Citrus Sinensis ID: 041602

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220---
Protein Sequence
MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKNGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRIGSRGLGSGRRRSPSPRRRRSPSYGYGRRCGSRAMSSSAMAQGSYTYESCNSINVESVSSPLQLQRYGYQFREICVMSLIFYPSNLFSIFLVLYCIQLYLSSILLGGEFNTPLSTF
Secondary Structure (PSIPRED)
cccEEEccccccccHHHHHHHHHccccEEEEEEEcccccEEEEEEccHHHHHHHHHHHHcccccEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHEEEEEEEEcccHHHHHHHHHHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEcccccccHHHHHHHHHHccccEEEEEccccccEEEEEEccHccHHHHHHccccccEEEEEEEccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccEEEEccccEEEEEcccHHHHHHHcccHHHHEEEEEEEccHHHHHHHHHHHHHHHHHHHHHHccccccccccc
Coil and Loop (DISEMBL)
msrvyvgnldprvserdleDEFRMFGVLRSVWvarrppgyafvefddRRDAVDAIRALdgkngwrvelshnskggggrggrgrgggedlkcyecgepghfaRECRLRIgsrglgsgrrrspsprrrrspsygygrrcgsramsssamaqgsytyescnsinvesvssplqlqryGYQFREICVMSLIFYPSNLFSIFLVLYCIQLYLSSILlggefntplstf
Flexible Loop (DISEMBL)
msrvyvgnldprvserdledeFRMFGvlrsvwvarrPPGYafvefddrrDAVDAIRaldgkngwrvelshnskggggrggrgrgggEDLKCYECGEPGHFARECRLrigsrglgsgrrrspsprrrrspsygygrrcgsramSSSAMAQGSYTYESCNSINVESVSSPLQLQRYGYQFREICVMSLIFYPSNLFSIFLVLYCIQLYLSSIllggefntplstf
Low Complexity Region (SEG)
MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFddrrdavdairaldGKNGWRVELSHNSKggggrggrgrgggEDLKCYECGEPGHFAREcrlrigsrglgsgrrrspsprrrrspsygygrrcgsrAMSSSAMAQGSYTYESCNSINVESVSSPLQLQRYGYQFREICVMSLIFYPSNLFSIFLVLYCIQLYLSSILLGGEFNTPLSTF
Disordered region (IsUnstruct)
*****************LEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKNGWRV***********************KCYECGEPGHFARECRLRI*******************************************YTYESCNSINVESVSSPLQLQRYGYQFREICVMSLIFYPSNLFSIFLVLYCIQLYLSSILLGGEF*******
Disordered Region (DISOPRED)
MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKNGW*******************************EPGH*****************************************************************************QFREICVMSLIFYPSNLFSIFLVLYCIQLYLSSILLGGEFNTPL***
Disordered Region (DISEMBL)
MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKNGWRVELSHNS*************GEDLKCYECGEPGHFARECRLRIGSRG***************************************YTYESCNSINVESVSSPLQLQRYGYQFREICVMSLIFYPSNLFSIFLVLYCIQLYLSSILLGGEFNTPLSTF
Disordered Region (DISPRO)
*SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKNGWRVELSH*****************DLKCYECGEPGHFARECRLRIGSR**************************************GSYTYESCNSINVESVSSPLQLQRYGYQFREICVMSLIFYPSNLFSIFLVLYCIQLYLSSILLGGEFNTPLS*F
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKNGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRIGSRGLGSGRRRSPSPRRRRSPSYGYGRRCGSRAMSSSAMAQGSYTYESCNSINVESVSSPLQLQRYGYQFREICVMSLIFYPSNLFSIFLVLYCIQLYLSSILLGGEFNTPLSTF
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	223	2.2.26 [Sep-21-2011]
Q6K4N0	185	Serine/arginine-rich spli	yes	no	0.578	0.697	0.695	1e-45
Q6K9C3	200	Serine/arginine-rich spli	no	no	0.470	0.525	0.796	5e-45
Q69KL9	185	Serine/arginine-rich spli	no	no	0.475	0.572	0.768	5e-43
O81126	200	Serine/arginine-rich spli	yes	no	0.591	0.66	0.704	5e-39
O81127	187	Serine/arginine-rich spli	no	no	0.466	0.556	0.807	3e-38
Q9SJA6	196	Serine/arginine-rich spli	no	no	0.466	0.530	0.729	6e-36
Q16629	238	Serine/arginine-rich spli	yes	no	0.461	0.432	0.477	1e-17
Q8BL97	267	Serine/arginine-rich spli	no	no	0.461	0.385	0.477	2e-17
Q3T106	235	Serine/arginine-rich spli	yes	no	0.461	0.438	0.477	2e-17
Q02427	144	RNA-binding protein 1 OS=	no	no	0.260	0.402	0.637	7e-15

>sp|Q6K4N0|RSZ21_ORYSJ Serine/arginine-rich splicing factor RSZ21 OS=Oryza sativa subsp. japonica GN=RSZP21 PE=2 SV=1

 Score =  183 bits (464), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 96/138 (69%), Positives = 113/138 (81%), Gaps = 9/138 (6%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           M+R+YVGNLDPRV+  +LEDEFR+FGVLRSVWVAR+PPG+AF++FDD+RDA DA+R LDG
Sbjct: 1   MARLYVGNLDPRVTSGELEDEFRVFGVLRSVWVARKPPGFAFIDFDDKRDAEDALRDLDG 60

Query: 61  KNGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRIGSRGLGSGR--- 117
           KNGWRVELS NS     RGGR R GG ++KCYECGE GHFARECRLRIG  GLGSG+   
Sbjct: 61  KNGWRVELSRNSS---SRGGRDRHGGSEMKCYECGETGHFARECRLRIGPGGLGSGKRRS 117

Query: 118 ---RRSPSPRRRRSPSYG 132
               RS SP+ R+SP+YG
Sbjct: 118 RSRSRSRSPQYRKSPTYG 135

Involved in pre-mRNA splicing.
Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q6K9C3|RZP23_ORYSJ Serine/arginine-rich splicing factor RSZ23 OS=Oryza sativa subsp. japonica GN=RSZ23 PE=2 SV=1

 Score =  181 bits (458), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 86/108 (79%), Positives = 97/108 (89%), Gaps = 3/108 (2%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           M+RVYVGNLDPRV+ R++EDEFR+FGVLRSVWVAR+PPG+AF++FDDRRDA DAIR LDG
Sbjct: 1   MARVYVGNLDPRVTAREIEDEFRVFGVLRSVWVARKPPGFAFIDFDDRRDAEDAIRDLDG 60

Query: 61  KNGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRI 108
           KNGWRVELS  +K G GR GR R GG D+KCYECGEPGHFARECRLRI
Sbjct: 61  KNGWRVELS--TKAGSGR-GRDRSGGSDMKCYECGEPGHFARECRLRI 105

Involved in pre-mRNA splicing. In protoplast assay, enhances splicing efficiency of WAXY intron 1 and alters the selection of the 5'-splice sites by stimulating site 1 (proximal site).

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q69KL9|RZ21A_ORYSJ Serine/arginine-rich splicing factor RSZ21A OS=Oryza sativa subsp. japonica GN=RSZ21A PE=2 SV=1

 Score =  174 bits (440), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 83/108 (76%), Positives = 94/108 (87%), Gaps = 2/108 (1%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           M+RVYVGNLDPRV+ R+LEDEFR+FGVLRSVWVAR+PPG+AF++FDDRRDA DAIR +DG
Sbjct: 1   MARVYVGNLDPRVTARELEDEFRVFGVLRSVWVARKPPGFAFIDFDDRRDAQDAIRDIDG 60

Query: 61  KNGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRI 108
           KNGWRVELS N+    GRGGR R G  + KCYECGE GHFARECRLRI
Sbjct: 61  KNGWRVELSRNA--SSGRGGRDRYGSSESKCYECGETGHFARECRLRI 106

Involved in pre-mRNA splicing.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|O81126|RZP22_ARATH Serine/arginine-rich splicing factor RSZ22 OS=Arabidopsis thaliana GN=RSZ22 PE=1 SV=1

 Score =  160 bits (406), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 100/142 (70%), Positives = 107/142 (75%), Gaps = 10/142 (7%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           MSRVYVGNLDPRV+ER+LEDEFR FGV+RSVWVARRPPGYAF++F+D RDA DAIRALDG
Sbjct: 1   MSRVYVGNLDPRVTERELEDEFRAFGVVRSVWVARRPPGYAFLDFEDPRDARDAIRALDG 60

Query: 61  KNGWRVELSHN----------SKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRIGS 110
           KNGWRVE SHN             GGG GGRG  GG DLKCYECGE GHFARECR R G+
Sbjct: 61  KNGWRVEQSHNRGERGGGGRGGDRGGGGGGRGGRGGSDLKCYECGETGHFARECRNRGGT 120

Query: 111 RGLGSGRRRSPSPRRRRSPSYG 132
               S  R    PR RRSPSYG
Sbjct: 121 GRRRSKSRSRTPPRYRRSPSYG 142

Sequence-specific RNA-binding protein probably involved in pre-mRNA splicing. In vitro, can complement efficiently splicing-deficient mammalian SRSF7-depleted HeLa cell extract.

Arabidopsis thaliana (taxid: 3702)

>sp|O81127|RZP21_ARATH Serine/arginine-rich splicing factor RSZ21 OS=Arabidopsis thaliana GN=RSZ21 PE=1 SV=1

 Score =  158 bits (400), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 84/104 (80%), Positives = 91/104 (87%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           M+RVYVGNLDPRV+ER+LEDEF+ FGVLR+VWVARRPPGYAF+EFDD RDA+DAI ALD 
Sbjct: 1   MTRVYVGNLDPRVTERELEDEFKAFGVLRNVWVARRPPGYAFLEFDDERDALDAISALDR 60

Query: 61  KNGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFAREC 104
           KNGWRVELSH  KGG G GG  RGG ED KCYECGE GHFAREC
Sbjct: 61  KNGWRVELSHKDKGGRGGGGGRRGGIEDSKCYECGELGHFAREC 104

Involved in pre-mRNA splicing.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SJA6|RZ22A_ARATH Serine/arginine-rich splicing factor RSZ22A OS=Arabidopsis thaliana GN=RSZ22A PE=1 SV=1

 Score =  150 bits (380), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 81/111 (72%), Positives = 88/111 (79%), Gaps = 7/111 (6%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           MSRVYVGNLDPRV+ER+LEDEFR FGV+RSVWVARRPPGYAF++F+D RDA DAIR +DG
Sbjct: 1   MSRVYVGNLDPRVTERELEDEFRSFGVIRSVWVARRPPGYAFLDFEDSRDARDAIREVDG 60

Query: 61  KNGWRVELSHN-------SKGGGGRGGRGRGGGEDLKCYECGEPGHFAREC 104
           KNGWRVE SHN         G GG  G    GG DLKCYECGE GHFAREC
Sbjct: 61  KNGWRVEQSHNRGGGGGRGGGRGGGDGGRGRGGSDLKCYECGESGHFAREC 111

Involved in pre-mRNA splicing.

Arabidopsis thaliana (taxid: 3702)

>sp|Q16629|SRSF7_HUMAN Serine/arginine-rich splicing factor 7 OS=Homo sapiens GN=SRSF7 PE=1 SV=1

 Score = 89.7 bits (221), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 52/109 (47%), Positives = 68/109 (62%), Gaps = 6/109 (5%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
           ++VYVGNL     + +LE  F  +G LR+VW+AR PPG+AFVEF+D RDA DA+R LDGK
Sbjct: 11  TKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGK 70

Query: 62  ----NGWRVELSHN--SKGGGGRGGRGRGGGEDLKCYECGEPGHFAREC 104
               +  RVELS     +    R    R    + +CYECGE GH+A +C
Sbjct: 71  VICGSRVRVELSTGMPRRSRFDRPPARRPFDPNDRCYECGEKGHYAYDC 119

Required for pre-mRNA splicing. Can also modulate alternative splicing in vitro. Represses the splicing of MAPT/Tau exon 10.

Homo sapiens (taxid: 9606)

>sp|Q8BL97|SRSF7_MOUSE Serine/arginine-rich splicing factor 7 OS=Mus musculus GN=Srsf7 PE=1 SV=1

 Score = 89.7 bits (221), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 52/109 (47%), Positives = 68/109 (62%), Gaps = 6/109 (5%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
           ++VYVGNL     + +LE  F  +G LR+VW+AR PPG+AFVEF+D RDA DA+R LDGK
Sbjct: 40  TKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGK 99

Query: 62  ----NGWRVELSHN--SKGGGGRGGRGRGGGEDLKCYECGEPGHFAREC 104
               +  RVELS     +    R    R    + +CYECGE GH+A +C
Sbjct: 100 VICGSRVRVELSTGMPRRSRFDRPPARRPFDPNDRCYECGEKGHYAYDC 148

Required for pre-mRNA splicing. Represses the splicing of MAPT/Tau exon 10.

Mus musculus (taxid: 10090)

>sp|Q3T106|SRSF7_BOVIN Serine/arginine-rich splicing factor 7 OS=Bos taurus GN=SRSF7 PE=2 SV=1

 Score = 89.4 bits (220), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 52/109 (47%), Positives = 68/109 (62%), Gaps = 6/109 (5%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
           ++VYVGNL     + +LE  F  +G LR+VW+AR PPG+AFVEF+D RDA DA+R LDGK
Sbjct: 11  TKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGK 70

Query: 62  ----NGWRVELSHN--SKGGGGRGGRGRGGGEDLKCYECGEPGHFAREC 104
               +  RVELS     +    R    R    + +CYECGE GH+A +C
Sbjct: 71  VICGSRVRVELSTGMPRRSRFDRPPARRPFDPNDRCYECGEKGHYAYDC 119

Required for pre-mRNA splicing. Represses the splicing of MAPT/Tau exon 10.

Bos taurus (taxid: 9913)

>sp|Q02427|RBP1_DROME RNA-binding protein 1 OS=Drosophila melanogaster GN=Rbp1 PE=2 SV=3

 Score = 80.9 bits (198), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 37/58 (63%), Positives = 45/58 (77%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          +VYVGNL    S+ ++E  F  +G LR+VWVAR PPG+AFVEF+DRRDA DA RALDG
Sbjct: 12 KVYVGNLGSSASKHEIEGAFAKYGPLRNVWVARNPPGFAFVEFEDRRDAEDATRALDG 69

Contributes to the activation of female-specific DSX splicing in vivo by recognizing the RBP1 target sequences within the purine-rich polypyrimidine tract of the female-specific 3' splice site.

Drosophila melanogaster (taxid: 7227)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	223
255587593	184	arginine/serine-rich splicing factor, pu	0.609	0.739	0.893	1e-49
224144714	179	predicted protein [Populus trichocarpa]	0.609	0.759	0.913	1e-47
356526819	176	PREDICTED: serine/arginine-rich splicing	0.511	0.647	0.887	1e-47
363807806	177	uncharacterized protein LOC100776329 [Gl	0.511	0.644	0.853	5e-46
225424701	182	PREDICTED: serine/arginine-rich splicing	0.520	0.637	0.860	3e-45
115449145	185	Os02g0789400 [Oryza sativa Japonica Grou	0.578	0.697	0.695	5e-44
115447241	200	Os02g0610600 [Oryza sativa Japonica Grou	0.470	0.525	0.796	3e-43
222623220	203	hypothetical protein OsJ_07486 [Oryza sa	0.470	0.517	0.796	3e-43
218197725	264	hypothetical protein OsI_21961 [Oryza sa	0.475	0.401	0.768	8e-42
222635100	264	hypothetical protein OsJ_20394 [Oryza sa	0.475	0.401	0.768	1e-41

>gi|255587593|ref|XP_002534324.1| arginine/serine-rich splicing factor, putative [Ricinus communis] gi|223525498|gb|EEF28060.1| arginine/serine-rich splicing factor, putative [Ricinus communis]

 Score =  202 bits (513), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 126/141 (89%), Positives = 130/141 (92%), Gaps = 5/141 (3%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           M+RVYVGNLDPRVSERDLEDEFRM+GVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG
Sbjct: 1   MARVYVGNLDPRVSERDLEDEFRMYGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60

Query: 61  KNGWRVELSHNSK-----GGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRIGSRGLGS 115
           KNGWRVELSHNSK     GGG  GG    GGED+KCYECGEPGHFARECRLRIGSRGLGS
Sbjct: 61  KNGWRVELSHNSKGGGGRGGGSGGGGRGRGGEDMKCYECGEPGHFARECRLRIGSRGLGS 120

Query: 116 GRRRSPSPRRRRSPSYGYGRR 136
           GRRRSPSP+RRRSPSYGYGRR
Sbjct: 121 GRRRSPSPKRRRSPSYGYGRR 141

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224144714|ref|XP_002325387.1| predicted protein [Populus trichocarpa] gi|222862262|gb|EEE99768.1| predicted protein [Populus trichocarpa]

 Score =  195 bits (496), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 126/138 (91%), Positives = 128/138 (92%), Gaps = 2/138 (1%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           MSRVYVGNLDPRVSERDLEDEFRM+GVLRSVWVARRPPGYAFVEFDDRRDA+DAIRALDG
Sbjct: 1   MSRVYVGNLDPRVSERDLEDEFRMYGVLRSVWVARRPPGYAFVEFDDRRDAIDAIRALDG 60

Query: 61  KNGWRVELSHNSK--GGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRIGSRGLGSGRR 118
           KNGWRVELSHNSK  GG    G GRGGGED KCYECGEPGHFARECRLRIGSRGLGS RR
Sbjct: 61  KNGWRVELSHNSKGGGGRSGDGHGRGGGEDSKCYECGEPGHFARECRLRIGSRGLGSSRR 120

Query: 119 RSPSPRRRRSPSYGYGRR 136
           RSPSPRRR SPSYGYGRR
Sbjct: 121 RSPSPRRRGSPSYGYGRR 138

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356526819|ref|XP_003532014.1| PREDICTED: serine/arginine-rich splicing factor 7-like [Glycine max]

 Score =  195 bits (495), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 103/116 (88%), Positives = 108/116 (93%), Gaps = 2/116 (1%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           MSRVYVGNLDPRVSERDLEDEFR++GVLRSVWVARRPPGYAF+EFDDRRDA+DAI+ALDG
Sbjct: 1   MSRVYVGNLDPRVSERDLEDEFRIYGVLRSVWVARRPPGYAFIEFDDRRDALDAIQALDG 60

Query: 61  KNGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRIGSRGLGSG 116
           KNGWRVELSHNSKGGG   G    GGED KCYECGEPGHFARECRLRIGSRGLGSG
Sbjct: 61  KNGWRVELSHNSKGGG--RGGRGRGGEDTKCYECGEPGHFARECRLRIGSRGLGSG 114

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363807806|ref|NP_001242436.1| uncharacterized protein LOC100776329 [Glycine max] gi|255640857|gb|ACU20711.1| unknown [Glycine max]

