3ulh_A		107	THO complex subunit 4; nuclear protein, RNA bindin	99.24
2d9p_A		103	Polyadenylate-binding protein 3; RRM domain, struc	99.24
3s8s_A		110	Histone-lysine N-methyltransferase SETD1A; chromat	99.24
1oo0_B		110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.24
3p5t_L		90	Cleavage and polyadenylation specificity factor S;	99.23
2cpe_A		113	RNA-binding protein EWS; RNA recognition motif, RR	99.23
2ek1_A		95	RNA-binding protein 12; RNA recognition motif, dim	99.23
1x4h_A		111	RNA-binding protein 28; structural genomics, RRM d	99.23
2la6_A		99	RNA-binding protein FUS; structural genomics, nort	99.23
2cph_A		107	RNA binding motif protein 19; RNA recognition moti	99.22
1x5o_A		114	RNA binding motif, single-stranded interacting pro	99.22
3ex7_B		126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.22
2fc8_A		102	NCL protein; structure genomics, RRM_1 domain, str	99.21
4a8x_A		88	RNA-binding protein with serine-rich domain 1; tra	99.21
1h2v_Z		156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.21
2dgv_A		92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.21
2dgs_A		99	DAZ-associated protein 1; RRM domain, structural g	99.2
2dnh_A		105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.2
2kt5_A		124	RNA and export factor-binding protein 2; chaperone	99.2
2ku7_A		140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.2
2cqd_A		116	RNA-binding region containing protein 1; RNA recog	99.19
3ns6_A		100	Eukaryotic translation initiation factor 3 subuni;	99.19
2fy1_A		116	RNA-binding motif protein, Y chromosome, family 1	99.19
2cpx_A		115	Hypothetical protein FLJ11016; RRM domain, structu	99.18
2dh8_A		105	DAZ-associated protein 1; RRM domain, structural g	99.18
2l08_A		97	Regulator of nonsense transcripts 3A; NESG, nonsen	99.17
2do0_A		114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.17
2cqi_A		103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.17
2cq3_A		103	RNA-binding protein 9; RRM domain, structural geno	99.17
3ucg_A		89	Polyadenylate-binding protein 2; ferredoxin-like,	99.16
2m2b_A		131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.16
2dng_A		103	Eukaryotic translation initiation factor 4H; RRM d	99.16
2kxn_B		129	Transformer-2 protein homolog beta; SR protein, RR	99.15
1x4e_A		85	RNA binding motif, single-stranded interacting pro	99.14
2dgw_A		91	Probable RNA-binding protein 19; RRM domain, struc	99.14
3s7r_A		87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.14
2fc9_A		101	NCL protein; structure genomics, RRM_1 domain, str	99.14
4f25_A		115	Polyadenylate-binding protein 1; RRM fold, transla	99.14
3n9u_C		156	Cleavage and polyadenylation specificity factor S;	99.13
2dgx_A		96	KIAA0430 protein; RRM domain, structural genomics,	99.13
2lea_A		135	Serine/arginine-rich splicing factor 2; SR protein	99.13
1fxl_A		167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.13
1wi8_A		104	EIF-4B, eukaryotic translation initiation factor 4	99.13
2kn4_A		158	Immunoglobulin G-binding protein G, splicing FACT	99.12
2dhg_A		104	TRNA selenocysteine associated protein (SECP43); R	99.12
1uaw_A		77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.12
1x4a_A		109	Splicing factor, arginine/serine-rich 1 (splicing	99.12
3md3_A		166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.12
2ki2_A		90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.12
2mss_A		75	Protein (musashi1); RNA-binding domain, RNA bindin	99.12
2cqg_A		103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.11
1rk8_A		165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.11
1x4b_A		116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.1
2hvz_A		101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.1
2dis_A		109	Unnamed protein product; structural genomics, RRM	99.1
2cq4_A		114	RNA binding motif protein 23; RRM domain, structur	99.09
2err_A		109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.09
1b7f_A		168	Protein (SXL-lethal protein), RNA (5'-R(PGPUP*UP	99.09
1wel_A		124	RNA-binding protein 12; structural genomics, NPPSF	99.08
2dnq_A		90	RNA-binding protein 4B; RRM domain,RBD, structural	99.07
2db1_A		118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.07