 Score =  189 bits (481), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 99/116 (85%), Positives = 105/116 (90%), Gaps = 2/116 (1%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           MSRVYVGNL PRV+ERDLEDEFR++GVL SVWVARRPPGYAF+EFDDRRDA+DAI+ALDG
Sbjct: 1   MSRVYVGNLHPRVNERDLEDEFRIYGVLMSVWVARRPPGYAFIEFDDRRDALDAIQALDG 60

Query: 61  KNGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRIGSRGLGSG 116
           KNGWRVELSHNSK  GG  G    GGED KCYECGEPGHFARECRLRIGSRGLGSG
Sbjct: 61  KNGWRVELSHNSK--GGGRGGRGRGGEDTKCYECGEPGHFARECRLRIGSRGLGSG 114

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225424701|ref|XP_002264105.1| PREDICTED: serine/arginine-rich splicing factor 7 [Vitis vinifera] gi|296086540|emb|CBI32129.3| unnamed protein product [Vitis vinifera]

 Score =  187 bits (475), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 105/122 (86%), Positives = 111/122 (90%), Gaps = 6/122 (4%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           MSRVYVGNLDPRVSER+LEDEFR++GV+RSVWVARRPPGYAFVEF DRRDAVDAIR LDG
Sbjct: 1   MSRVYVGNLDPRVSERELEDEFRVYGVIRSVWVARRPPGYAFVEFADRRDAVDAIRGLDG 60

Query: 61  KNGWRVELSHNSK------GGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRIGSRGLG 114
           K+GWRVELSHNSK      GGGG   RGRGGGEDLKCYECGEPGHFARECRLRIGSRG+G
Sbjct: 61  KSGWRVELSHNSKGGGGGGGGGGGRDRGRGGGEDLKCYECGEPGHFARECRLRIGSRGMG 120

Query: 115 SG 116
           SG
Sbjct: 121 SG 122

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115449145|ref|NP_001048352.1| Os02g0789400 [Oryza sativa Japonica Group] gi|75324004|sp|Q6K4N0.1|RSZ21_ORYSJ RecName: Full=Serine/arginine-rich splicing factor RSZ21; AltName: Full=RS-containing zinc finger protein 21; Short=Os-RSZ21; Short=Os-RSZp21 gi|47497051|dbj|BAD19103.1| putative Splicing factor, arginine/serine-rich 7 [Oryza sativa Japonica Group] gi|47497773|dbj|BAD19873.1| putative Splicing factor, arginine/serine-rich 7 [Oryza sativa Japonica Group] gi|113537883|dbj|BAF10266.1| Os02g0789400 [Oryza sativa Japonica Group] gi|215706489|dbj|BAG93345.1| unnamed protein product [Oryza sativa Japonica Group] gi|215706955|dbj|BAG93415.1| unnamed protein product [Oryza sativa Japonica Group] gi|218191722|gb|EEC74149.1| hypothetical protein OsI_09229 [Oryza sativa Indica Group] gi|222623815|gb|EEE57947.1| hypothetical protein OsJ_08668 [Oryza sativa Japonica Group]

 Score =  183 bits (464), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 96/138 (69%), Positives = 113/138 (81%), Gaps = 9/138 (6%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           M+R+YVGNLDPRV+  +LEDEFR+FGVLRSVWVAR+PPG+AF++FDD+RDA DA+R LDG
Sbjct: 1   MARLYVGNLDPRVTSGELEDEFRVFGVLRSVWVARKPPGFAFIDFDDKRDAEDALRDLDG 60

Query: 61  KNGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRIGSRGLGSGR--- 117
           KNGWRVELS NS     RGGR R GG ++KCYECGE GHFARECRLRIG  GLGSG+   
Sbjct: 61  KNGWRVELSRNSS---SRGGRDRHGGSEMKCYECGETGHFARECRLRIGPGGLGSGKRRS 117

Query: 118 ---RRSPSPRRRRSPSYG 132
               RS SP+ R+SP+YG
Sbjct: 118 RSRSRSRSPQYRKSPTYG 135

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115447241|ref|NP_001047400.1| Os02g0610600 [Oryza sativa Japonica Group] gi|75324099|sp|Q6K9C3.1|RZP23_ORYSJ RecName: Full=Serine/arginine-rich splicing factor RSZ23; AltName: Full=RS-containing zinc finger protein 23; Short=Os-RSZ23; Short=Os-RSZp23 gi|47497180|dbj|BAD19227.1| putative splicing factor RSZp22 (RSZP22) [Oryza sativa Japonica Group] gi|113536931|dbj|BAF09314.1| Os02g0610600 [Oryza sativa Japonica Group] gi|215704568|dbj|BAG94201.1| unnamed protein product [Oryza sativa Japonica Group] gi|215737778|dbj|BAG96908.1| unnamed protein product [Oryza sativa Japonica Group] gi|215765616|dbj|BAG87313.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  181 bits (458), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 86/108 (79%), Positives = 97/108 (89%), Gaps = 3/108 (2%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           M+RVYVGNLDPRV+ R++EDEFR+FGVLRSVWVAR+PPG+AF++FDDRRDA DAIR LDG
Sbjct: 1   MARVYVGNLDPRVTAREIEDEFRVFGVLRSVWVARKPPGFAFIDFDDRRDAEDAIRDLDG 60

Query: 61  KNGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRI 108
           KNGWRVELS  +K G GR GR R GG D+KCYECGEPGHFARECRLRI
Sbjct: 61  KNGWRVELS--TKAGSGR-GRDRSGGSDMKCYECGEPGHFARECRLRI 105

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222623220|gb|EEE57352.1| hypothetical protein OsJ_07486 [Oryza sativa Japonica Group]

 Score =  180 bits (457), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 86/108 (79%), Positives = 97/108 (89%), Gaps = 3/108 (2%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           M+RVYVGNLDPRV+ R++EDEFR+FGVLRSVWVAR+PPG+AF++FDDRRDA DAIR LDG
Sbjct: 1   MARVYVGNLDPRVTAREIEDEFRVFGVLRSVWVARKPPGFAFIDFDDRRDAEDAIRDLDG 60

Query: 61  KNGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRI 108
           KNGWRVELS  +K G GR GR R GG D+KCYECGEPGHFARECRLRI
Sbjct: 61  KNGWRVELS--TKAGSGR-GRDRSGGSDMKCYECGEPGHFARECRLRI 105

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218197725|gb|EEC80152.1| hypothetical protein OsI_21961 [Oryza sativa Indica Group]

 Score =  176 bits (445), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 83/108 (76%), Positives = 94/108 (87%), Gaps = 2/108 (1%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           M+RVYVGNLDPRV+ R+LEDEFR+FGVLRSVWVAR+PPG+AF++FDDRRDA DAIR +DG
Sbjct: 80  MARVYVGNLDPRVTARELEDEFRVFGVLRSVWVARKPPGFAFIDFDDRRDAQDAIRDIDG 139

Query: 61  KNGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRI 108
           KNGWRVELS N+    GRGGR R G  + KCYECGE GHFARECRLRI
Sbjct: 140 KNGWRVELSRNAS--SGRGGRDRYGSSESKCYECGETGHFARECRLRI 185

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222635100|gb|EEE65232.1| hypothetical protein OsJ_20394 [Oryza sativa Japonica Group]

 Score =  175 bits (444), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 83/108 (76%), Positives = 94/108 (87%), Gaps = 2/108 (1%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           M+RVYVGNLDPRV+ R+LEDEFR+FGVLRSVWVAR+PPG+AF++FDDRRDA DAIR +DG
Sbjct: 80  MARVYVGNLDPRVTARELEDEFRVFGVLRSVWVARKPPGFAFIDFDDRRDAQDAIRDIDG 139

Query: 61  KNGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRI 108
           KNGWRVELS N+    GRGGR R G  + KCYECGE GHFARECRLRI
Sbjct: 140 KNGWRVELSRNAS--SGRGGRDRYGSSESKCYECGETGHFARECRLRI 185

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	223
TAIR|locus:2199837	187	RSZ21 "RS-containing zinc fing	0.461	0.550	0.621	1.8e-30
TAIR|locus:2046638	196	RSZ22a "RS-containing zinc fin	0.461	0.525	0.590	5.6e-29
UNIPROTKB|Q6K9C3	200	RSZ23 "Serine/arginine-rich sp	0.448	0.5	0.582	9.1e-29
TAIR|locus:2124799	200	RSZ22 "RS-containing zinc fing	0.461	0.515	0.575	3.1e-28
FB|FBgn0028554	258	x16 [Drosophila melanogaster (	0.300	0.259	0.450	2.8e-14
UNIPROTKB|E1BRL9	226	LOC100859609 "Uncharacterized	0.197	0.194	0.545	5.5e-14
ZFIN|ZDB-GENE-040426-1798	258	zgc:77155 "zgc:77155" [Danio r	0.443	0.383	0.394	7.1e-13
UNIPROTKB|Q3T106	235	SRSF7 "Serine/arginine-rich sp	0.448	0.425	0.386	1.2e-12
UNIPROTKB|J9P2I8	238	SRSF7 "Uncharacterized protein	0.448	0.420	0.386	1.2e-12
UNIPROTKB|C9JAB2	235	SRSF7 "Serine/arginine-rich-sp	0.448	0.425	0.386	1.2e-12

TAIR|locus:2199837 RSZ21 "RS-containing zinc finger protein 21" [Arabidopsis thaliana (taxid:3702)]

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 64/103 (62%), Positives = 70/103 (67%)

Query:     1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFXXXXXXXXXXXXXXG 60
             M+RVYVGNLDPRV+ER+LEDEF+ FGVLR+VWVARRPPGYAF+EF               
Sbjct:     1 MTRVYVGNLDPRVTERELEDEFKAFGVLRNVWVARRPPGYAFLEFDDERDALDAISALDR 60

Query:    61 KNGWRVELSHNSKXXXXXXXXXXXXXEDLKCYECGEPGHFARE 103
             KNGWRVELSH  K             ED KCYECGE GHFARE
Sbjct:    61 KNGWRVELSHKDKGGRGGGGGRRGGIEDSKCYECGELGHFARE 103

GO:0005634 "nucleus" evidence=ISM;IPI

GO:0000398 "mRNA splicing, via spliceosome" evidence=RCA;TAS

GO:0005515 "protein binding" evidence=IPI

GO:0016607 "nuclear speck" evidence=IDA

GO:0000278 "mitotic cell cycle" evidence=RCA

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

GO:0006396 "RNA processing" evidence=RCA

GO:0030422 "production of siRNA involved in RNA interference" evidence=RCA

GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

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

GO:0048573 "photoperiodism, flowering" evidence=RCA

TAIR|locus:2046638 RSZ22a "RS-containing zinc finger protein 22a" [Arabidopsis thaliana (taxid:3702)]

 Score = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 65/110 (59%), Positives = 70/110 (63%)

Query:     1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFXXXXXXXXXXXXXXG 60
             MSRVYVGNLDPRV+ER+LEDEFR FGV+RSVWVARRPPGYAF++F              G
Sbjct:     1 MSRVYVGNLDPRVTERELEDEFRSFGVIRSVWVARRPPGYAFLDFEDSRDARDAIREVDG 60

Query:    61 KNGWRVELSHN-------SKXXXXXXXXXXXXXEDLKCYECGEPGHFARE 103
             KNGWRVE SHN                       DLKCYECGE GHFARE
Sbjct:    61 KNGWRVEQSHNRGGGGGRGGGRGGGDGGRGRGGSDLKCYECGESGHFARE 110

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0008380 "RNA splicing" evidence=NAS

GO:0005829 "cytosol" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=RCA

UNIPROTKB|Q6K9C3 RSZ23 "Serine/arginine-rich splicing factor RSZ23" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 320 (117.7 bits), Expect = 9.1e-29, P = 9.1e-29
 Identities = 60/103 (58%), Positives = 71/103 (68%)

Query:     1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFXXXXXXXXXXXXXXG 60
             M+RVYVGNLDPRV+ R++EDEFR+FGVLRSVWVAR+PPG+AF++F              G
Sbjct:     1 MARVYVGNLDPRVTAREIEDEFRVFGVLRSVWVARKPPGFAFIDFDDRRDAEDAIRDLDG 60

Query:    61 KNGWRVELSHNSKXXXXXXXXXXXXXEDLKCYECGEPGHFARE 103
             KNGWRVELS  +               D+KCYECGEPGHFARE
Sbjct:    61 KNGWRVELSTKA---GSGRGRDRSGGSDMKCYECGEPGHFARE 100

GO:0000398 "mRNA splicing, via spliceosome" evidence=IDA

TAIR|locus:2124799 RSZ22 "RS-containing zinc finger protein 22" [Arabidopsis thaliana (taxid:3702)]

 Score = 315 (115.9 bits), Expect = 3.1e-28, P = 3.1e-28
 Identities = 65/113 (57%), Positives = 70/113 (61%)

Query:     1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFXXXXXXXXXXXXXXG 60
             MSRVYVGNLDPRV+ER+LEDEFR FGV+RSVWVARRPPGYAF++F              G
Sbjct:     1 MSRVYVGNLDPRVTERELEDEFRAFGVVRSVWVARRPPGYAFLDFEDPRDARDAIRALDG 60

Query:    61 KNGWRVELSHN----------SKXXXXXXXXXXXXXEDLKCYECGEPGHFARE 103
             KNGWRVE SHN                          DLKCYECGE GHFARE
Sbjct:    61 KNGWRVEQSHNRGERGGGGRGGDRGGGGGGRGGRGGSDLKCYECGETGHFARE 113

GO:0005634 "nucleus" evidence=ISM;ISS

GO:0000398 "mRNA splicing, via spliceosome" evidence=RCA;TAS

GO:0005515 "protein binding" evidence=IPI

GO:0016607 "nuclear speck" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0008380 "RNA splicing" evidence=NAS

GO:0005829 "cytosol" evidence=RCA

FB|FBgn0028554 x16 [Drosophila melanogaster (taxid:7227)]

 Score = 135 (52.6 bits), Expect = 2.8e-14, Sum P(2) = 2.8e-14
 Identities = 32/71 (45%), Positives = 39/71 (54%)

Query:     3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFXXXXXXXXXXXXXXGKN 62
             +VYVG+L     + DLE  F  +G LRSVW+AR PPG+AFVEF              G+ 
Sbjct:     9 KVYVGDLGNNARKNDLEYVFGAYGSLRSVWIARNPPGFAFVEFESARDAADAVRGLDGRT 68

Query:    63 --GWR--VELS 69
               G R  VELS
Sbjct:    69 VCGRRARVELS 79

GO:0005634 "nucleus" evidence=IDA;NAS

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC;ISS;NAS

GO:0005681 "spliceosomal complex" evidence=NAS

GO:0003723 "RNA binding" evidence=ISM

GO:0003729 "mRNA binding" evidence=ISS

GO:0006376 "mRNA splice site selection" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0007399 "nervous system development" evidence=NAS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IPI

GO:0071011 "precatalytic spliceosome" evidence=IDA

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

UNIPROTKB|E1BRL9 LOC100859609 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 133 (51.9 bits), Expect = 5.5e-14, Sum P(2) = 5.5e-14
 Identities = 24/44 (54%), Positives = 32/44 (72%)

Query:     2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEF 45
             ++VYVGNL     + +LE  F  +G LR+VW+AR PPG+AFVEF
Sbjct:    11 TKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEF 54

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

ZFIN|ZDB-GENE-040426-1798 zgc:77155 "zgc:77155" [Danio rerio (taxid:7955)]

 Score = 170 (64.9 bits), Expect = 7.1e-13, P = 7.1e-13
 Identities = 41/104 (39%), Positives = 55/104 (52%)

Query:     3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFXXXXXXXXXXXXXXGKN 62
             +VYVG+L    ++ +LE  F  +G LRSVWVAR PPG+AFVE+              GK 
Sbjct:    15 KVYVGDLGNGAAKGELERAFSYYGPLRSVWVARNPPGFAFVEYEDARDAEDAVKGMDGKV 74

Query:    63 --GWRV--ELSHN-SKXXXXXXXXXXXXXEDLKCYECGEPGHFA 101
               G RV  ELS+  S+              + +CY+CGE GH+A
Sbjct:    75 LCGARVRVELSNGMSRKSRYGRPSRRQFDPNDRCYQCGETGHYA 118

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|Q3T106 SRSF7 "Serine/arginine-rich splicing factor 7" [Bos taurus (taxid:9913)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 41/106 (38%), Positives = 52/106 (49%)

Query:     2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFXXXXXXXXXXXXXXGK 61
             ++VYVGNL     + +LE  F  +G LR+VW+AR PPG+AFVEF              GK
Sbjct:    11 TKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGK 70

Query:    62 ----NGWRVELSHNSKXXXXXXXXXXXXXEDL--KCYECGEPGHFA 101
                 +  RVELS                  D   +CYECGE GH+A
Sbjct:    71 VICGSRVRVELSTGMPRRSRFDRPPARRPFDPNDRCYECGEKGHYA 116

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|J9P2I8 SRSF7 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 41/106 (38%), Positives = 52/106 (49%)

Query:     2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFXXXXXXXXXXXXXXGK 61
             ++VYVGNL     + +LE  F  +G LR+VW+AR PPG+AFVEF              GK
Sbjct:    11 TKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGK 70

Query:    62 ----NGWRVELSHNSKXXXXXXXXXXXXXEDL--KCYECGEPGHFA 101
                 +  RVELS                  D   +CYECGE GH+A
Sbjct:    71 VICGSRVRVELSTGMPRRSRFDRPPARRPFDPNDRCYECGEKGHYA 116

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|C9JAB2 SRSF7 "Serine/arginine-rich-splicing factor 7" [Homo sapiens (taxid:9606)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 41/106 (38%), Positives = 52/106 (49%)

Query:     2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFXXXXXXXXXXXXXXGK 61
             ++VYVGNL     + +LE  F  +G LR+VW+AR PPG+AFVEF              GK
Sbjct:    11 TKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGK 70

Query:    62 ----NGWRVELSHNSKXXXXXXXXXXXXXEDL--KCYECGEPGHFA 101
                 +  RVELS                  D   +CYECGE GH+A
Sbjct:    71 VICGSRVRVELSTGMPRRSRFDRPPARRPFDPNDRCYECGEKGHYA 116

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O81126	RZP22_ARATH	No assigned EC number	0.7042	0.5919	0.66	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	gw1.XIX.900.1	hypothetical protein (179 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	fgenesh4_pg.C_LG_II002243	hypothetical protein (274 aa)			•			•			0.463
	gw1.IV.3602.1	hypothetical protein (264 aa)			•			•			0.422