2cpy_A		114	RNA-binding protein 12; RRM domain, structural gen	99.07
2la4_A		101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.07
1x4g_A		109	Nucleolysin TIAR; structural genomics, RRM domain,	99.06
2cpj_A		99	Non-POU domain-containing octamer-binding protein;	99.05
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	99.05
1iqt_A		75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.05
3lqv_A		115	PRE-mRNA branch site protein P14; cysless mutant,	99.05
2cqh_A		93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.05
2f3j_A		177	RNA and export factor binding protein 2; RRM domai	99.05
2g4b_A		172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.04
2jwn_A		124	Embryonic polyadenylate-binding protein 2-B; epabp	99.04
1x4c_A		108	Splicing factor, arginine/serine-rich 1; structura	99.04
2dha_A		123	FLJ20171 protein; RRM domain, structural genomics,	99.03
2jvo_A		108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.03
3q2s_C		229	Cleavage and polyadenylation specificity factor S;	99.03
1wg1_A		88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.03
2cpi_A		111	CCR4-NOT transcription complex subunit 4; RNA reco	99.03
1fxl_A		167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.03
1nu4_A		97	U1A RNA binding domain; RNA recognition motif, U1	99.03
1fjc_A		96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.02
2cpd_A		99	Apobec-1 stimulating protein; RNA recognition moti	99.02
1b7f_A		168	Protein (SXL-lethal protein), RNA (5'-R(PGPUP*UP	99.02
2dgu_A		103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.01
2ytc_A		85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.0
2dgt_A		92	RNA-binding protein 30; RRM domain, structural gen	99.0
1fj7_A		101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.0
2e5j_A		97	Methenyltetrahydrofolate synthetase domain contain	98.99
2yh0_A		198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	98.99
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	98.99
2rs2_A		109	Musashi-1, RNA-binding protein musashi homolog 1;	98.98
2hgl_A		136	HNRPF protein, heterogeneous nuclear ribonucleopro	98.98
1wg5_A		104	Heterogeneous nuclear ribonucleoprotein H; structu	98.98
3egn_A		143	RNA-binding protein 40; RNA recognition motif (RRM	98.98
1whx_A		111	Hypothetical protein riken cDNA 1200009A02; RNA re	98.97
2lcw_A		116	RNA-binding protein FUS; RRM, nucleic acid binding	98.52
2nlw_A		105	Eukaryotic translation initiation factor 3 subunit	98.97
2lmi_A		107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	98.97
1why_A		97	Hypothetical protein riken cDNA 1810017N16; RNA re	98.96
2xnq_A		97	Nuclear polyadenylated RNA-binding protein 3; tran	98.95
3nmr_A		175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	98.95
2j76_E		100	EIF-4B, EIF4B, eukaryotic translation initiation f	98.94
4f02_A		213	Polyadenylate-binding protein 1; mRNA, eukaryotic	98.94
1wf1_A		110	RNA-binding protein RALY; structural genomics, RRM	98.92
1l3k_A		196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	98.92
2jvr_A		111	Nucleolar protein 3; RNA recognition motif, nucleu	98.92
2xs2_A		102	Deleted in azoospermia-like; RNA binding protein-R	98.92
2dnp_A		90	RNA-binding protein 14; RRM domain, RBD, structura	98.92
1sjq_A		105	Polypyrimidine tract-binding protein 1; babbab mot	98.9
3nmr_A		175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	98.9
2kvi_A		96	Nuclear polyadenylated RNA-binding protein 3; RNA-	98.89
2i2y_A		150	Fusion protein consists of immunoglobin G- binding	98.89
1l3k_A		196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	98.89
2cjk_A		167	Nuclear polyadenylated RNA-binding protein 4; HRP1	98.89
2cq1_A		101	PTB-like protein L; RRM domain, structural genomic	98.87
2a3j_A		127	U1 small nuclear ribonucleoprotein A; computationa	98.87
1s79_A		103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	98.87
1wez_A		102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	98.86
2cq2_A		114	Hypothetical protein LOC91801; RRM domain, structu	98.86
1wex_A		104	Hypothetical protein (riken cDNA 2810036L13); stru	98.86
3beg_B		115	Splicing factor, arginine/serine-rich 1; kinase, S	98.86
3md3_A		166	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.85