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	223
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-37
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	1e-18
smart00360	73	smart00360, RRM, RNA recognition motif	2e-17
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	7e-17
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-16
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	5e-16
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	2e-15
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	4e-15
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	8e-15
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-12
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-10
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	1e-10
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-10
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	2e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-10
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	4e-10
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	9e-10
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	1e-09
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-09
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	1e-09
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	1e-09
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-09
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-09
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-09
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	3e-09
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	4e-09
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	7e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-08
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-08
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	2e-08
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-08
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	2e-08
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-08
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	3e-08
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	4e-08
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	4e-08
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	6e-08
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	8e-08
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	8e-08
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	1e-07
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	2e-07
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	2e-07
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	2e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	2e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-07
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	3e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	5e-07
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	5e-07
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	5e-07
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	6e-07
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	6e-07
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	6e-07
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	6e-07
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	7e-07
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	8e-07
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	8e-07
cd12600	72	cd12600, RRM2_SRSF4_like, RNA recognition motif 2	8e-07
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	1e-06
cd12626	77	cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in	1e-06
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-06
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	1e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	1e-06
cd12625	77	cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in	2e-06
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-06
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	2e-06
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	2e-06
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	2e-06
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	2e-06
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	2e-06
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	2e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-06
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	3e-06
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	3e-06
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	3e-06
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	3e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	3e-06
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	3e-06
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	4e-06
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	4e-06
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	5e-06
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	5e-06
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	5e-06
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	5e-06
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	6e-06
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	6e-06
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	6e-06
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	7e-06
cd12627	77	cd12627, RRM1_IGF2BP3, RNA recognition motif 1 in	8e-06
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	8e-06
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	9e-06
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	1e-05
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-05
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	1e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	1e-05
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	2e-05
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	2e-05
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	2e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	2e-05
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	2e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	3e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-05
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	3e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	3e-05
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	4e-05
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	4e-05
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	4e-05
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	6e-05
pfam00098	18	pfam00098, zf-CCHC, Zinc knuckle	6e-05
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	7e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	7e-05
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	8e-05
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	9e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-04
cd12724	92	cd12724, RRM1_CPEB2_like, RNA recognition motif 1	1e-04
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-04
smart00343	17	smart00343, ZnF_C2HC, zinc finger	1e-04
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	1e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	1e-04
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	1e-04
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	2e-04
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	2e-04
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	2e-04
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	2e-04
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-04
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-04
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-04
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	3e-04
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	3e-04
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	3e-04
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	3e-04
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	4e-04
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	4e-04
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	4e-04
cd12248	74	cd12248, RRM_RBM44, RNA recognition motif in RNA-b	5e-04
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	5e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	6e-04
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	6e-04
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	6e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	6e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	6e-04
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	6e-04
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	7e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	8e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	8e-04
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	8e-04
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	8e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	8e-04
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	9e-04
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.001
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	0.001
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.001
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	0.001
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	0.001
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	0.002
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.002
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	0.002
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	0.002
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	0.002
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	0.002
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	0.003
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	0.003
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	0.003
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	0.003
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	0.003
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	0.003
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	0.003
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	0.003
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	0.004
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	0.004
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	0.004
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	0.004
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	0.004

>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score =  124 bits (313), Expect = 3e-37
 Identities = 48/73 (65%), Positives = 57/73 (78%), Gaps = 4/73 (5%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK- 61
          +VYVGNL PR ++R+LEDEF  +G LRSVWVAR PPG+AFVEF+D RDA DA+RALDG+ 
Sbjct: 1  KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRR 60

Query: 62 ---NGWRVELSHN 71
             N  RVELS  
Sbjct: 61 ICGNRVRVELSRG 73

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 76.6 bits (188), Expect = 1e-18
 Identities = 42/75 (56%), Positives = 52/75 (69%), Gaps = 4/75 (5%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN 62
          +VYVGNL    ++ +LE  F  +G LRSVWVAR PPG+AFVEF+D RDA DA+R LDG+ 
Sbjct: 6  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 65

Query: 63 ----GWRVELSHNSK 73
                RVELS+  K
Sbjct: 66 LCGCRVRVELSNGEK 80

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 81

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 73.4 bits (181), Expect = 2e-17
 Identities = 26/64 (40%), Positives = 38/64 (59%), Gaps = 5/64 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
           ++VGNL P  +E +L + F  FG + SV + R     +  G+AFVEF+   DA  A+ A
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 58 LDGK 61
          L+GK
Sbjct: 61 LNGK 64

Length = 73

>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 72.0 bits (176), Expect = 7e-17
 Identities = 40/71 (56%), Positives = 50/71 (70%), Gaps = 4/71 (5%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK- 61
          +VYVGNL     + +LE  F  +G LR+VW+AR PPG+AFVEF+D RDA DA+R LDGK 
Sbjct: 1  KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 60

Query: 62 ---NGWRVELS 69
             +  RVELS
Sbjct: 61 ICGSRVRVELS 71

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 77

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 71.1 bits (175), Expect = 1e-16
 Identities = 29/62 (46%), Positives = 40/62 (64%), Gaps = 4/62 (6%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALD 59
          ++VGNL P  +E DL+D F  FG + S+ + R    R  G+AFVEF+D  DA  A+ AL+
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 60 GK 61
          GK
Sbjct: 61 GK 62

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 70.8 bits (174), Expect = 2e-16
 Identities = 29/72 (40%), Positives = 45/72 (62%), Gaps = 6/72 (8%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALD 59
          ++VGNL P  +E DL + F  FG + SV + R    +  G+AFVEF+   DA  A+ AL+
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 60 GK--NGWRVELS 69
          GK  +G ++++S
Sbjct: 61 GKELDGRKLKVS 72

RRM, 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. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 69.7 bits (171), Expect = 5e-16
 Identities = 30/60 (50%), Positives = 41/60 (68%), Gaps = 2/60 (3%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSV--WVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          R+YVGNL   + ERD+ED F  +G ++++     RR P +AFVEF+D RDA DA+R  DG
Sbjct: 1  RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDG 60

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 68.3 bits (167), Expect = 2e-15
 Identities = 35/72 (48%), Positives = 44/72 (61%), Gaps = 6/72 (8%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSV--WVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           VYVGNL   + ER++ED F  +G +  +   +  RPPGYAF+EF+D RDA DAIR  DG
Sbjct: 1  TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDG 60

Query: 61 ----KNGWRVEL 68
                  RVEL
Sbjct: 61 YDFDGQRLRVEL 72

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 67.5 bits (165), Expect = 4e-15
 Identities = 31/71 (43%), Positives = 46/71 (64%), Gaps = 3/71 (4%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-RRPPGYAFVEFDDRRDAVDAIRALDGK 61
          R+YVGNL P +  +D+ED F  +G +R + +  RR P +AFVEF+D RDA DA+   DG 
Sbjct: 1  RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPPFAFVEFEDPRDAEDAVYGRDGY 60

Query: 62 N--GWRVELSH 70
          +  G+R+ +  
Sbjct: 61 DYDGYRLRVEF 71

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 66.6 bits (163), Expect = 8e-15
 Identities = 31/70 (44%), Positives = 43/70 (61%), Gaps = 5/70 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN 62
          RVY+G L  R  ERD+E  F+ +G +R + +     G+ FVEF+D RDA DA+  L+GK 
Sbjct: 1  RVYIGRLPYRARERDVERFFKGYGRIREINLKN---GFGFVEFEDPRDADDAVYELNGKE 57

Query: 63 --GWRVELSH 70
            G RV + H
Sbjct: 58 LCGERVIVEH 67

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

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

 Score = 58.8 bits (143), Expect = 7e-12
 Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP-----GYAFVEFDDRRDAVDAIR 56
          ++++V  L  R +E++LE  F  FG +  V + + P      G+ FV F+   DA  AIR
Sbjct: 2  NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 57 ALDGK 61
           L+GK
Sbjct: 62 DLNGK 66

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 55.6 bits (135), Expect = 1e-10
 Identities = 24/63 (38%), Positives = 33/63 (52%), Gaps = 5/63 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
           + V NL     E DL + FR FG +  V++A+     +  G+AFV F  R DA  AI  
Sbjct: 1  TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 58 LDG 60
          L+G
Sbjct: 61 LNG 63

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 55.3 bits (134), Expect = 1e-10
 Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 4/65 (6%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWV----ARRPPGYAFVEFDDRRDAVDAIRA 57
          +R+ V NL   V+E DLE+ F   G ++ V +    + R  G A V F+ R DA  AI+ 
Sbjct: 1  TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQ 60

Query: 58 LDGKN 62
           +G  
Sbjct: 61 FNGVL 65

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

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

 Score = 55.4 bits (134), Expect = 1e-10
 Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 8/67 (11%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWV--------ARRPPGYAFVEFDDRRDAVDA 54
          R+++GNLD R++E  L   F  +G ++              +P GY FV F+ + +A  A
Sbjct: 1  RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 55 IRALDGK 61
          +++L+GK
Sbjct: 61 LKSLNGK 67

This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. . Length = 80

>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 55.0 bits (132), Expect = 2e-10
 Identities = 31/70 (44%), Positives = 44/70 (62%), Gaps = 5/70 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN 62
          RV++G L+P   E+D+E  F+ +G +R + + R   G+ FVEFDD RDA DA+  LDGK 
Sbjct: 1  RVFIGRLNPAAREKDVERFFKGYGRIRDIDLKR---GFGFVEFDDPRDADDAVYELDGKE 57

Query: 63 --GWRVELSH 70
              RV + H
Sbjct: 58 LCNERVTIEH 67

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 54.9 bits (133), Expect = 2e-10
 Identities = 26/62 (41%), Positives = 36/62 (58%), Gaps = 3/62 (4%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDAVDAIRALDG 60
          +YV NL P V+E DL + F  +G +  V + R   RP G+AFVEF    DA  A++ L+G
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 61 KN 62
            
Sbjct: 61 LV 62

k.a. RRM, RBD, or RNP domain). Length = 69

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

 Score = 53.8 bits (130), Expect = 4e-10
 Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 5/68 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK-- 61
          +YV NL    +E  L + F  +G +  V   ++   YAFV F++R DAV A+  ++GK  
Sbjct: 4  LYVRNLPLSTTEEQLRELFSEYGEVERV---KKIKDYAFVHFEERDDAVKAMEEMNGKEL 60

Query: 62 NGWRVELS 69
           G  +E+S
Sbjct: 61 EGSPIEVS 68

This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Length = 72

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

 Score = 53.0 bits (128), Expect = 9e-10
 Identities = 25/59 (42%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN 62
          VYVGNL   ++E +L+  F  FG +  V V +   GYAFV FD    A  AI A++G +
Sbjct: 3  VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-KGYAFVRFDTHEAAATAIVAVNGTS 60

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 52.7 bits (127), Expect = 1e-09
 Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 2/61 (3%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPG--YAFVEFDDRRDAVDAIRALDGK 61
          +YVGNLD  V+E  L + F   G ++S  + R      YAFVE+ D R A  A++ ++G+
Sbjct: 1  LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60

Query: 62 N 62
           
Sbjct: 61 L 61

This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 72

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 52.6 bits (127), Expect = 1e-09
 Identities = 25/65 (38%), Positives = 34/65 (52%), Gaps = 5/65 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
           +YVGNL   V+E DL+D F  FG + S  V       R  G+ FVE +   +A  AI  
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 58 LDGKN 62
          L+G +
Sbjct: 61 LNGTD 65

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 52.6 bits (127), Expect = 1e-09
 Identities = 30/68 (44%), Positives = 37/68 (54%), Gaps = 6/68 (8%)

Query: 5  YVGNLDPRVSERDLEDEFRMFGVLRSV-WVARRPPGYAFVEFDDRRDAVDAIRALDGK-- 61
          YVG L  RV+E+DL D F  FG +RS+  V R+    AFV F  R  A  A   L  K  
Sbjct: 5  YVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQ--QCAFVTFTTREAAEKAAERLFNKLI 62

Query: 62 -NGWRVEL 68
           NG R++L
Sbjct: 63 INGRRLKL 70

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 52.7 bits (127), Expect = 1e-09
 Identities = 29/66 (43%), Positives = 36/66 (54%), Gaps = 8/66 (12%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWV--------ARRPPGYAFVEFDDRRDAVDAI 55
          +YVGNL+P+V+E  L  EF  FG L SV +         RR     FV F +R DA  A+
Sbjct: 4  LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 56 RALDGK 61
            LDGK
Sbjct: 64 DELDGK 69

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 52.5 bits (127), Expect = 2e-09
 Identities = 25/60 (41%), Positives = 33/60 (55%), Gaps = 8/60 (13%)

Query: 5  YVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALD 59
          YVG+L P V+E  L + F   G + S+ V R     R  GYA+V F   ++  DA RALD
Sbjct: 3  YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNF---QNPADAERALD 59

This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 51.8 bits (125), Expect = 3e-09
 Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 5/57 (8%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSV-----WVARRPPGYAFVEFDDRRDAVDAI 55
          +YVG L   V E+ L   F  FG ++ +     +  ++  G+AFVEF++  DA  AI
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAI 57

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 51.8 bits (125), Expect = 3e-09
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 12/78 (15%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP----------GYAFVEFDDRRDAVD 53
          ++V NL+ + +E  L+  F   G +RSV +A++            GY FVEF  +  A  
Sbjct: 3  LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 54 AIRALDGK--NGWRVELS 69
          A++ L G   +G  +EL 
Sbjct: 63 ALKRLQGTVLDGHALELK 80

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 51.5 bits (124), Expect = 3e-09
 Identities = 24/61 (39%), Positives = 39/61 (63%), Gaps = 4/61 (6%)

Query: 2  SRVYVGNLDP-RVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          SRV+VGNL+  +VS+ DLE+ F  +G +  + + +   GY FV+FD+  DA  A+   +G
Sbjct: 1  SRVFVGNLNTDKVSKEDLEEIFSKYGKILGISLHK---GYGFVQFDNEEDARAAVAGENG 57

Query: 61 K 61
          +
Sbjct: 58 R 58

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 51.5 bits (124), Expect = 4e-09
 Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 7/69 (10%)

Query: 5  YVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALD 59
          +V  L+   +E  L  EF  +G ++ + + R     +P GYAF+EF+  RD   A +  D
Sbjct: 5  FVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYAD 64

Query: 60 GK--NGWRV 66
          GK  +G RV
Sbjct: 65 GKKIDGRRV 73

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 50.9 bits (122), Expect = 7e-09
 Identities = 19/62 (30%), Positives = 37/62 (59%), Gaps = 4/62 (6%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWV----ARRPPGYAFVEFDDRRDAVDAIRAL 58
          +++V  L   V++ +LE  F+  GV++SV +    + +P G A+VE+++   A  A+  +
Sbjct: 4  KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 59 DG 60
          DG
Sbjct: 64 DG 65

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

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

 Score = 53.8 bits (128), Expect = 1e-08
 Identities = 25/65 (38%), Positives = 38/65 (58%), Gaps = 5/65 (7%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
           + ++VGNL   V+E DL + F+ FG ++ V + R     +  G+AFVEF+    A  AI 
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIE 175

Query: 57  ALDGK 61
            L+GK
Sbjct: 176 ELNGK 180

Length = 306

>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 49.5 bits (119), Expect = 1e-08
 Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 3/60 (5%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN 62
          +++VGNL    +  +L   F  +G +    V +    Y FV  ++  DA DAI+AL+G  
Sbjct: 1  KLFVGNLPDATTSEELRALFEKYGTVTECDVVKN---YGFVHMEEEEDAEDAIKALNGYE 57

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 53.7 bits (129), Expect = 2e-08
 Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 4/62 (6%)

Query: 4   VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALD 59
           +YV NLDP V+E  L + F  FG + S  V +    R  G+AFV F+   DA  A+  ++
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMN 240

Query: 60  GK 61
           GK
Sbjct: 241 GK 242

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 49.2 bits (117), Expect = 2e-08
 Identities = 32/70 (45%), Positives = 43/70 (61%), Gaps = 5/70 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN 62
          RVY+G L  +  ERD+E  F+ +G +  V +     GY FVEFDD RDA DA+  L+GK+
Sbjct: 1  RVYIGRLSYQARERDVERFFKGYGKILEVDLKN---GYGFVEFDDLRDADDAVYELNGKD 57

Query: 63 --GWRVELSH 70
            G RV + H
Sbjct: 58 LCGERVIVEH 67

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 49.2 bits (118), Expect = 2e-08
 Identities = 25/62 (40%), Positives = 34/62 (54%), Gaps = 5/62 (8%)

Query: 6  VGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDG 60
          V NL  R +  DL   F  +G +  V++ R        G+AFV F D+RDA DA+ A+DG
Sbjct: 3  VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 61 KN 62
          K 
Sbjct: 63 KE 64

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 49.0 bits (117), Expect = 2e-08
 Identities = 29/64 (45%), Positives = 40/64 (62%), Gaps = 5/64 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPG--YAFVEFDDRRDAVDAIRALDG 60
          R+YVGNL   V E+DLED F  +G +R + +  R     +AFV F+D RDA DA+    G
Sbjct: 1  RIYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVF---G 57

Query: 61 KNGW 64
          +NG+
Sbjct: 58 RNGY 61

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 49.2 bits (118), Expect = 2e-08
 Identities = 26/66 (39%), Positives = 39/66 (59%), Gaps = 9/66 (13%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGV-LRSVWVARRP-----PGYAFVEFDDRRDAVDAIRA 57
          +++GNLDP V E+ L D F  FGV L++  + R P      G+AF+ +D   +A DA  A
Sbjct: 4  LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDS-FEASDA--A 60

Query: 58 LDGKNG 63
          ++  NG
Sbjct: 61 IEAMNG 66

This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 83

>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 48.7 bits (117), Expect = 3e-08
 Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 5/62 (8%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRAL 58
          VYVGNLD +V+E  L + F   G + +V + +        GY FVEF    DA  AI+ +
Sbjct: 1  VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 59 DG 60
          + 
Sbjct: 61 NM 62

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 48.8 bits (116), Expect = 4e-08
 Identities = 30/70 (42%), Positives = 42/70 (60%), Gaps = 5/70 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN 62
          RVY+G L   V E+D++  F  +G L  + +     GY FVEF+D RDA DA+  L+GK+
Sbjct: 1  RVYIGRLSYHVREKDIQRFFGGYGKLLEIDLKN---GYGFVEFEDSRDADDAVYELNGKD 57

Query: 63 --GWRVELSH 70
            G RV + H
Sbjct: 58 LCGERVIVEH 67

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 48.5 bits (116), Expect = 4e-08
 Identities = 27/69 (39%), Positives = 37/69 (53%), Gaps = 5/69 (7%)

Query: 5  YVGNLDPRVSERDLEDEFRMFGV-LRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK-- 61
          Y+GNL   V+E DL   F    + + SV V +   GYAFV+  D+  A  AI  L+GK  
Sbjct: 2  YIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKG--GYAFVDCPDQSWADKAIEKLNGKIL 59

Query: 62 NGWRVELSH 70
           G  +E+ H
Sbjct: 60 QGKVIEVEH 68

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 47.9 bits (115), Expect = 6e-08
 Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 5/62 (8%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-RPP----GYAFVEFDDRRDAVDAIRAL 58
          ++VG L   V++  L++ F  +G ++ V +   R      GYA+VEF+   DA  AI+ +
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 59 DG 60
          DG
Sbjct: 61 DG 62

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 47.9 bits (114), Expect = 8e-08
 Identities = 23/62 (37%), Positives = 38/62 (61%), Gaps = 4/62 (6%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVA----RRPPGYAFVEFDDRRDAVDAIRALD 59
          +YVGNLDPRV+E  L+  F++ G +++V +      +   Y FVE+    DA  A++ L+
Sbjct: 1  LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 60 GK 61
          G+
Sbjct: 61 GR 62

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp

 Score = 47.8 bits (114), Expect = 8e-08
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSV-WVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
           VY G         D++  F   G +R V  ++R    +AF+ F++   A  AI  L+G 
Sbjct: 1  TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGA 60

Query: 62 N 62
          +
Sbjct: 61 S 61

This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 47.8 bits (114), Expect = 1e-07
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 5/63 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRAL 58
          ++VG+L P +    L   F  FG +    V +     +  GY FV F  + DA +AI+++
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 59 DGK 61
          +G+
Sbjct: 62 NGQ 64

This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 75

>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 46.5 bits (111), Expect = 2e-07
 Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 7/64 (10%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAI-----RA 57
          R+ V NL P V+E D+ + F   G L+   + R  PG A V +  + DA+ AI     R 
Sbjct: 2  RLVVSNLHPSVTEDDIVELFSAIGALKRARLVR--PGVAEVVYVRKDDALTAIDKYNNRE 59

Query: 58 LDGK 61
          LDG+
Sbjct: 60 LDGQ 63

This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Length = 69

>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 46.7 bits (111), Expect = 2e-07
 Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 3/59 (5%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          R+YV    P  SE  + + F  +G ++ V +      +AFVEF+    A+ A  ++ GK
Sbjct: 1  RLYVRPFPPDTSESAIREIFSPYGAVKEVKMIS---NFAFVEFESLESAIRAKDSVHGK 56

This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 67

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 46.6 bits (110), Expect = 2e-07
 Identities = 27/64 (42%), Positives = 37/64 (57%), Gaps = 6/64 (9%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKNG 63
          ++V NL   V+E  LE  F  FG L  V   ++   YAFV F++ RDA  A+RA+D  NG
Sbjct: 4  LFVRNLATTVTEEILEKSFSEFGKLERV---KKLKDYAFVHFEE-RDA--AVRAMDEMNG 57

Query: 64 WRVE 67
            +E
Sbjct: 58 KEIE 61

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 46.6 bits (111), Expect = 2e-07
 Identities = 28/65 (43%), Positives = 34/65 (52%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIR 56
           R++V NL     E DLE  F  FG L  V VA      +  G+A+V F D  DAV A +
Sbjct: 3  GRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYK 62

Query: 57 ALDGK 61
           LDGK
Sbjct: 63 ELDGK 67

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

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

 Score = 46.5 bits (111), Expect = 2e-07
 Identities = 26/64 (40%), Positives = 34/64 (53%), Gaps = 8/64 (12%)

Query: 5  YVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALD 59
          YVGNL   ++E DL   F  FG +  V + R     R  GY F++F    DA DA +AL+
Sbjct: 2  YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQF---ADAEDAKKALE 58

Query: 60 GKNG 63
            NG
Sbjct: 59 QLNG 62

This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 46.1 bits (110), Expect = 3e-07
 Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 5/64 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRA 57
          R++V NL    +E +L + F  FG +  V +      +R  G+AFV F     AV A   
Sbjct: 1  RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 58 LDGK 61
          LDG 
Sbjct: 61 LDGS 64

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 46.2 bits (110), Expect = 3e-07
 Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 5/66 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWV-----ARRPPGYAFVEFDDRRDAVDAIR 56
          + +YV N+       DL   F  +G +  V++      RRP G+A+V+F+D RDA DA+ 
Sbjct: 1  TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 57 ALDGKN 62
           LD   
Sbjct: 61 YLDRTR 66

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 49.4 bits (118), Expect = 4e-07
 Identities = 28/66 (42%), Positives = 37/66 (56%), Gaps = 8/66 (12%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
          + +YVG+LDP V+E  L D F+ FG + SV V R     R  GY +V F +  DA    R
Sbjct: 1  ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAE---R 57

Query: 57 ALDGKN 62
          AL+  N
Sbjct: 58 ALETMN 63

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 45.2 bits (108), Expect = 5e-07
 Identities = 14/43 (32%), Positives = 23/43 (53%)

Query: 20 DEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN 62
            F  FG +  + + ++ PG+AFVEF     A  A++ L+G  
Sbjct: 3  KLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVL 45

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 45.6 bits (109), Expect = 5e-07
 Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 4/62 (6%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP----GYAFVEFDDRRDAVDAIRALD 59
          +++ NLD  +  + L D F  FG + S  VA        GY FV F+    AV AI  ++
Sbjct: 5  IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVN 64

Query: 60 GK 61
          G 
Sbjct: 65 GM 66

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 45.4 bits (107), Expect = 5e-07
 Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 3/59 (5%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN 62
          ++V NL   V+E  LE  F  FG L  V   ++   YAF+ FD+R  AV A+  ++GK 
Sbjct: 4  LFVRNLANTVTEEILEKAFGQFGKLERV---KKLKDYAFIHFDERDGAVKAMEEMNGKE 59

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 45.3 bits (108), Expect = 6e-07
 Identities = 21/60 (35%), Positives = 32/60 (53%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
            + V NLD  +S+++L   F  FG ++ +      P   FVEF D R A  A+ AL+G+
Sbjct: 2  GTLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNGR 61

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 45.3 bits (108), Expect = 6e-07
 Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 2  SRV-YVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          SR  +V N++  V + +L   F  FG +R+++ A +  G+  V + D R A  A RAL G
Sbjct: 1  SRTLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQG 60

Query: 61 KNGWR 65
               
Sbjct: 61 TELGG 65

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 45.7 bits (108), Expect = 6e-07
 Identities = 26/65 (40%), Positives = 37/65 (56%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWV-----ARRPPGYAFVEFDDRRDAVDAIR 56
          S ++V N+       DL  EF  +G +  V+V      RRP G+A+V+F+D RDA DA+ 
Sbjct: 1  SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 57 ALDGK 61
           LD K
Sbjct: 61 NLDRK 65

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 45.2 bits (107), Expect = 6e-07
 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK- 61
          +++VGN+D   S+ +L   F  +G + S  V R+   +AFV       A  AI  L+G+ 
Sbjct: 2  KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ---FAFVHLRGEAAADRAIEELNGRE 58

Query: 62 -NGWR--VELS 69
           +G +  VE S
Sbjct: 59 LHGRKLVVEHS 69

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 45.2 bits (108), Expect = 7e-07
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 5/49 (10%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP-----GYAFVEFD 46
          R++VG L P V+E DLE+ F  FG +  V + ++       G+A+++  
Sbjct: 1  RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLR 49

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 44.9 bits (107), Expect = 8e-07
 Identities = 22/59 (37%), Positives = 27/59 (45%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          RV V  L    S +DL+D  R  G +    V R   G   VEF  + D   A+R LDG 
Sbjct: 2  RVVVSGLPEGASWQDLKDFGRQAGDVTYADVDRDQEGEGVVEFTSQEDMERALRKLDGT 60

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 45.0 bits (107), Expect = 8e-07
 Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWV-----ARRPPGYAFVEFDDRRDAVDAIR 56
          S VYV NL   ++  DL   F  +G +  V +      R+  G AF+ F DR DA   ++
Sbjct: 2  STVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVK 61

Query: 57 ALDGK 61
          AL+ K
Sbjct: 62 ALNNK 66

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 45.1 bits (107), Expect = 8e-07
 Identities = 25/69 (36%), Positives = 34/69 (49%), Gaps = 2/69 (2%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK- 61
          R+ V NL  RVS +DL+D  R  G +      ++ P    VEF    D   AI  LDG  
Sbjct: 2  RLIVENLSSRVSWQDLKDFMRKAGEVTYADAHKQRPNEGVVEFATYSDMKRAIEKLDGTE 61

Query: 62 -NGWRVELS 69
           NG +++L 
Sbjct: 62 LNGRKIKLI 70

This subfamily corresponds to the RRM2 of three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and is essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 44.8 bits (106), Expect = 1e-06
 Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 3/56 (5%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALD 59
          V+ GN +    + ++E  F  +G +  V       G+AFV  +D RDA DAIR LD
Sbjct: 3  VFCGNFEYDARQSEIERLFGKYGRVDRV---DMKSGFAFVYMEDERDAEDAIRGLD 55

This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 72

>gnl|CDD|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2)

 Score = 45.0 bits (106), Expect = 1e-06
 Identities = 24/63 (38%), Positives = 35/63 (55%), Gaps = 5/63 (7%)

Query: 1  MSRVYVGNLDPRVSERDLEDEF--RMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRAL 58
          M+++Y+GNL P V+  DL   F  R   +   V +     GYAFV++ D+  A+ AI  L
Sbjct: 1  MNKLYIGNLSPAVTAEDLRQLFGDRKLPLTGQVLLKS---GYAFVDYPDQNWAIRAIETL 57

Query: 59 DGK 61
           GK
Sbjct: 58 SGK 60

This subgroup corresponds to the RRM1 of IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also termed hepatocellular carcinoma autoantigen p62, or VICKZ family member 2, which is a ubiquitously expressed RNA-binding protein involved in the stimulation of insulin action. It is predominantly nuclear. SNPs in IGF2BP2 gene are implicated in susceptibility to type 2 diabetes. IGF2BP2 plays an important role in cellular motility; it regulates the expression of PINCH-2, an important mediator of cell adhesion and motility, and MURF-3, a microtubule-stabilizing protein, through direct binding to their mRNAs. IGF2BP2 may be involved in the regulation of mRNA stability through the interaction with the AU-rich element-binding factor AUF1. IGF2BP2 binds initially to nascent beta-actin transcripts and facilitates the subsequent binding of the shuttling IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. . Length = 77

>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 44.6 bits (106), Expect = 1e-06
 Identities = 22/58 (37%), Positives = 32/58 (55%), Gaps = 6/58 (10%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWV-----ARRPPGYAFVEFDDRRDAVDAI 55
          +++VG L   V+E DL + F  +G + SV +       +  G+AFV FDD  D VD I
Sbjct: 1  KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDD-YDPVDKI 57

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 44.5 bits (106), Expect = 1e-06
 Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 3/63 (4%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSV-WVARRPPGYAFVEFDDRRDAVDAIRALDGKN 62
          ++VG L P  S  +LE EF  FG +R + +   R   YA++E++    A  A  AL G  
Sbjct: 1  LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRN--YAYIEYESIEAAQAAKEALRGFP 58

Query: 63 GWR 65
             
Sbjct: 59 LGG 61

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 44.6 bits (106), Expect = 1e-06
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 5/63 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP-----GYAFVEFDDRRDAVDAIRA 57
          R+YV ++ P +SE D++  F  FG ++S  +A  P      GY F+E+++ + A DAI +
Sbjct: 2  RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61

Query: 58 LDG 60
          ++ 
Sbjct: 62 MNL 64

This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 77

>gnl|CDD|241069 cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1)

 Score = 44.3 bits (104), Expect = 2e-06
 Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 4/74 (5%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          M+++Y+GNL+  V+  DLE  F    +  S     +  GYAFV+  D + A+ AI    G
Sbjct: 1  MNKLYIGNLNESVTPADLEKVFEDHKISYSGQFLVK-SGYAFVDCPDEQWAMKAIETFSG 59

Query: 61 K---NGWRVELSHN 71
          K   +G R+E+ H+
Sbjct: 60 KVELHGKRLEIEHS 73

This subgroup corresponds to the RRM1 of IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also termed coding region determinant-binding protein (CRD-BP), or VICKZ family member 1, or zipcode-binding protein 1 (ZBP-1). IGF2BP1 is a multi-functional regulator of RNA metabolism that has been implicated in the control of aspects of localization, stability, and translation for many mRNAs. It is predominantly located in cytoplasm and was initially identified as a trans-acting factor that interacts with the zipcode in the 3'- untranslated region (UTR) of the beta-actin mRNA, which is important for its localization and translational regulation. It inhibits IGF-II mRNA translation through binding to the 5'-UTR of the transcript. IGF2BP1 also acts as human immunodeficiency virus type 1 (HIV-1) Gag-binding factor that interacts with HIV-1 Gag protein and blocks the formation of infectious HIV-1 particles. IGF2BP1 promotes mRNA stabilization; it functions as a coding region determinant (CRD)-binding protein that binds to the coding region of betaTrCP1 mRNA and prevents miR-183-mediated degradation of betaTrCP1 mRNA. It also promotes c-myc mRNA stability by associating with the CRD and stabilizes CD44 mRNA via interaction with the 3'-UTR of the transcript. In addition, IGF2BP1 specifically interacts with both Hepatitis C virus (HCV) 5'-UTR and 3'-UTR, further recruiting eIF3 and enhancing HCV internal ribosome entry site (IRES)-mediated translation initiation via the 3'-UTR. IGF2BP1 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. It also contains two putative nuclear export signals (NESs) and a putative nuclear localization signal (NLS). . Length = 77

>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 6/63 (9%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRP---PGYAFVEFDDRRDAVDAIRALDG 60
          ++VG L P V++ +L + F   G +  V + +R      +AF++F+       A RA++ 
Sbjct: 6  IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFE---REQAAARAVES 62

Query: 61 KNG 63
          +N 
Sbjct: 63 ENH 65

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 44.3 bits (105), Expect = 2e-06
 Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 4/61 (6%)

Query: 5  YVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPG----YAFVEFDDRRDAVDAIRALDG 60
          +VGNL+  ++E +L   F  +GV+  V + R P G    YAFV+F +   A  A  A+ G
Sbjct: 6  FVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAMSG 65

Query: 61 K 61
          +
Sbjct: 66 Q 66

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 47.7 bits (113), Expect = 2e-06
 Identities = 45/167 (26%), Positives = 66/167 (39%), Gaps = 39/167 (23%)

Query: 1   MSRV---YVGNLDPRVSERDLEDEFRMF--GVLRSVWVARRPPGYAFVEFDDRRDAVDAI 55
           M++V   YV NL    +E  +E  F  F  G +  V   ++   YAFV F+DR DAV A+
Sbjct: 230 MAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERV---KKIRDYAFVHFEDREDAVKAM 286

Query: 56  RALDGK--NGWRVEL-----------SHNSKGGGGRGGRGRGGGEDL-KCYEC-----GE 96
             L+GK   G  +E+              ++G GGRG   +   + L + Y+        
Sbjct: 287 DELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAY 346

Query: 97  PGHFARECRLR----------IGSRGLGSGRRRSPSPRRRRSPSYGY 133
             ++                 I  RG G    R+     R  P YGY
Sbjct: 347 EDYYYHPPYAPSLHFPRMPGPIRGRGRGGAPSRAAGG--RGYPPYGY 391

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 44.1 bits (104), Expect = 2e-06
 Identities = 18/62 (29%), Positives = 39/62 (62%), Gaps = 4/62 (6%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRAL 58
          +++VG L+ + +E+++E+ F  +G +  +++ R    +  G AFV++  +  A  AI+AL
Sbjct: 1  KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKAL 60

Query: 59 DG 60
          +G
Sbjct: 61 NG 62

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 44.3 bits (104), Expect = 2e-06
 Identities = 29/66 (43%), Positives = 35/66 (53%), Gaps = 8/66 (12%)

Query: 1  MSRV---YVGNLDPRVSERDLEDEFRMF--GVLRSVWVARRPPGYAFVEFDDRRDAVDAI 55
          MS V   YV NL    +E  +E EF     G +  V   R    YAFV F +R DAVDA+
Sbjct: 5  MSSVKILYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIR---DYAFVHFSNREDAVDAM 61

Query: 56 RALDGK 61
           AL+GK
Sbjct: 62 NALNGK 67

This subgroup corresponds to the RRM3 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 83

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 43.6 bits (103), Expect = 2e-06
 Identities = 23/59 (38%), Positives = 31/59 (52%), Gaps = 4/59 (6%)

Query: 4  VYVGNLDP-RVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          ++V   DP    E D+E  F  FG L    + R+   +AFVEF+D  DA  A+ AL G 
Sbjct: 2  LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI-RKT--FAFVEFEDSEDATKALEALHGS 57

This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. Length = 70

>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 43.9 bits (104), Expect = 2e-06
 Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 17/83 (20%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLR--------SVWVAR-----RPPGYAFVEFDDRRD 50
          V+V NL P  +E+DL + F   G+++         +W+ +      P G A V +DD   
Sbjct: 1  VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 51 AVDAIRALDGK----NGWRVELS 69
          A  AI   + K    N  +V L+
Sbjct: 61 ASAAIEWFNNKDFMGNTIKVSLA 83

This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 46.7 bits (111), Expect = 3e-06
 Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 4/61 (6%)

Query: 4   VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALD 59
           ++V NLD  V  + L D F  FG + S  VA     +  GY FV F+    A  AI+ ++
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVN 150

Query: 60  G 60
           G
Sbjct: 151 G 151

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 43.4 bits (103), Expect = 3e-06
 Identities = 25/59 (42%), Positives = 32/59 (54%), Gaps = 5/59 (8%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGY--AFVEFDDRRDAVDAIRALDG 60
          V+VG LDP V+E +L   F  FG +  V +   PPG    FV+F  R  A  AI+ L G
Sbjct: 4  VFVGGLDPAVTEDELRSLFGPFGEIVYVKI---PPGKGCGFVQFVHRAAAEAAIQQLQG 59

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 43.9 bits (104), Expect = 3e-06
 Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 6/66 (9%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
           SR+++      V+E DL + F  FG ++ +WV +        G A+V+F     A  A+
Sbjct: 3  NSRLFI-VCGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAM 61

Query: 56 RALDGK 61
            ++GK
Sbjct: 62 EEMNGK 67

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 43.4 bits (103), Expect = 3e-06
 Identities = 15/62 (24%), Positives = 34/62 (54%), Gaps = 6/62 (9%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRAL 58
          ++VGN+D   +  +L++ F+  G +  + +       +P G+A++EF D + +V+    L
Sbjct: 2  IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLD-KSSVENALLL 60

Query: 59 DG 60
          + 
Sbjct: 61 NE 62

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 43.5 bits (103), Expect = 3e-06
 Identities = 22/57 (38%), Positives = 32/57 (56%), Gaps = 6/57 (10%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFG-VL----RSVWVARRPPGYAFVEFDDRRDAVDAI 55
          ++VGNL   ++E +L++ F+ FG VL     S     R P + FV FDD  +AV  I
Sbjct: 6  LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDD-PEAVQKI 61