2e44_A		96	Insulin-like growth factor 2 mRNA binding protein	98.83
2krb_A		81	Eukaryotic translation initiation factor 3 subunit	98.82
1x4f_A		112	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.82
2ad9_A		119	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.81
3pgw_S		437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	98.81
4f02_A		213	Polyadenylate-binding protein 1; mRNA, eukaryotic	98.8
2dnn_A		109	RNA-binding protein 12; RRM domain, RBD, structura	98.78
2dnl_A		114	Cytoplasmic polyadenylation element binding protei	98.78
1x4d_A		102	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.78
1fje_B		175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	98.77
1x5p_A		97	Negative elongation factor E; structure genomics,	98.76
3smz_A		284	Protein raver-1, ribonucleoprotein PTB-binding 1;	98.75
3r27_A		100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	98.75
2ghp_A		292	U4/U6 snRNA-associated splicing factor PRP24; RNA	98.74
2cjk_A		167	Nuclear polyadenylated RNA-binding protein 4; HRP1	98.73
3smz_A		284	Protein raver-1, ribonucleoprotein PTB-binding 1;	98.73
3d2w_A		89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	98.72
1fje_B		175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	98.72
1qm9_A		198	Polypyrimidine tract-binding protein; ribonucleopr	98.71
1wf0_A		88	TDP-43, TAR DNA-binding protein-43; structural gen	98.69
2adc_A		229	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.68
3pgw_A		282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	98.67
2wbr_A		89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	98.67
2hgm_A		126	HNRPF protein, heterogeneous nuclear ribonucleopro	98.66
3tyt_A		205	Heterogeneous nuclear ribonucleoprotein L; ferredo	98.65
3sde_A		261	Paraspeckle component 1; RRM, anti parallel right	98.64
2hgn_A		139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	98.64
3pgw_A		282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	98.63
2ghp_A		292	U4/U6 snRNA-associated splicing factor PRP24; RNA	98.61
2e5g_A		94	U6 snRNA-specific terminal uridylyltransferase 1;	98.6
2hzc_A		87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	98.58
3sde_A		261	Paraspeckle component 1; RRM, anti parallel right	98.58
1sjr_A		164	Polypyrimidine tract-binding protein 1; extended b	98.57
2bz2_A		121	Negative elongation factor E; NELF E, RNA recognit	98.56
2pe8_A		105	Splicing factor 45; RRM, protein binding; 2.00A {H	98.54
1qm9_A		198	Polypyrimidine tract-binding protein; ribonucleopr	98.53
2adc_A		229	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.51
2yh0_A		198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	98.49
2dit_A		112	HIV TAT specific factor 1 variant; structural geno	98.45
3zzy_A		130	Polypyrimidine tract-binding protein 1; protein bi	98.44
2voo_A		193	Lupus LA protein; RNA-binding protein, RNA recogni	98.41
3tyt_A		205	Heterogeneous nuclear ribonucleoprotein L; ferredo	98.4
2g4b_A		172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	98.39
3u1l_A		240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	98.38
3v4m_A		105	Splicing factor U2AF 65 kDa subunit; canonical RNA	98.37
2diu_A		96	KIAA0430 protein; structural genomics, RRM domain,	98.34
3ue2_A		118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.3
2e5i_A		124	Heterogeneous nuclear ribonucleoprotein L-like; RR	98.28
2j8a_A		136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	98.22
1jmt_A		104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.16
2d9o_A		100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.05
3tht_A		345	Alkylated DNA repair protein ALKB homolog 8; struc	98.04
3s6e_A		114	RNA-binding protein 39; ferredoxin-like, structura	97.86
3dxb_A		222	Thioredoxin N-terminally fused to PUF60(UHM); spli	96.84
1owx_A		121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	95.84
1wey_A		104	Calcipressin 1; structural genomics, RRM domain, r	95.72
2dnr_A		91	Synaptojanin-1; RRM domain, RBD, structural genomi	95.55
1ufw_A		95	Synaptojanin 2; RNP domain, structural genomics, r	93.98
2l9w_A		117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	89.82
2dhx_A		104	Poly (ADP-ribose) polymerase family, member 10 var	85.6
2kn4_A		158	Immunoglobulin G-binding protein G, splicing FACT	80.01