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 43.4 bits (103), Expect = 3e-06
 Identities = 24/69 (34%), Positives = 33/69 (47%), Gaps = 15/69 (21%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP-----------GYAFVEFDDRRDAV 52
          +YV NLD ++ E DL   F  FG + S+   R P            G+AFV F D   A 
Sbjct: 3  IYVRNLDFKLDEDDLRGIFSKFGEVESI---RIPKKQDEKQGRLNNGFAFVTFKDASSAE 59

Query: 53 DAIRALDGK 61
          +A+  L+G 
Sbjct: 60 NAL-QLNGT 67

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 43.5 bits (103), Expect = 3e-06
 Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 12/71 (16%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWV-----------ARRPPGYAFVEFDDRRDA 51
          RVY+ NL    SE DLE+  + F  + SV +             RP G A+ EF     A
Sbjct: 1  RVYISNLSYSSSEEDLEEFLKDFEPV-SVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59

Query: 52 VDAIRALDGKN 62
             ++ L+GK 
Sbjct: 60 EKVVKDLNGKV 70

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 43.1 bits (102), Expect = 4e-06
 Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 14 SERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
           +  LED F  FG L  V++      Y + ++ DR  A  AI  L GK
Sbjct: 12 PDYILEDVFCRFGGLIDVYLVPGK-NYGYAKYADRESAERAITTLHGK 58

This subfamily corresponds to the RRM4 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 68

>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score = 42.9 bits (101), Expect = 4e-06
 Identities = 24/59 (40%), Positives = 34/59 (57%), Gaps = 6/59 (10%)

Query: 6  VGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP---GYAFVEFDDRRDAVDAIRALDGK 61
          + NLDP VS   L   F+++G ++ +   R  P      FVEF D RDA  A+RA++GK
Sbjct: 6  IFNLDPTVSSETLRSIFQVYGDVKEL---RETPCKREQRFVEFFDVRDAAKALRAMNGK 61

This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 43.1 bits (102), Expect = 5e-06
 Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 4/61 (6%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALD 59
          ++VGNLD RV+E  L + F   G L  V + +    +P  +AFV F        AI+ L+
Sbjct: 4  LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLN 63

Query: 60 G 60
          G
Sbjct: 64 G 64

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 42.6 bits (101), Expect = 5e-06
 Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
           R++VGNL   ++E + ++ F  +G +  V++ +   G+ F+  D R +A  A   LDG 
Sbjct: 2  CRLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-KGFGFIRLDTRTNAEKAKAELDGI 60

Query: 62 NG 63
            
Sbjct: 61 MR 62

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 42.6 bits (101), Expect = 5e-06
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 9/70 (12%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWV----ARRPPGYAFVEFDDRRDAVDAIR- 56
          +++ V NLD  VS+ D+++ F  FG L+   V    + R  G A V F+ R DA+ A++ 
Sbjct: 1  TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60

Query: 57 ----ALDGKN 62
               LDG+ 
Sbjct: 61 YNGVPLDGRP 70

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 43.0 bits (102), Expect = 5e-06
 Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 5/70 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRAL 58
          V++ NL    +E +L++ F  FG ++   + +        G AFV+F  +  A   + A 
Sbjct: 3  VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 59 DGKNGWRVEL 68
          D      + L
Sbjct: 63 DNAEDSGLSL 72

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 42.6 bits (101), Expect = 6e-06
 Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 6/63 (9%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVW-----VARRPPGYAFVEFDDRRDAVDAIRAL 58
          V+V  L  +V ERDL + F   G +R V       +RR  G A+VEF D      A+  L
Sbjct: 2  VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GL 60

Query: 59 DGK 61
           G+
Sbjct: 61 TGQ 63

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 42.6 bits (101), Expect = 6e-06
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 5/62 (8%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWV----ARRPPGYAFVEFDDRRDAVDAIRA 57
          +R++VG + P  +E +L D F  FG ++ V +    A    GY FV F+  ++  + I A
Sbjct: 3  NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFET-QEDAEKILA 61

Query: 58 LD 59
          + 
Sbjct: 62 MG 63

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 42.4 bits (100), Expect = 6e-06
 Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 4/68 (5%)

Query: 5  YVGNLDPRVSERDLEDEFRMFGVLRSVWVARRP--PGYAFVEFDDRRDAVDAIRALDGK- 61
          ++GNL+   +  DL + F  FG +  + + ++   P YAF+++ D    V A+R +DG+ 
Sbjct: 6  FIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKMDGEY 65

Query: 62 -NGWRVEL 68
              RV+L
Sbjct: 66 LGNNRVKL 73

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 42.6 bits (101), Expect = 7e-06
 Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 5/63 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVA--RRP---PGYAFVEFDDRRDAVDAIRAL 58
          ++V  +     E D+ D+F  FG ++++ +   RR     GYA +E++ +++A  AI  L
Sbjct: 9  IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 59 DGK 61
          +GK
Sbjct: 69 NGK 71

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

>gnl|CDD|241071 cd12627, RRM1_IGF2BP3, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3)

 Score = 42.3 bits (99), Expect = 8e-06
 Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 4/74 (5%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          M+++Y+GNL    S  DLE  F+   +  S     +  GYAFV+  D   A+ AI  L G
Sbjct: 1  MNKLYIGNLSENASPLDLESIFKDSKIPFSGPFLVKS-GYAFVDCPDESWAMKAIDTLSG 59

Query: 61 K---NGWRVELSHN 71
          K   +G  +E+ H+
Sbjct: 60 KVELHGKVIEVEHS 73

This subgroup corresponds to the RRM1 of IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also termed KH domain-containing protein overexpressed in cancer (KOC), or VICKZ family member 3, an RNA-binding protein that plays an important role in the differentiation process during early embryogenesis. It is known to bind to and repress the translation of IGF2 leader 3 mRNA. IGF2BP3 also acts as a Glioblastoma-specific proproliferative and proinvasive marker acting through IGF2 resulting in the activation of oncogenic phosphatidylinositol 3-kinase/mitogen-activated protein kinase (PI3K/MAPK) pathways. IGF2BP3 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. . Length = 77

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 42.4 bits (100), Expect = 8e-06
 Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWV-----ARRPPGYAFVEFDDRRDAVDAIRA 57
           ++VGNL   V +  L+ EF  FG +    V       R  G+ +V+F+   DA  AI A
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 58 LDGK 61
          +DGK
Sbjct: 61 MDGK 64

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 42.1 bits (99), Expect = 9e-06
 Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 5/63 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVL---RSVWVAR--RPPGYAFVEFDDRRDAVDAIRAL 58
          ++VG+L P V++  L   F  F      R +W  +  R  GY FV F  ++DA +AI  +
Sbjct: 2  IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 59 DGK 61
          +GK
Sbjct: 62 NGK 64

This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 75

>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 42.1 bits (100), Expect = 1e-05
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 5/62 (8%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVW-----VARRPPGYAFVEFDDRRDAVDAIRAL 58
          +YVGNL    +E  + + F   G ++ +        + P G+ FVE+  R DA +A++ L
Sbjct: 1  LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 59 DG 60
          +G
Sbjct: 61 NG 62

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 4/62 (6%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALD 59
          VYV NL   + +  L++ F  +G + S  V +    +  G+ FV F++   A  A+  L+
Sbjct: 4  VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELN 63

Query: 60 GK 61
          GK
Sbjct: 64 GK 65

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 41.8 bits (98), Expect = 1e-05
 Identities = 24/61 (39%), Positives = 34/61 (55%), Gaps = 6/61 (9%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWV-----ARRPPGYAFVEFDDRRDAVDAIRAL 58
          VYVGN+D   +  +LE  F   G +  V +     +  P GYA++EF   RD+V+A  AL
Sbjct: 2  VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFAT-RDSVEAAVAL 60

Query: 59 D 59
          D
Sbjct: 61 D 61

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 12/23 (52%), Positives = 17/23 (73%)

Query: 39 GYAFVEFDDRRDAVDAIRALDGK 61
          GYAFVEF    +A +A++AL+G 
Sbjct: 51 GYAFVEFATPEEAKEAVKALNGY 73

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 5/55 (9%)

Query: 5  YVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDA 54
          +V  L+P  ++ DLE  F  FG ++S  V R         YAF+EF+ + D  +A
Sbjct: 7  FVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 41.3 bits (97), Expect = 2e-05
 Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 6/57 (10%)

Query: 6  VGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPG---YAFVEFDDRRDAVDAIRALD 59
          V NLDP VS  DL   F  +G ++ +   R  P    + F+EF D R A  A++AL+
Sbjct: 6  VFNLDPSVSNDDLHQIFGAYGEIKEI---RETPNKRHHKFIEFYDVRSAEAALKALN 59

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 5/66 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPG--YAFVEFDDRRDAVDAIRALDGK 61
          +YVG +    +  +L   F+ FG +  + +  R  G  Y FV +   R A DA RA++  
Sbjct: 5  IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTY---RYACDAFRAIEHG 61

Query: 62 NGWRVE 67
          N    E
Sbjct: 62 NDDPTE 67

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 41.2 bits (97), Expect = 2e-05
 Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 5/63 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVW-----VARRPPGYAFVEFDDRRDAVDAIRA 57
          R+++ NL    +E DLE  F  +G L  V      + ++P G+AFV +     AV A   
Sbjct: 4  RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 58 LDG 60
          LDG
Sbjct: 64 LDG 66

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 41.3 bits (97), Expect = 2e-05
 Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP--GYAFVEFDDRRDAVDAIRALD 59
          + VYVGN+ P  ++ DL   F+ FG +      R  P  G+AFV+ D    A  AI  L 
Sbjct: 1  TTVYVGNIPPYTTQADLIPLFQNFGYILE---FRHQPDRGFAFVKLDTHEQAAMAIVQLQ 57

Query: 60 GKN 62
          G  
Sbjct: 58 GFP 60

This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 41.0 bits (97), Expect = 3e-05
 Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
          +++VG L    +E D+   F  +G +  V + R     +  G AFV+F  R +A  AI A
Sbjct: 1  KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 58 LDGK 61
          L GK
Sbjct: 61 LHGK 64

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 5/59 (8%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
          ++VG L  + +E  L + F  +G +R + + R        GYAFVE++  RDA+ A R 
Sbjct: 6  LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 40.6 bits (95), Expect = 3e-05
 Identities = 20/63 (31%), Positives = 37/63 (58%), Gaps = 4/63 (6%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR----PPGYAFVEFDDRRDAVDAIRA 57
          +++ V NL    +++D+   F  +G L+SV V ++      G+AFVEF   ++A++A+ A
Sbjct: 1  TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNA 60

Query: 58 LDG 60
          L  
Sbjct: 61 LKD 63

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 40.8 bits (96), Expect = 3e-05
 Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 6/58 (10%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWV-----ARRPPGYAFVEFDDRRDAVDAI 55
          +++VG L P V+E DL   F  FG +  V V      +RP G+ F+ F+   D+VD +
Sbjct: 4  KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFES-EDSVDQV 60

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 40.5 bits (95), Expect = 4e-05
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKNG 63
          VY+GNL    SE +L ++   FG +  + + +     AFV F    +A+  +  L  +  
Sbjct: 6  VYIGNLPESYSEEELREDLEKFGPIDQIKIVKE-KNIAFVHFLSIANAIKVVTTLPCEPD 64

Query: 64 W 64
          +
Sbjct: 65 Y 65

This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 78

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 40.6 bits (95), Expect = 4e-05
 Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 5/64 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
          ++++G L    +E+ LE  F  +G +  V V +     R  G+ FV F++  DA DA+ A
Sbjct: 2  KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 58 LDGK 61
          ++GK
Sbjct: 62 MNGK 65

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 43.9 bits (103), Expect = 4e-05
 Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 5/62 (8%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP-----GYAFVEFDDRRDAVDAIRA 57
           R+YV ++ P +SE D++  F  FG +    +AR P      GY F+E+++ +   +AI +
Sbjct: 206 RIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS 265

Query: 58  LD 59
           ++
Sbjct: 266 MN 267

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 39.9 bits (94), Expect = 6e-05
 Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 9/73 (12%)

Query: 6  VGNLDPRVSERDLEDEFRMFGVLRSVWV-----ARRPPGYAFVEFDDRRDAVDAIRALDG 60
          V  L    +ERDL + F  +G +  V V       R  G+ FV F+   DA +A   L+G
Sbjct: 4  VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNG 63

Query: 61 KNGW----RVELS 69
                  RV+ S
Sbjct: 64 MEIDGRRIRVDYS 76

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

>gnl|CDD|189387 pfam00098, zf-CCHC, Zinc knuckle

 Score = 38.6 bits (91), Expect = 6e-05
 Identities = 10/16 (62%), Positives = 12/16 (75%)

Query: 90  KCYECGEPGHFARECR 105
           KCY CG+ GH AR+C 
Sbjct: 2   KCYNCGKEGHLARDCP 17

The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger. Length = 18

>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 39.8 bits (93), Expect = 7e-05
 Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 5/62 (8%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRAL 58
          +Y+G+L     E++L+  F  FG +++V VAR         Y F++F +   A  A +++
Sbjct: 2  IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 59 DG 60
          + 
Sbjct: 62 NN 63

This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 40.0 bits (93), Expect = 7e-05
 Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWV-----ARRPPGYAFVEFDDRRDAVDAIR 56
          + ++V N+       DL  EF  +G +  V+V      RRP G+A+++F+D RDA DA+ 
Sbjct: 1  TSLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALY 60

Query: 57 ALDGK 61
           L+ K
Sbjct: 61 NLNRK 65

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 39.8 bits (94), Expect = 8e-05
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 15 ERDLEDEFRMFGVLRSVWVARRPP-GYAFVEFDDRRDAVDAIRALDG 60
          + D+ +E   FG +  + V +  P G  +V+F     A   I+AL+G
Sbjct: 25 KEDVLEECSKFGPVEHIKVDKNSPEGVVYVKFKTVEAAQKCIQALNG 71

This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 39.1 bits (91), Expect = 9e-05
 Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 3/56 (5%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRAL 58
          +++VGNL P  +E+++   F  +G +    + +    Y FV  DD+  A +AIR L
Sbjct: 2  KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIK---NYGFVHMDDKTAADEAIRNL 54

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 42.1 bits (99), Expect = 1e-04
 Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 4/64 (6%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP----GYAFVEFDDRRDAVDAIRA 57
             +YV NLD  V++  L + F   G + S  V         G+ FV F +  +A  A+  
Sbjct: 286 VNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTE 345

Query: 58  LDGK 61
           + G+
Sbjct: 346 MHGR 349

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|241168 cd12724, RRM1_CPEB2_like, RNA recognition motif 1 in cytoplasmic polyadenylation element-binding protein CPEB-2, CPEB-3, CPEB-4 and similar protiens

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 7/62 (11%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR------RPP-GYAFVEFDDRRDAVDAI 55
          +V+VG L P + E ++   FR FG L   W  +       PP GYAF+ F +       I
Sbjct: 2  KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 61

Query: 56 RA 57
           A
Sbjct: 62 DA 63

This subgroup corresponds to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and CPEB-4, all well-conserved in both, vertebrates and invertebrates. Due to the high sequence similarity, members in this family may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. Moreover, CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All family members contain an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. In addition, they do have conserved nuclear export signals that are not present in CPEB-1. . Length = 92

>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 10/67 (14%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP-------GYAFVEFDDRRDAVDAI 55
          R+ V NL  + +E DL+  F  FG    VW    P        G+AFV+F  + DA  AI
Sbjct: 1  RLIVRNLPFKCTEADLKKLFSPFG---FVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAI 57

Query: 56 RALDGKN 62
          + ++GK 
Sbjct: 58 KGVNGKK 64

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

>gnl|CDD|197667 smart00343, ZnF_C2HC, zinc finger

 Score = 37.4 bits (88), Expect = 1e-04
 Identities = 10/16 (62%), Positives = 12/16 (75%)

Query: 90  KCYECGEPGHFARECR 105
           KCY CG+ GH AR+C 
Sbjct: 1   KCYNCGKEGHIARDCP 16

Length = 17

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 38.7 bits (91), Expect = 1e-04
 Identities = 18/61 (29%), Positives = 38/61 (62%), Gaps = 4/61 (6%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP----GYAFVEFDDRRDAVDAIRA 57
          +++ V N+    ++++L + F  FG ++SV + ++      G+AFVEF  +++A +A+ A
Sbjct: 1  TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

Query: 58 L 58
          L
Sbjct: 61 L 61

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 38.7 bits (91), Expect = 1e-04
 Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 4/63 (6%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPG----YAFVEFDDRRDAVDAIRA 57
          SR+ V NL   V+E  L + F   G +  V V R   G    + FV F    DA  A++ 
Sbjct: 1  SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKY 60

Query: 58 LDG 60
           + 
Sbjct: 61 FNK 63

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 11/27 (40%), Positives = 13/27 (48%)

Query: 82  GRGGGEDLKCYECGEPGHFARECRLRI 108
              G     CY CG+ GH +REC  R 
Sbjct: 71  APPGSGPRSCYNCGQTGHISRECPNRA 97

Length = 148

>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 3/54 (5%)

Query: 8  NLDPRVSERDLEDEFRMFGVLRSV-WVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          NL    ++  LE  F  F   + V  V RR  G AFVEF+    A  A++AL G
Sbjct: 9  NLPEETTKEMLEMLFNQFPGFKEVRLVPRR--GIAFVEFETEEQATVALQALQG 60

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 7/64 (10%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFG-------VLRSVWVARRPPGYAFVEFDDRRDAVDA 54
           R++VG +    ++ ++ +EF           V RS     +  G+AFVE++  R A  A
Sbjct: 2  CRLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMA 61

Query: 55 IRAL 58
           R L
Sbjct: 62 RRKL 65

This subfamily corresponds to the RRM2 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains); DND1 harbors only two RRMs. . Length = 82

>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 38.5 bits (89), Expect = 2e-04
 Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 3/58 (5%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALD 59
          ++++VGN+    + ++L  +F  +G +    + +    YAFV  +   DAV+AIR LD
Sbjct: 1  TKLHVGNISSSCTNQELRAKFEEYGPVIECDIVK---DYAFVHMERAEDAVEAIRGLD 55

This subgroup corresponds to the RRM2 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 6/72 (8%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVL-RSVWVAR----RPPGYAFVEFDDRRDAVDAIRAL 58
          V +  L    +E D+ D F    +    + +      RP G A+VEF    DA  A+R  
Sbjct: 2  VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKH 61

Query: 59 DGKNGWR-VELS 69
          + K G R +E+ 
Sbjct: 62 NNKMGGRYIEVF 73

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWV-----ARRPPGYAFVEFDDRRDAVDAIRAL 58
          V+VGN+    +E  L + F   G + S  +       +P GY F EF+D   A  AIR L
Sbjct: 1  VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 59 DGK 61
          +G 
Sbjct: 61 NGY 63

This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. Length = 75

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

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 5/56 (8%)

Query: 12 RVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN 62
           +++ +L   F   G + S  + R     +  GY FV++ D  DA  AI  L+G  
Sbjct: 11 DMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFE 66

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 5/62 (8%)

Query: 5  YVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALD 59
          ++G+L+P + E  +   F   G + SV + R     +  GY FVEF     A  A+++L+
Sbjct: 3  WMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLN 62

Query: 60 GK 61
          GK
Sbjct: 63 GK 64

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 12/67 (17%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP-----GYAFVEFDDRRDAV--DAIR 56
          ++V NL    ++  LE+ F   G ++  +V +        G+ +V F     A+  DA R
Sbjct: 2  LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTF-----ALEEDAKR 56

Query: 57 ALDGKNG 63
          AL+ K  
Sbjct: 57 ALEEKKK 63

This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 79

>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 7/64 (10%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVW------VARRPPGYAFVEFDDRRDAVDAIR 56
           V+VGN+   VS+  +       G + S W         +   + F EF+D   A+ A+R
Sbjct: 2  TVFVGNIPEGVSDDFIRKLLEKCGKVLS-WKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 57 ALDG 60
           L+G
Sbjct: 61 LLNG 64

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 37.9 bits (88), Expect = 3e-04
 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 6/62 (9%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWV-----ARRPPGYAFVEFDDRRDAVDAIRAL 58
          VYVGN+D   +  +LE  F   G +  V +     +  P G+A++EF D +++V    AL
Sbjct: 2  VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTALAL 60

Query: 59 DG 60
          D 
Sbjct: 61 DE 62

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 5/64 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP-----GYAFVEFDDRRDAVDAIRA 57
          R++VG+L   V++  L   F  +   +   V R        GY FV F D  D + A++ 
Sbjct: 8  RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKE 67

Query: 58 LDGK 61
          ++GK
Sbjct: 68 MNGK 71

This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 37.7 bits (87), Expect = 3e-04
 Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 4/61 (6%)

Query: 2  SRVYVGNLDPR-VSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          SRV++GNL+   V + D+E  F  +G +    V +   G+AFV++ + R+A  A+   DG
Sbjct: 2  SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK---GFAFVQYVNERNARAAVAGEDG 58

Query: 61 K 61
          +
Sbjct: 59 R 59

This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex. They are involved in the packaging of hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site. . Length = 71

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 37.7 bits (88), Expect = 4e-04
 Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 4/63 (6%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALD 59
          ++V NLD +V  + L++ F++ G +    +      +  G   V+F+   +AV AI   +
Sbjct: 1  IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 60 GKN 62
          G+ 
Sbjct: 61 GQM 63

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 4/61 (6%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFG-VLRS---VWVARRPPGYAFVEFDDRRDAVDAIRALD 59
          ++V NL   V+ +DL+D FR  G VLR+        R  G+  V F+   DA  AI   +
Sbjct: 1  IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 60 G 60
          G
Sbjct: 61 G 61

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate RNA-binding protein 46 (RBM46)

 Score = 37.7 bits (87), Expect = 4e-04
 Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 7/70 (10%)

Query: 4  VYVGNLDPRVSERDLEDEFRMF--GVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          +YV NL    +E  ++ EF  F  GV+  V   ++   YAFV F +R DAV A+  ++GK
Sbjct: 4  LYVRNLMISTTEETIKAEFNKFKPGVVERV---KKLRDYAFVHFFNREDAVAAMSVMNGK 60

Query: 62 --NGWRVELS 69
            +G  +E++
Sbjct: 61 CIDGASIEVT 70

This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|240694 cd12248, RRM_RBM44, RNA recognition motif in RNA-binding protein 44 (RBM44) and similar proteins

 Score = 37.2 bits (86), Expect = 5e-04
 Identities = 20/58 (34%), Positives = 29/58 (50%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          V+VG L P VSE DL   F+ + V            YA + FD   DA+ A++ ++G 
Sbjct: 2  VHVGGLSPSVSEGDLRSHFQKYQVSVISLCKLSNYRYASLHFDRASDALLAVKKMNGG 59

This subgroup corresponds to the RRM of RBM44, a novel germ cell intercellular bridge protein that is localized in the cytoplasm and intercellular bridges from pachytene to secondary spermatocyte stages. RBM44 interacts with itself and testis-expressed gene 14 (TEX14). Unlike TEX14, RBM44 does not function in the formation of stable intercellular bridges. It carries an RNA recognition motif (RRM) that could potentially bind a multitude of RNA sequences in the cytoplasm and help to shuttle them through the intercellular bridge, facilitating their dispersion into the interconnected neighboring cells. Length = 74

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 37.4 bits (86), Expect = 5e-04
 Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 5/63 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRAL 58
          V+VG+L P ++  D++  F  FG +    V +     +  GY FV F ++ DA +AI+ +
Sbjct: 4  VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 59 DGK 61
           G+
Sbjct: 64 GGQ 66

This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 37.2 bits (86), Expect = 6e-04
 Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 5/64 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
          + +YV  L   +++++LE  F  +G + +  + R        G  F+ FD R +A +AI+
Sbjct: 1  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 57 ALDG 60
           L+G
Sbjct: 61 GLNG 64

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 37.4 bits (86), Expect = 6e-04
 Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 5/63 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRAL 58
          V+VG+L P ++  D++  F  FG +    V +     +  GY FV F ++ DA +AI  +
Sbjct: 4  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 59 DGK 61
           G+
Sbjct: 64 GGQ 66

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 37.3 bits (87), Expect = 6e-04
 Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 5/69 (7%)

Query: 5  YVGNLDPRVSERDLEDEFRMFGVLRSVWVARRP-----PGYAFVEFDDRRDAVDAIRALD 59
           VGNL    ++    +    FG +   ++          GY FVE+  +  A+ A   LD
Sbjct: 3  CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62

Query: 60 GKNGWRVEL 68
          GK     +L
Sbjct: 63 GKQIGGRKL 71

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 36.9 bits (86), Expect = 6e-04
 Identities = 19/59 (32%), Positives = 37/59 (62%), Gaps = 3/59 (5%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP-GYAFVEFDDRRDAVDAIRALDGK 61
          +++G+L  +V+E DL++ F  +G ++S+ +   PP G A+V  + R+DA  A++ L   
Sbjct: 5  LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI--PPRGCAYVCMETRQDAHRALQKLRNV 61

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 36.9 bits (86), Expect = 6e-04
 Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 4/58 (6%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIR 56
           ++VGNL     + DLE+ F+  G +  V +A+    R  G+  VEF     A  A+ 
Sbjct: 1  TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE 58

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 37.0 bits (86), Expect = 6e-04
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 4/62 (6%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGY----AFVEFDDRRDAVDAIRAL 58
          +++VG L  + +E D+   F  FG +    + R P G     AFV+F    +A  AI AL
Sbjct: 3  KLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINAL 62

Query: 59 DG 60
           G
Sbjct: 63 HG 64

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 36.9 bits (86), Expect = 7e-04
 Identities = 22/55 (40%), Positives = 26/55 (47%), Gaps = 4/55 (7%)

Query: 6  VGNLDPRVSERDLEDEFRMFG-VLRSVWVAR---RPPGYAFVEFDDRRDAVDAIR 56
          V NL P VS   LE  F  FG V R+V +     R  G   VEF  +  A  AI+
Sbjct: 4  VKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIK 58

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 39.5 bits (92), Expect = 8e-04
 Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 8/69 (11%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRP-----PGYAFVEFDDRRDAVDAIRA 57
           ++YVGNL   ++E++L   F  FG +  V + R P      G+ F++F    DA +A  A
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQF---HDAEEAKEA 244

Query: 58  LDGKNGWRV 66
           L+  NG+ +
Sbjct: 245 LEVMNGFEL 253

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 36.8 bits (85), Expect = 8e-04
 Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 5/64 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
          + +YV NL  +++E +L   F  +G +    + R      P G AFV +D R +A  AI 
Sbjct: 1  TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 57 ALDG 60
          +L+G
Sbjct: 61 SLNG 64

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 38.1 bits (88), Expect = 8e-04
 Identities = 36/108 (33%), Positives = 48/108 (44%), Gaps = 23/108 (21%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFG--VLRSVWVAR---RPPGYAFVEFDDRRDAVDAIR 56
           +++++G L     +  L D F  FG  V   V V R   R  G+ FV F+D   A  AI 
Sbjct: 35  TKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAIS 94

Query: 57  ALDGK--NGWRVELS----------------HNSKGGGGRGGRGRGGG 86
            +DGK  NG  + ++                  S GGGG GG G GGG
Sbjct: 95  EMDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGGGGYGGGGDGGG 142

Length = 144

>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 36.8 bits (85), Expect = 8e-04
 Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 8/73 (10%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWV-----ARRPPGYAFVEFDDRRDAVD--AI 55
          +++VG L   V E DL + F  FG +    V       +  G+ FV F +  D+ D  A+
Sbjct: 1  KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQN-HDSADKAAV 59

Query: 56 RALDGKNGWRVEL 68
                NG RVE+
Sbjct: 60 VKFHPINGHRVEV 72

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 36.9 bits (86), Expect = 8e-04
 Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 11/66 (16%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFG------VL--RSVWVARRPPGYAFVEFDDRRDAVDAI 55
          +YV  L   +++++LE  F  +G      +L      ++R   G  F+ FD R +A  AI
Sbjct: 3  LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSR---GVGFIRFDKRIEAERAI 59

Query: 56 RALDGK 61
          +AL+G 
Sbjct: 60 KALNGT 65

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 36.4 bits (84), Expect = 9e-04
 Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 4/55 (7%)

Query: 4  VYVGNLDP-RVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRA 57
          ++V N DP     RDLE  F  +G L +V + R    +AFV+++ + DA  A+ +
Sbjct: 2  LFVINFDPINTRTRDLERHFEPYGKLVNVRIRR---NFAFVQYETQEDATKALES 53

This subgroup corresponds to the RRM2 in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 70

>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 5/53 (9%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDA 51
          VY+G+L     E +L   F  FG +  + ++R     +  GYAFVEF+    A
Sbjct: 2  VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVA 54

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 4/61 (6%)

Query: 5  YVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDG 60
          YV NLD  + +  L +EF  FG + S  V      R  G+ FV F    +A  A+  ++G
Sbjct: 5  YVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMNG 64

Query: 61 K 61
          +
Sbjct: 65 R 65

This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 7/65 (10%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGV--LRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
          +YVGNL    ++ DLE      GV  ++S+         +  G+A+VEF     A     
Sbjct: 1  LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 57 ALDGK 61
           L+G+
Sbjct: 61 KLEGR 65

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 36.3 bits (84), Expect = 0.001
 Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 4/55 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWV----ARRPPGYAFVEFDDRRDAV 52
          +R++VG +D + +E DL   F  +G ++ V +    A    GY FV F+ + DA 
Sbjct: 3  NRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQ 57

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins

 Score = 36.3 bits (84), Expect = 0.001
 Identities = 21/62 (33%), Positives = 28/62 (45%), Gaps = 4/62 (6%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVL-RSVWVARRPPG---YAFVEFDDRRDAVDAIRALD 59
          +YV         RDL  EF  +G L R      R      +AFVE++  RDA DA   + 
Sbjct: 2  LYVTGFGAETRARDLAYEFERYGRLVRCDIPPPRTFQSRPFAFVEYESHRDAEDAYEEMH 61

Query: 60 GK 61
          G+
Sbjct: 62 GR 63

This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but not essential for growth. Srp1p is closely related to the SR protein family found in metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. Some family members also contain another RRM domain. Length = 78

>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 5/64 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWV-----ARRPPGYAFVEFDDRRDAVDAIRAL 58
          VY+  L P  ++ DLE   + FG + S          +  GY FV+FD    A+ AI  L
Sbjct: 3  VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62

Query: 59 DGKN 62
          +G+ 
Sbjct: 63 NGRG 66

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 38.4 bits (89), Expect = 0.002
 Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 5/64 (7%)

Query: 4   VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP-----GYAFVEFDDRRDAVDAIRAL 58
           ++V NL P   E  L   F  FG +++V + R        GY FV   +  +A  AI +L
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 59  DGKN 62
           +G  
Sbjct: 332 NGYT 335

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 5/50 (10%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSV---W--VARRPPGYAFVEFD 46
           RVYVG++   + E  +   F  FG ++S+   W  V  +  G+AFVE++
Sbjct: 1  CRVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYE 50

This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 76

>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 4/62 (6%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPG----YAFVEFDDRRDAVDAIRALD 59
          +++GNLD  V+E DL   F  FGV+  V + R   G    Y F++F++   A  A  A+ 
Sbjct: 10 LFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKLAMS 69

Query: 60 GK 61
          GK
Sbjct: 70 GK 71

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 3/59 (5%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          +++VGN+    +  +L   F  FG +      +    YAFV  +   +A+ AI AL+GK
Sbjct: 2  KIFVGNVSATCTSDELRGLFEEFGRVVECDKVK---DYAFVHMEREEEALAAIEALNGK 57

This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 68

>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 35.5 bits (82), Expect = 0.002
 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 5/62 (8%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRAL 58
          V+VGN+    +E  L+D F   G + S  +       +P GY F E+ D+  A+ A+R L
Sbjct: 1  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 59 DG 60
          +G
Sbjct: 61 NG 62

This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. . Length = 75

>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 11/24 (45%), Positives = 14/24 (58%)

Query: 81  RGRGGGEDLKCYECGEPGHFAREC 104
              GG  +  CY CG+ GH +REC
Sbjct: 45  SAPGGRGERSCYNCGKTGHLSREC 68

Length = 148

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 35.1 bits (81), Expect = 0.003
 Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 6/70 (8%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR-A 57
          ++VGNL    +E +L   F   G +R V +       +  G+AFV+F++   A +A++  
Sbjct: 1  LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60

Query: 58 LDGKNGWRVE 67
                 RVE
Sbjct: 61 HLNGRALRVE 70

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 35.0 bits (80), Expect = 0.003
 Identities = 25/70 (35%), Positives = 34/70 (48%), Gaps = 7/70 (10%)

Query: 4  VYVGNLDPRVSERDLEDEFRMF--GVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          +YV NL    SE  ++  F  F  G +  V   R    YAFV F  R DAV A+  L+G 
Sbjct: 4  LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIR---DYAFVHFTSREDAVHAMNNLNGT 60

Query: 62 --NGWRVELS 69
             G  +E++
Sbjct: 61 ELEGSCIEVT 70

This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 35.2 bits (82), Expect = 0.003
 Identities = 24/73 (32%), Positives = 33/73 (45%), Gaps = 17/73 (23%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLR-------------SVWVARRPPGYAFVEFDD 47
            R+YVGNL P ++E +L D F     +              SV +      +AFVEF  
Sbjct: 1  ARRLYVGNLPPGITEEELVDFFN--QAMLAAGLNQAPGNPVLSVQIN-PEKNFAFVEFRT 57

Query: 48 RRDAVDAIRALDG 60
            +A  A+ ALDG
Sbjct: 58 VEEATAAL-ALDG 69

The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 82

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 35.1 bits (81), Expect = 0.003
 Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 6/63 (9%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP------GYAFVEFDDRRDAVDAI 55
          S++ V N+    + ++L + F  FG L++V + ++        G+ FV+F  ++DA  A 
Sbjct: 1  SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAF 60

Query: 56 RAL 58
          +AL
Sbjct: 61 KAL 63

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 34.9 bits (81), Expect = 0.003
 Identities = 17/50 (34%), Positives = 26/50 (52%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDA 51
           +V+VG L   ++E DL   F  FG +  V++ +    +AFV F D   A
Sbjct: 1  RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTFADPEVA 50

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 35.0 bits (81), Expect = 0.003
 Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 7/61 (11%)

Query: 5  YVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALD 59
          +VGNL     + DL+  F+   V +SV + R     +  G+ +VEF+D     +A+   D
Sbjct: 5  FVGNLPFNTVQGDLDAIFKDLSV-KSVRLVRDKETDKFKGFCYVEFEDVESLKEAL-EYD 62

Query: 60 G 60
          G
Sbjct: 63 G 63

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)

 Score = 35.0 bits (80), Expect = 0.003
 Identities = 26/60 (43%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 6  VGNLDPRVSERDLEDEFRMFG-VLRSVWVAR---RPPGYAFVEFDDRRDAVDAI-RALDG 60
          V NL P VS   LE  F  FG V R+V +     RP G  FVEF  +  A  A+ R  DG
Sbjct: 4  VKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKALERCADG 63

This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 35.1 bits (80), Expect = 0.004
 Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 3/61 (4%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPG---YAFVEFDDRRDAVDAIRALDG 60
          +YVGNL   V+E  +   F   G  +S  +         Y FVEF + RDA  A+ A++G
Sbjct: 2  LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNG 61

Query: 61 K 61
          +
Sbjct: 62 R 62

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 81

>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 34.8 bits (80), Expect = 0.004
 Identities = 21/58 (36%), Positives = 30/58 (51%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          ++V N+   V+E  L   F ++G +R V   R   G   V F D RDA  A+R L G+
Sbjct: 4  LFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVRELCGR 61

This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

 Score = 36.8 bits (85), Expect = 0.004
 Identities = 21/89 (23%), Positives = 34/89 (38%), Gaps = 7/89 (7%)

Query: 87  EDLKCYECGEPGHFARECRLRIGSRGLGSGRRRSPSPRRRRSPSYG----YGRRC---GS 139
           E+  C+ CG+ GH  R+C   I       G R +  P+ ++  + G      R C     
Sbjct: 59  ENPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSKD 118

Query: 140 RAMSSSAMAQGSYTYESCNSINVESVSSP 168
           +  S        ++ E C SI    V + 
Sbjct: 119 QQKSCFDCNSTRHSSEDCPSIWKHYVLNN 147

Length = 190

>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 34.7 bits (80), Expect = 0.004
 Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 6/64 (9%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAI-----RAL 58
          V+V       SE  L D F  FG + +V + +    YA VEFD  ++ VD +       L
Sbjct: 5  VFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKDKGVYAIVEFDS-KEGVDKVLSEPQHTL 63

Query: 59 DGKN 62
          +G  
Sbjct: 64 NGHR 67

This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS). . Length = 74

>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 34.6 bits (80), Expect = 0.004
 Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 5/62 (8%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP-----GYAFVEFDDRRDAVDAIRAL 58
          ++V NL P   E  L   F  FG + +V V R        GY FV   +  +A  AI +L
Sbjct: 4  IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 59 DG 60
          +G
Sbjct: 64 NG 65