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

Probab=99.44  E-value=3.2e-13  Score=112.23  Aligned_cols=81  Identities=23%  Similarity=0.348  Sum_probs=76.1

Q ss_pred             CccceEEEecCCCccCHHHHHHHHhhcCCCcCceEeecccCCCCcceeEEEEeccChhhHHHHHHHhcCCccccCCCccE
Q 009947          360 DTRTTLMIKNIPNKYTSKMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMVSPSHIISFYEAFNGKKWEKFNSEKV  439 (522)
Q Consensus       360 D~RTTLMIRNIPNKyTq~mLl~iIDe~~~G~YDFlYLPiDFknkcNvGYAFVNF~spe~a~~F~~~FnGkkW~~fnS~KV  439 (522)
                      -..|||.|+|||..+|+++|++++.++  |+...+.++.|..++.+.|||||.|.++++|.++++.+||+.|.    .+.
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~--G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~----gr~   90 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSI--GEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQ----SKT   90 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTT--SCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEET----TEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEEC----CEE
Confidence            346899999999999999999999875  88999999999999999999999999999999999999999997    789


Q ss_pred             EEEEeec
Q 009947          440 ASLAYAR  446 (522)
Q Consensus       440 c~VsYAr  446 (522)
                      +.|.||+
T Consensus        91 l~V~~Ak   97 (99)
T 4fxv_A           91 IKVSYAR   97 (99)
T ss_dssp             CEEEECC
T ss_pred             EEEEEee
Confidence            9999997

PyMOL of 4fxv

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>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	Back alignment and structure

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

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

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

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

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

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

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

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

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

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

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

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

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

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

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

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

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

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

>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}	Back alignment and structure

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

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

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

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

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

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}	Back alignment and structure

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>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	Back alignment and structure

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A	Back alignment and structure

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

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

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

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A	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	Back alignment and structure

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	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} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A	Back alignment and structure

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

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}	Back alignment and structure

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3	Back alignment and structure

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*	Back alignment and structure

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A	Back alignment and structure

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}	Back alignment and structure

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

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

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}	Back alignment and structure

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

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

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		522
d2cqpa1		86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	7e-05
d1b7fa2		85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-04
d1uw4a_		91	d.58.7.4 (A:) RNA processing protein UPF3x, RRM do	0.001
d1fxla1		82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	0.004

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.3 bits (91), Expect = 7e-05
 Identities = 10/75 (13%), Positives = 21/75 (28%), Gaps = 2/75 (2%)

Query: 357 SGEDTRTTLMIKNIPNKYTSKMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMVSP 416
           SG+   T + ++N+P   +   +L                    +     G A +   S 
Sbjct: 4   SGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVC--LKYNEKGMPTGEAMVAFESR 61