This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	223
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.9
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.7
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.64
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.57
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.55
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.52
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.51
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.49
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.47
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.47
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.47
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.46
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.44
PLN03120	260	nucleic acid binding protein; Provisional	99.42
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.41
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.39
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.36
smart00362	72	RRM_2 RNA recognition motif.	99.33
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.33
PLN03213	759	repressor of silencing 3; Provisional	99.31
KOG0122	270	consensus Translation initiation factor 3, subunit	99.31
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.3
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.3
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.27
PLN03121	243	nucleic acid binding protein; Provisional	99.26
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.26
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.25
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.24
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.24
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.23
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.22
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.22
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.22
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.21
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.16
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.16
smart00360	71	RRM RNA recognition motif.	99.15
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.15
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.14
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.14
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.13
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.09
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.08
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.07
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.05
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.0
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.98
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.96
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	98.95
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.95
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.93
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.93
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.92
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	98.91
smart00361	70	RRM_1 RNA recognition motif.	98.85
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	98.85
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.84
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.81
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.81
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.8
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.8
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.73
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.73
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.7
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.63
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.61
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.61
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.6
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.57
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.55
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.55
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.48
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.44
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.41
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.4
KOG0151	877	consensus Predicted splicing regulator, contains R	98.38
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.37
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.36
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.34
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.29
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.24
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.23
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.22
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.11
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.1
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.08
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.03
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.91
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.83
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.81
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	97.73
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.61
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.54
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	97.53
KOG0226	290	consensus RNA-binding proteins [General function p	97.32
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.32
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.32
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.06
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	96.99
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.99
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.8
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.79
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.75
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	96.7
KOG4210	285	consensus Nuclear localization sequence binding pr	96.62
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.47
KOG2314	698	consensus Translation initiation factor 3, subunit	96.44
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.37
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.33
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.31
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	96.3
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	96.23
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	96.05
KOG1548	382	consensus Transcription elongation factor TAT-SF1	96.03
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.71
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	95.55
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	94.99
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	94.75
KOG3152	278	consensus TBP-binding protein, activator of basal	94.62
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	94.59
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	94.49
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	94.42
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	94.37
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	94.24
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.09
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	93.42
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	93.42
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	92.69
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	92.46
KOG1996	378	consensus mRNA splicing factor [RNA processing and	92.05
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	91.98
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	90.39
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	89.77
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	88.06
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	87.36
KOG4660	549	consensus Protein Mei2, essential for commitment t	87.16
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	86.7
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	86.33
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	85.61
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	84.76
KOG2591	684	consensus c-Mpl binding protein, contains La domai	84.72
KOG2068	327	consensus MOT2 transcription factor [Transcription	82.33
KOG4210	285	consensus Nuclear localization sequence binding pr	80.93
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	80.88

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

Probab=99.90  E-value=2.1e-22  Score=162.12  Aligned_cols=109  Identities=53%  Similarity=0.944  Sum_probs=89.1

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--c--EEEEEeeccCCCC
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--G--WRVELSHNSKGGG   76 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g--~~V~v~~~~~~~r   76 (223)
                      .++||||||+..+++.||+.+|.+||+|..|.|...+.|||||+|+++.||++|+..|+|+.  +  ++||++...+...
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r~~   89 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPRGS   89 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCcccc
Confidence            47999999999999999999999999999999988999999999999999999999999998  5  7788777766533


Q ss_pred             CCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCC
Q 041602           77 GRGGRGRGGGEDLKCYECGEPGHFARECRLRIGS  110 (223)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~g~~G~~~r~~~~~~~r  110 (223)
                      ..++.. ...+..-|+.||..||+.++|.+...+
T Consensus        90 r~gg~~-~~~g~~~~~r~G~rg~~~r~~~~sy~r  122 (195)
T KOG0107|consen   90 RRGGSR-PPRGRGFCYRCGERGHIGRNCKDSYSR  122 (195)
T ss_pred             ccCCCC-CcccccccccCCCcccccccccccccc
Confidence            322222 223333488999999999888774333

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.70  E-value=4.3e-16  Score=124.17  Aligned_cols=73  Identities=29%  Similarity=0.563  Sum_probs=64.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||+++||++|+++|++||+|+.|.|+.     +++|||||+|.+.++|++|++.||+.+  +..|+|.++.++
T Consensus        35 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~  114 (144)
T PLN03134         35 TKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDR  114 (144)
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcC
Confidence            6899999999999999999999999999999974     458999999999999999999999887  666777666543

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

Probab=99.64  E-value=2.6e-15  Score=124.17  Aligned_cols=70  Identities=41%  Similarity=0.731  Sum_probs=63.2

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--c--EEEEEee
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--G--WRVELSH   70 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g--~~V~v~~   70 (223)
                      |++|-|-||.+.|+.++|+.+|++||.|-+|.|+.     +++|||||.|.+..||++|+++|+|..  +  +.|++++
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            78999999999999999999999999999999974     679999999999999999999999998  4  4555554

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

Probab=99.57  E-value=9.6e-14  Score=120.20  Aligned_cols=74  Identities=28%  Similarity=0.568  Sum_probs=65.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      +||||+-|+.+|+|..|+..|++||+|+.|.|+.     +++|||||+|+++.++++|.+..+|..  +..|-|......
T Consensus       102 ~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvERgR  181 (335)
T KOG0113|consen  102 KTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVERGR  181 (335)
T ss_pred             ceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEecccc
Confidence            6999999999999999999999999999999874     689999999999999999999999887  666666655444


Q ss_pred             C
Q 041602           75 G   75 (223)
Q Consensus        75 ~   75 (223)
                      +
T Consensus       182 T  182 (335)
T KOG0113|consen  182 T  182 (335)
T ss_pred             c
Confidence            3

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

Probab=99.55  E-value=8e-15  Score=126.56  Aligned_cols=100  Identities=34%  Similarity=0.689  Sum_probs=86.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeeccCCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHNSKGGGG   77 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~~~~~r~   77 (223)
                      +||+||||.+.++.++|++.|++||+|.+|+|+   ++|+||+|+..++|..|++.||+.+    .++|+++.++-....
T Consensus        79 tkl~vgNis~tctn~ElRa~fe~ygpviecdiv---kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlrtap  155 (346)
T KOG0109|consen   79 TKLHVGNISPTCTNQELRAKFEKYGPVIECDIV---KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTAP  155 (346)
T ss_pred             cccccCCCCccccCHHHhhhhcccCCceeeeee---cceeEEEEeeccchHHHHhcccccccccceeeeeeeccccccCC
Confidence            689999999999999999999999999999999   7899999999999999999999998    456666665444333


Q ss_pred             CCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCC
Q 041602           78 RGGRGRGGGEDLKCYECGEPGHFARECRLRIGS  110 (223)
Q Consensus        78 ~~~~~~~~~~~~~~~~~g~~G~~~r~~~~~~~r  110 (223)
                            +.++...|++||+.|||..+||.....
T Consensus       156 ------gmgDq~~cyrcGkeghwskEcP~~~~~  182 (346)
T KOG0109|consen  156 ------GMGDQSGCYRCGKEGHWSKECPVDRTG  182 (346)
T ss_pred             ------CCCCHHHheeccccccccccCCccCCC
Confidence                  356788999999999999999976543

>PF00076 RRM_1: RNA recognition motif

Probab=99.52  E-value=6.1e-14  Score=96.26  Aligned_cols=59  Identities=49%  Similarity=0.852  Sum_probs=55.1

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC----CCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            4 VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR----PPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         4 LfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~----~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      |||+|||.++|+++|+++|++||+|..+.+..+    .+++|||+|++.++|++|++.|++..
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~   63 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKK   63 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCE
Confidence            799999999999999999999999999988753    57899999999999999999999876

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.51  E-value=5.1e-13  Score=120.52  Aligned_cols=73  Identities=27%  Similarity=0.474  Sum_probs=63.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~~   72 (223)
                      ++|||+|||..+||++|+++|++||+|+.|.|+.     +++|||||+|++.++|++||++||+..    .+.|+|..+.
T Consensus       194 ~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~  273 (346)
T TIGR01659       194 TNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAE  273 (346)
T ss_pred             ceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECC
Confidence            5799999999999999999999999999999874     347999999999999999999999985    3566666655


Q ss_pred             CC
Q 041602           73 KG   74 (223)
Q Consensus        73 ~~   74 (223)
                      ..
T Consensus       274 ~~  275 (346)
T TIGR01659       274 EH  275 (346)
T ss_pred             cc
Confidence            43

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

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

Probab=99.49  E-value=1.4e-13  Score=112.29  Aligned_cols=70  Identities=43%  Similarity=0.774  Sum_probs=60.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee--CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR--RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~--~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||||||.++.|.+|+++|.+||.|..|.+..  .+..||||+|+++-+|+.||..-+|..  +.++.|..+
T Consensus         7 ~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    7 RRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             ceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            5899999999999999999999999999998853  346799999999999999999888887  544444444

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.47  E-value=2.9e-13  Score=121.05  Aligned_cols=72  Identities=29%  Similarity=0.447  Sum_probs=65.1

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      +|||+|||+++++++|.++|++||+|..|+|+.+     ++|||||+|.+.++|.+||+.|||..  +..|+|.+...+
T Consensus       271 ~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~  349 (352)
T TIGR01661       271 CIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNK  349 (352)
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCC
Confidence            5999999999999999999999999999999753     59999999999999999999999998  777777776543

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.47  E-value=2.3e-13  Score=121.72  Aligned_cols=71  Identities=23%  Similarity=0.422  Sum_probs=63.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||.++||++|+++|++||+|..|+|+.     +++|||||+|.+.++|++||+.||+..  +..|.+.++.
T Consensus         4 ~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         4 TNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            6899999999999999999999999999999974     357999999999999999999999987  6666665554

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.47  E-value=2.3e-13  Score=122.74  Aligned_cols=70  Identities=30%  Similarity=0.518  Sum_probs=61.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+|||+++||++|+++|++||+|++|+|+.     +++|||||+|.++++|++||+.||+..  +..|++.++
T Consensus       108 ~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a  184 (346)
T TIGR01659       108 TNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYA  184 (346)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecc
Confidence            6899999999999999999999999999999975     357999999999999999999999987  555555543

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

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

Probab=99.46  E-value=2e-13  Score=105.46  Aligned_cols=75  Identities=32%  Similarity=0.553  Sum_probs=64.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe-----eCCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~-----~~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~~   72 (223)
                      +|||||||+..|+|+.|.++|+++|+|..|.|-     +.+.|||||+|.+.++|+.|++-++++.    .+.|.+....
T Consensus        37 ~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~GF  116 (153)
T KOG0121|consen   37 CTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDAGF  116 (153)
T ss_pred             ceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccccc
Confidence            799999999999999999999999999999772     3568999999999999999999999986    5666666554


Q ss_pred             CCCC
Q 041602           73 KGGG   76 (223)
Q Consensus        73 ~~~r   76 (223)
                      ..++
T Consensus       117 ~eGR  120 (153)
T KOG0121|consen  117 VEGR  120 (153)
T ss_pred             hhhh
Confidence            4443

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.44  E-value=2.6e-12  Score=122.31  Aligned_cols=70  Identities=37%  Similarity=0.568  Sum_probs=63.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcC--CCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMF--GVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~--G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+||+.++||++|+++|++|  |+|+.|.++   ++||||+|++.++|++|++.||+.+  +..|+|.++.+.
T Consensus       234 k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~---rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~  307 (578)
T TIGR01648       234 KILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI---RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPV  307 (578)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee---cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCC
Confidence            579999999999999999999999  999999876   7899999999999999999999998  777777766554

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.42  E-value=1.1e-12  Score=113.08  Aligned_cols=72  Identities=25%  Similarity=0.380  Sum_probs=64.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC--CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR--PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~--~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      +.+|||+|||+.+||++|+++|+.||+|.+|.|+.+  ++|||||+|.++++|+.||. |+|..  +..|.|..+..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            368999999999999999999999999999999764  57999999999999999995 99887  77777777643

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.41  E-value=5.1e-13  Score=117.02  Aligned_cols=72  Identities=28%  Similarity=0.452  Sum_probs=66.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee---CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~---~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|+|+|||+...|.||+.+|++||+|.+|.|+-   .+||||||+|++.+||++|-++|||..  |++|||..+..
T Consensus        97 kRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATa  173 (376)
T KOG0125|consen   97 KRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATA  173 (376)
T ss_pred             ceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccch
Confidence            5799999999999999999999999999999974   579999999999999999999999997  89999887643

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.39  E-value=6e-13  Score=112.01  Aligned_cols=72  Identities=26%  Similarity=0.429  Sum_probs=61.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe-----eCCCCEEEEEEcCHHHHHHHHHHhCCCC-cEEEEEeecc
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRALDGKN-GWRVELSHNS   72 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~-----~~~rGfaFV~F~~~e~A~~Al~~lng~~-g~~V~v~~~~   72 (223)
                      .||||||||+++|+.++|+++|++||+|.+..|+     +++||||||+|.+.+.|..|++..|-.. |++..+..+.
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLAS   89 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhh
Confidence            4799999999999999999999999999998876     3679999999999999999998777665 6555544443

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.36  E-value=3.5e-12  Score=88.30  Aligned_cols=63  Identities=40%  Similarity=0.738  Sum_probs=54.4

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEE
Q 041602            4 VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRV   66 (223)
Q Consensus         4 LfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V   66 (223)
                      |||+|||+++++++|.++|+.+|.|..+.+..+    .+++|||+|.++++|++|++.+++..  +..|
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l   69 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKL   69 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEc
Confidence            799999999999999999999999999999865    36899999999999999999888655  5554

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>smart00362 RRM_2 RNA recognition motif

Probab=99.33  E-value=1.2e-11  Score=83.62  Aligned_cols=66  Identities=42%  Similarity=0.776  Sum_probs=58.2

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC---CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEE
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR---PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVEL   68 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~---~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v   68 (223)
                      +|||+|||..+++++|+++|.+||+|..+.+..+   ++++|||+|.+.++|++|++.+++..  +..|.+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            5899999999999999999999999999988754   36999999999999999999999765  555543

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

Probab=99.33  E-value=5e-12  Score=108.47  Aligned_cols=72  Identities=33%  Similarity=0.593  Sum_probs=67.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      |+|||||++..+||++|++.|+.||+|.+|++-++ +|||||.|++.|.|..||..||+++  +..|+..+.+..
T Consensus       165 tsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~-qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~  238 (321)
T KOG0148|consen  165 TSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD-QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEG  238 (321)
T ss_pred             ceEEeCCcCccccHHHHHHhcccCCcceEEEEecc-cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccC
Confidence            79999999999999999999999999999999765 8999999999999999999999998  888999987654

>PLN03213 repressor of silencing 3; Provisional

Probab=99.31  E-value=6.9e-12  Score=115.09  Aligned_cols=71  Identities=24%  Similarity=0.413  Sum_probs=63.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-CCCCEEEEEEcCH--HHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-RPPGYAFVEFDDR--RDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-~~rGfaFV~F~~~--e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      .+||||||++.++++||+..|+.||.|..|.|++ ..+|||||+|.+.  +++.+||..|||.+  |..|+|..++
T Consensus        11 MRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK   86 (759)
T PLN03213         11 VRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence            4799999999999999999999999999999985 3489999999987  78999999999998  7677776664

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

Probab=99.31  E-value=8.2e-12  Score=105.74  Aligned_cols=71  Identities=44%  Similarity=0.634  Sum_probs=62.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeec
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHN   71 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~   71 (223)
                      .++|-|.||+.+++|++|+++|.+||.|..|.|..     .++|||||+|.+.++|.+||+.|||.-    .++|+++++
T Consensus       189 ~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwskP  268 (270)
T KOG0122|consen  189 EATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSKP  268 (270)
T ss_pred             cceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecCC
Confidence            36899999999999999999999999999999864     469999999999999999999999885    556666554

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

Probab=99.30  E-value=8.5e-12  Score=119.29  Aligned_cols=71  Identities=28%  Similarity=0.570  Sum_probs=64.1

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      +++|||+||++++++++|+++|++||+|..|.|+.     +++|||||+|.+.++|++|++.|||..  +..|++.++
T Consensus       107 ~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       107 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            47999999999999999999999999999999864     479999999999999999999999987  677777643

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.30  E-value=1.4e-11  Score=115.59  Aligned_cols=72  Identities=22%  Similarity=0.304  Sum_probs=65.3

Q ss_pred             cEEEEecCCC-CCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDP-RVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~-~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+||++ .+|+++|+++|++||.|..|+++.+.+|||||+|.+.++|++|++.||+..  +..|.|..+..
T Consensus       276 ~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~  350 (481)
T TIGR01649       276 SVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQ  350 (481)
T ss_pred             CEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccc
Confidence            4899999998 699999999999999999999988778999999999999999999999987  77777766543

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=99.27  E-value=1.9e-11  Score=116.43  Aligned_cols=71  Identities=38%  Similarity=0.653  Sum_probs=63.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||.++||++|+++|++||+|..|+|+.     +++|||||+|.+.++|++|++.+|+..  +..|.+.++.
T Consensus         1 ~sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~   78 (562)
T TIGR01628         1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQ   78 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccc
Confidence            4899999999999999999999999999999974     457999999999999999999999885  6666666653

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.26  E-value=2.8e-11  Score=103.11  Aligned_cols=69  Identities=29%  Similarity=0.385  Sum_probs=61.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee--CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR--RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~--~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      .+|||+||++.+||++|+++|+.||+|.+|.|+.  +.++||||+|.++++|+.|+ .|+|..  +..|.|...
T Consensus         6 ~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~   78 (243)
T PLN03121          6 YTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRW   78 (243)
T ss_pred             eEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeC
Confidence            4799999999999999999999999999999985  34689999999999999999 599887  667777665

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.26  E-value=1.6e-11  Score=116.95  Aligned_cols=61  Identities=26%  Similarity=0.475  Sum_probs=57.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ++|||+|||.+++|++|+++|++||+|.+|+|+.    +++|||||+|.+.++|++||+.||+.+
T Consensus        59 ~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~  123 (578)
T TIGR01648        59 CEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYE  123 (578)
T ss_pred             CEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCe
Confidence            7899999999999999999999999999999874    578999999999999999999999765

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

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

Probab=99.25  E-value=2.7e-11  Score=115.87  Aligned_cols=72  Identities=26%  Similarity=0.549  Sum_probs=64.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+||+.++++++|+++|++||+|+.+.|..     +++|||||+|.+.++|.+|++.||+.+  |..|.|.++..
T Consensus       205 ~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~  283 (612)
T TIGR01645       205 NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  283 (612)
T ss_pred             ceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCC
Confidence            5899999999999999999999999999999974     368999999999999999999999997  66777766543

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

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

Probab=99.24  E-value=1.1e-11  Score=107.34  Aligned_cols=70  Identities=27%  Similarity=0.542  Sum_probs=62.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      +.+|||||||.++++.+|+.+|++||+|.+|+|+   |.||||+.++...|+.||..|++..  +..|+|..++.
T Consensus         2 ~~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv---KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSks   73 (346)
T KOG0109|consen    2 PVKLFIGNLPREATEQELRSLFEQYGKVLECDIV---KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKS   73 (346)
T ss_pred             ccchhccCCCcccchHHHHHHHHhhCceEeeeee---cccceEEeecccccHHHHhhcccceecceEEEEEeccc
Confidence            4589999999999999999999999999999999   7799999999999999999999987  65555554433