Query: 417 SHIISFYEAFNGKKW 431
               +     N +  
Sbjct: 62  DEATAAVIDLNDRPI 76

PyMOL of d2cqpa1

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

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]} Length = 91	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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		522
d1fxla1		82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.51
d1b7fa1		82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.44
d1rk8a_		88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.4
d2cq0a1		90	Eukaryotic translation initiation factor 3 subunit	99.39
d1b7fa2		85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.37
d2cqba1		89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.36
d1x5ua1		93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.31
d1whwa_		99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.3
d1uw4a_		91	RNA processing protein UPF3x, RRM domain {Human (H	99.3
d1h2vz_		93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.3
d2ghpa1		81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.29
d1fxla2		85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.29
d2cpha1		94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.28
d2cpza1		102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.28
d1cvja1		80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.27
d1u6fa1		139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.26
d2cpea1		101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.25
d1p1ta_		104	Cleavage stimulation factor, 64 kda subunit {Human	99.24
d2u2fa_		85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.22
d2cqca1		83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.21
d1whxa_		111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.21
d2cpxa1		102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.19
d1x5sa1		90	Cold-inducible RNA-binding protein {Human (Homo sa	99.17
d2cqga1		90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.17
d2cqpa1		86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.15
d1x5ta1		83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.15
d2cq3a1		93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.14
d2cpfa1		85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.13
d1cvja2		89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.13
d2cqia1		90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.12
d1no8a_		78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.12
d2cqda1		103	RNA-binding region containing protein 1 {Human (Ho	99.1
d1wg1a_		88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.1
d1x4ha1		98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.1
d1x4aa1		95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.1
d2msta_		75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.07
d1x4ba1		103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.06
d1x4ga1		96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.05
d1l3ka1		84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.05
d1fjca_		96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.04
d2cq4a1		101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.04
d1uawa_		77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.03
d2cpja1		86	Non-POU domain-containing octamer-binding protein,	99.03
d2f9da1		114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.03
d2ghpa3		86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.03
d2cqha1		80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.02
d1fjeb1		91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.01
d2cpda1		86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.0
d1wi8a_		104	Eukaryotic translation initiation factor 4B {Human	98.99
d2b0ga1		83	Splicesomal U1A protein {Drosophila melanogaster [	98.99
d1x5oa1		101	RNA-binding motif, single-stranded-interacting pro	98.98
d1wi6a1		75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	98.93
d1hd0a_		75	Heterogeneous nuclear ribonucleoprotein d0 {Human	98.93
d1zh5a2		85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.92
d2adca1		109	Polypyrimidine tract-binding protein {Human (Homo	98.92
d1wg4a_		98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	98.91
d1nu4a_		91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	98.91
d2disa1		96	Hypothetical protein FLJ20273 {Human (Homo sapiens	98.9
d2adca2		88	Polypyrimidine tract-binding protein {Human (Homo	98.9
d1whya_		97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	98.89
d1u1qa_		183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.89
d1l3ka2		79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.89
d2bz2a1		79	Negative elongation factor E, NELF-E {Human (Homo	98.89
d2ghpa2		75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.88
d1x0fa1		75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	98.87
d2cpia1		89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	98.85
d2adba1		108	Polypyrimidine tract-binding protein {Human (Homo	98.85
d3begb1		87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.85
d1wg5a_		104	Heterogeneous nuclear ribonucleoprotein H' {Human	98.81
d1weza_		102	Heterogeneous nuclear ribonucleoprotein H' {Human	98.78
d2cpya1		103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.76
d1wela1		112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.71
d1wexa_		104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	98.7
d1wf2a_		98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	98.69
d1x4ea1		72	RNA-binding motif, single-stranded-interacting pro	98.68
d1wf0a_		88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.67
d2cq1a1		88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	98.64
d1weya_		104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	98.62
d1x4fa1		99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.54
d2cq2a1		101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	98.52
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	98.46
d1u2fa_		90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.38
d1x4da1		89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.27
d1o0pa_		104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.2
d1owxa_		113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.15
d1u1qa_		183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.15
d2dita1		99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.04
d1wwha1		81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	96.65

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=2.2e-14  Score=112.72  Aligned_cols=80  Identities=23%  Similarity=0.412  Sum_probs=75.6

Q ss_pred             ccceEEEecCCCccCHHHHHHHHhhcCCCcCceEeecccCCCCcceeEEEEeccChhhHHHHHHHhcCCccccCCCccEE
Q 009947          361 TRTTLMIKNIPNKYTSKMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMVSPSHIISFYEAFNGKKWEKFNSEKVA  440 (522)
Q Consensus       361 ~RTTLMIRNIPNKyTq~mLl~iIDe~~~G~YDFlYLPiDFknkcNvGYAFVNF~spe~a~~F~~~FnGkkW~~fnS~KVc  440 (522)
                      .||||.|+|||..+|+++|++++.++  |....+.++.|..++.+.|||||.|.++++|.++++.+||+.|.    .+.+
T Consensus         1 s~t~l~V~nLp~~~te~~l~~~f~~~--G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~----g~~l   74 (82)
T d1fxla1           1 SKTNLIVNYLPQNMTQEEFRSLFGSI--GEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQ----TKTI   74 (82)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTT--SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET----TEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHh--CCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEEC----CEEE
Confidence            48999999999999999999999985  78888999999999999999999999999999999999999997    7899


Q ss_pred             EEEeec
Q 009947          441 SLAYAR  446 (522)
Q Consensus       441 ~VsYAr  446 (522)
                      .|.||+
T Consensus        75 ~v~~Ak   80 (82)
T d1fxla1          75 KVSYAR   80 (82)
T ss_dssp             EEEECC
T ss_pred             EEEEee
Confidence            999997

PyMOL of d1fxla1

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

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

>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

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}	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

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {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

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

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

>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

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {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

>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

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

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

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {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

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

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

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

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

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {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

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

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

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {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

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {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

>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

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {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

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

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}	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

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	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

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

>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

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

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

>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

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

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA 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

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

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {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

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

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

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

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

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {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

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

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

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

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

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

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

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

>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

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}	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

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

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {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

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

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 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

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {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

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