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.24  E-value=4.5e-11  Score=112.11  Aligned_cols=72  Identities=29%  Similarity=0.526  Sum_probs=63.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      .+|||+|||..+|+++|+++|++||+|..+.|+.     .++|||||+|.+.++|+.|++.|||..  +..|.|.++..
T Consensus       296 ~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~  374 (509)
T TIGR01642       296 DRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACV  374 (509)
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECcc
Confidence            4899999999999999999999999999998864     368999999999999999999999998  66666666543

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.23  E-value=4.2e-11  Score=110.97  Aligned_cols=71  Identities=30%  Similarity=0.636  Sum_probs=63.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||..+|+++|+++|++||+|..|.++.     +++|||||+|.+.++|++|++.|||..  +..|.|.++.
T Consensus       187 ~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       187 LKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            5899999999999999999999999999999874     457999999999999999999999987  6667776654

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

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

Probab=99.22  E-value=2.4e-11  Score=110.25  Aligned_cols=69  Identities=35%  Similarity=0.566  Sum_probs=61.3

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      |+.|||.||+.+|||+.|+++|++||.|+.|+.+   +.||||+|.+.++|.+|++.||+++  |-.|++..++
T Consensus       259 VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~---rDYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAK  329 (506)
T KOG0117|consen  259 VKVLYVRNLMESTTEETLKKLFNEFGKVERVKKP---RDYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAK  329 (506)
T ss_pred             eeeeeeeccchhhhHHHHHHHHHhccceEEeecc---cceeEEeecchHHHHHHHHHhcCceecCceEEEEecC
Confidence            4679999999999999999999999999999876   6699999999999999999999998  6555555544

>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

Probab=99.22  E-value=1.3e-10  Score=78.89  Aligned_cols=67  Identities=45%  Similarity=0.801  Sum_probs=59.2

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCC----CCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEe
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRP----PGYAFVEFDDRRDAVDAIRALDGKN--GWRVELS   69 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~----rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~   69 (223)
                      +|+|+|||..+++++|+++|+.+|+|..+.+....    +++|||+|.+.++|+.|++.+++..  +.++.+.
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~   73 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVE   73 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEe
Confidence            58999999999999999999999999999987643    7899999999999999999999885  5555543

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

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

Probab=99.22  E-value=3.1e-11  Score=94.17  Aligned_cols=73  Identities=27%  Similarity=0.525  Sum_probs=64.3

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCCC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKGG   75 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~~   75 (223)
                      -|||.++..++||++|.+.|..||+|+.+.+..     -.+|||+|+|++.++|++|+.+|||.+  +.+|+|.++.-.+
T Consensus        74 Ii~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~g  153 (170)
T KOG0130|consen   74 IIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVKG  153 (170)
T ss_pred             EEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEecC
Confidence            489999999999999999999999999998853     358999999999999999999999998  7777777765543

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=99.21  E-value=6.6e-11  Score=112.69  Aligned_cols=72  Identities=26%  Similarity=0.444  Sum_probs=63.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+||+..+|+++|+++|++||+|++|+++.    .++|||||+|.+.++|++|++.||+..  +..|.|..+..
T Consensus       286 ~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~  363 (562)
T TIGR01628       286 VNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQR  363 (562)
T ss_pred             CEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccC
Confidence            5799999999999999999999999999999974    458999999999999999999999987  66666665543

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

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

Probab=99.16  E-value=1.7e-10  Score=86.24  Aligned_cols=60  Identities=30%  Similarity=0.545  Sum_probs=55.9

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe--eCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA--RRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~--~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      -|||.|||..+|.++..++|.+||.|..|+|-  ...+|.|||.|++..+|++|+++|.|..
T Consensus        20 iLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n   81 (124)
T KOG0114|consen   20 ILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYN   81 (124)
T ss_pred             eEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccc
Confidence            48999999999999999999999999999983  4569999999999999999999999987

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.16  E-value=1.5e-10  Score=107.27  Aligned_cols=68  Identities=32%  Similarity=0.499  Sum_probs=59.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~   70 (223)
                      .+|||+|||..+++++|+++|++||+|..|.|+.     .++|||||+|.+.++|++||. |+|..  +..|.+..
T Consensus        90 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        90 RTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            4899999999999999999999999999999974     468999999999999999996 88876  55555544

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>smart00360 RRM RNA recognition motif

Probab=99.15  E-value=2.3e-10  Score=76.84  Aligned_cols=63  Identities=44%  Similarity=0.791  Sum_probs=54.2

Q ss_pred             EecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEE
Q 041602            6 VGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVEL   68 (223)
Q Consensus         6 VgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v   68 (223)
                      |+|||..+++++|+++|++||+|..+.+..+     ++|+|||+|.+.++|++|++.+++..  +..|.+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEe
Confidence            5799999999999999999999999988653     36899999999999999999998665  444443

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

Probab=99.15  E-value=1.3e-10  Score=105.55  Aligned_cols=61  Identities=30%  Similarity=0.500  Sum_probs=57.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      |-||||.||.++.|++|.-+|++.|+|-+++|+.     +++|||||+|.+.++|++||+.||+.+
T Consensus        84 ~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~E  149 (506)
T KOG0117|consen   84 CEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYE  149 (506)
T ss_pred             ceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCcc
Confidence            5799999999999999999999999999999975     579999999999999999999999996

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

Probab=99.14  E-value=2.4e-10  Score=95.35  Aligned_cols=71  Identities=37%  Similarity=0.692  Sum_probs=62.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      .+|||+|||..+|+++|.++|.+||.|..+.+..     ..+|||||+|.+.++|..|++.+++..  +..+.+....
T Consensus       116 ~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            6899999999999999999999999999988853     568999999999999999999999887  6666666643

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.14  E-value=2.4e-10  Score=107.26  Aligned_cols=71  Identities=23%  Similarity=0.212  Sum_probs=61.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCC-CCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRP-PGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~-rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~~   72 (223)
                      .+|||+||++.+|+++|+++|+.||+|..|.|..+. .++|||+|++.++|++|++.|||.+    ...+++.++.
T Consensus        97 ~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk  172 (481)
T TIGR01649        97 LRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAK  172 (481)
T ss_pred             EEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCCceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEec
Confidence            479999999999999999999999999999887643 4799999999999999999999997    2355555544

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

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

Probab=99.13  E-value=4.9e-11  Score=107.87  Aligned_cols=71  Identities=31%  Similarity=0.599  Sum_probs=63.3

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC-------cEEEEEeec
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN-------GWRVELSHN   71 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~-------g~~V~v~~~   71 (223)
                      +||||-|+..+||++++++|++||.|++|.|.+    .++|||||.|.+.|.|..||++||+..       .+.|+++..
T Consensus       126 KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADt  205 (510)
T KOG0144|consen  126 KLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADT  205 (510)
T ss_pred             hhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEeccc
Confidence            789999999999999999999999999999975    479999999999999999999999986       456666655


Q ss_pred             cC
Q 041602           72 SK   73 (223)
Q Consensus        72 ~~   73 (223)
                      .+
T Consensus       206 qk  207 (510)
T KOG0144|consen  206 QK  207 (510)
T ss_pred             CC
Confidence            43

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

Probab=99.09  E-value=8.8e-11  Score=98.40  Aligned_cols=73  Identities=27%  Similarity=0.550  Sum_probs=64.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      .+||||+|..++||.-|...|-.||.|++|.++.     +++|||||+|+..|||.+||..||+.+  |..|.|..+.+.
T Consensus        11 rtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~   90 (298)
T KOG0111|consen   11 RTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPE   90 (298)
T ss_pred             eeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCc
Confidence            4899999999999999999999999999999963     679999999999999999999999998  666665555443

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

Probab=99.08  E-value=1.9e-10  Score=93.82  Aligned_cols=71  Identities=34%  Similarity=0.539  Sum_probs=64.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      .|||||||+..++++.|.++|-+.|+|..+.+++     ..+|||||+|.++|+|+-|++-||...  +..|.+.++.
T Consensus        10 ~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen   10 ATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             ceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            5899999999999999999999999999999875     468999999999999999999999665  7777777775

>PF13893 RRM_5: RNA recognition motif

Probab=99.07  E-value=9.3e-10  Score=73.23  Aligned_cols=53  Identities=34%  Similarity=0.607  Sum_probs=45.7

Q ss_pred             HHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEee
Q 041602           18 LEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSH   70 (223)
Q Consensus        18 L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~   70 (223)
                      |.++|++||+|..+.+..+.+++|||+|.+.++|++|++.||+..  +..|++.+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~   55 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSY   55 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            678999999999999986656999999999999999999999997  66666654

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

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

Probab=99.05  E-value=4e-10  Score=102.03  Aligned_cols=61  Identities=28%  Similarity=0.586  Sum_probs=57.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      .++|||-+|..++|+||+++|++||.|.+|.|++     .++|||||.|.+.++|.+|+.+|++..
T Consensus        35 vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~k  100 (510)
T KOG0144|consen   35 VKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQK  100 (510)
T ss_pred             hhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhccc
Confidence            4799999999999999999999999999999976     358999999999999999999999876

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.00  E-value=9.8e-10  Score=103.08  Aligned_cols=68  Identities=28%  Similarity=0.426  Sum_probs=55.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcC------------CCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEE
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMF------------GVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVE   67 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~------------G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~   67 (223)
                      .+|||||||+.+|+++|+++|.++            +.|..+.+. +.+|||||+|.+.++|++|| +|||..  +..|+
T Consensus       176 r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~-~~kg~afVeF~~~e~A~~Al-~l~g~~~~g~~l~  253 (509)
T TIGR01642       176 RRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNIN-KEKNFAFLEFRTVEEATFAM-ALDSIIYSNVFLK  253 (509)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEEC-CCCCEEEEEeCCHHHHhhhh-cCCCeEeeCceeE
Confidence            479999999999999999999975            244444443 55899999999999999999 599887  66676


Q ss_pred             Eeec
Q 041602           68 LSHN   71 (223)
Q Consensus        68 v~~~   71 (223)
                      +..+
T Consensus       254 v~r~  257 (509)
T TIGR01642       254 IRRP  257 (509)
T ss_pred             ecCc
Confidence            6543

Members of this subfamily are found in plants, metazoa and fungi.

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

Probab=98.98  E-value=3.5e-10  Score=100.79  Aligned_cols=71  Identities=28%  Similarity=0.572  Sum_probs=65.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe-----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~-----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ||+||||.+.+++.|+.|+..|..||+|++|.+.     .+++|||||+|+-+|.|+-|++.|||..  |++|++..+
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCC
Confidence            7899999999999999999999999999999984     4679999999999999999999999998  778877654

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

Probab=98.96  E-value=1.8e-09  Score=95.48  Aligned_cols=72  Identities=32%  Similarity=0.577  Sum_probs=64.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC---cEEEEEeeccC
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN---GWRVELSHNSK   73 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~---g~~V~v~~~~~   73 (223)
                      |++|||+||...++|.+|+++|.+||+|..+.+... +++|||+|.+.++|+.|.++.-.+.   |.+|++.|..+
T Consensus       228 I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  228 IKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             eeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            589999999999999999999999999999988754 6799999999999999988765554   88888888766

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

Probab=98.95  E-value=1.5e-09  Score=93.38  Aligned_cols=70  Identities=30%  Similarity=0.633  Sum_probs=61.3

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      .+||+.|..+++.++|++.|.+||+|.+++|++     ++||||||.|.+.++|++||+.|||.=  ++.|.-.++.
T Consensus        64 hvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWAT  140 (321)
T KOG0148|consen   64 HVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWAT  140 (321)
T ss_pred             eEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccc
Confidence            489999999999999999999999999999985     679999999999999999999999885  4445444443

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

Probab=98.95  E-value=2.2e-09  Score=102.95  Aligned_cols=71  Identities=27%  Similarity=0.514  Sum_probs=63.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      +|||||+|+.+++|.||..+|+.||+|.+|.++ .+++||||.+....+|++|+.+|++..  ...|+++|+..
T Consensus       422 rTLwvG~i~k~v~e~dL~~~feefGeiqSi~li-~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  422 RTLWVGGIPKNVTEQDLANLFEEFGEIQSIILI-PPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeccccchhhHHHHHHHHHhcccceeEeec-cCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            699999999999999999999999999999887 459999999999999999999998766  67777777643

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

Probab=98.93  E-value=1e-08  Score=94.38  Aligned_cols=73  Identities=26%  Similarity=0.509  Sum_probs=57.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC-cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN-GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~-g~~V~v~~~~~~   74 (223)
                      .+|||.|||.++++++|+++|++||+|+...|..     +..+||||+|.+.++++.||++-.-.. ++++.|......
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEecccc
Confidence            4599999999999999999999999999887742     223899999999999999998663222 556665555443

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

Probab=98.93  E-value=2.6e-09  Score=98.74  Aligned_cols=72  Identities=35%  Similarity=0.548  Sum_probs=65.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe-----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~-----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ..|||||+|++++|++|.++|+..|.|..++++     ++++||||++|.+.++|+.|++.||+.+  +.++++.++..
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~   97 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASN   97 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeecccc
Confidence            579999999999999999999999999999997     3679999999999999999999999998  77777776643

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

Probab=98.92  E-value=1.3e-10  Score=94.79  Aligned_cols=69  Identities=26%  Similarity=0.578  Sum_probs=62.9

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      -|||||||++.||.||-..|++||+|.+|.+++     +++||||+.|++.-...-|+..|||..  ++.|.|.+.
T Consensus        37 ~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   37 YIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             EEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            589999999999999999999999999999974     679999999999999999999999998  777777664

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

Probab=98.91  E-value=1.8e-09  Score=92.60  Aligned_cols=72  Identities=28%  Similarity=0.549  Sum_probs=62.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe-----eCCCCEEEEEEcCHHHHHHHHHHhCCCC------cEEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRALDGKN------GWRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~-----~~~rGfaFV~F~~~e~A~~Al~~lng~~------g~~V~v~~   70 (223)
                      +.|||.+||..+|..+|+++|++||.|..-+|.     +-++|.+||.|+..++|++||+.|||..      .+.|+++.
T Consensus       128 aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFan  207 (360)
T KOG0145|consen  128 ANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFAN  207 (360)
T ss_pred             cceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecC
Confidence            479999999999999999999999987655443     3569999999999999999999999987      58888887


Q ss_pred             ccC
Q 041602           71 NSK   73 (223)
Q Consensus        71 ~~~   73 (223)
                      ...
T Consensus       208 nPs  210 (360)
T KOG0145|consen  208 NPS  210 (360)
T ss_pred             Ccc
Confidence            654

>smart00361 RRM_1 RNA recognition motif

Probab=98.85  E-value=1.2e-08  Score=71.18  Aligned_cols=54  Identities=30%  Similarity=0.569  Sum_probs=45.4

Q ss_pred             HHHHHHHHH----cCCCeEEEE-Ee-------eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEE
Q 041602           15 ERDLEDEFR----MFGVLRSVW-VA-------RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVEL   68 (223)
Q Consensus        15 e~~L~~~F~----~~G~I~~v~-i~-------~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v   68 (223)
                      +++|+++|.    +||+|..|. ++       ++++|||||+|.+.++|++|++.|||..  +..|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            678999998    999999985 32       3458999999999999999999999987  666553

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

Probab=98.85  E-value=8.6e-09  Score=88.45  Aligned_cols=73  Identities=25%  Similarity=0.423  Sum_probs=63.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      +.|.|--||.++|+++++.+|...|+|++|++++     ++.||+||.|-+++||++|+..|||-.  ...|+|+.+++.
T Consensus        42 TNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPS  121 (360)
T KOG0145|consen   42 TNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPS  121 (360)
T ss_pred             ceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccCC
Confidence            5688888999999999999999999999999975     568999999999999999999999886  456666666543

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

Probab=98.84  E-value=9e-09  Score=95.74  Aligned_cols=74  Identities=27%  Similarity=0.514  Sum_probs=66.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKGG   75 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~~   75 (223)
                      .+|.|.|||+.+.+.+|+.+|++||.|..|.|+.    +..|||||+|.+..+|.+|++.+|+.+  |+.|-+.|+-++.
T Consensus       118 ~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd  197 (678)
T KOG0127|consen  118 WRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKD  197 (678)
T ss_pred             ceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccc
Confidence            4789999999999999999999999999999985    346999999999999999999999998  8888888876553

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

Probab=98.81  E-value=5.2e-09  Score=88.22  Aligned_cols=69  Identities=45%  Similarity=0.755  Sum_probs=61.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      |..+|||+||+.+.+.+|+.+|..||+|.++.+.   .||+||+|++.-+|+.|+..+|+.+  +.++.+.++.
T Consensus         1 m~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk---~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r   71 (216)
T KOG0106|consen    1 MPRVYIGRLPYRARERDVERFFKGYGKIPDADMK---NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHAR   71 (216)
T ss_pred             CCceeecccCCccchhHHHHHHhhccccccceee---cccceeccCchhhhhcccchhcCceecceeeeeeccc
Confidence            6789999999999999999999999999999886   7899999999999999999999998  4444444444

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=98.81  E-value=4.8e-09  Score=97.42  Aligned_cols=71  Identities=32%  Similarity=0.609  Sum_probs=62.8

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      .||||||..+++|+.|+.+|+.||+|..|.++.     .++|||||+|.+.++|.+|++.|||.+  |..|+|+....
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~  357 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTE  357 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeee
Confidence            389999999999999999999999999998865     468999999999999999999999977  76666665433

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.80  E-value=2e-08  Score=89.39  Aligned_cols=70  Identities=30%  Similarity=0.479  Sum_probs=61.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~   71 (223)
                      +.|||..|.+.||.+||+-+|+.||+|..|.|+.     ++..||||+|++.+++++|..+|++..    .++|.++.+
T Consensus       240 NVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQS  318 (479)
T KOG0415|consen  240 NVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQS  318 (479)
T ss_pred             ceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhhh
Confidence            4699999999999999999999999999999985     346699999999999999999999886    566665554

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.80  E-value=5.4e-08  Score=88.67  Aligned_cols=71  Identities=24%  Similarity=0.366  Sum_probs=61.9

Q ss_pred             EEEEecCCCCCCHHHHHHHHH-cCCCeEEEEEe----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            3 RVYVGNLDPRVSERDLEDEFR-MFGVLRSVWVA----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~-~~G~I~~v~i~----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      .+||.|+|+++.+.+|+++|. +-|+|+.|.+.    ++++|||.|+|+++|.+++|++.||..+  ++.+.+.....
T Consensus        46 ~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d  123 (608)
T KOG4212|consen   46 SVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHD  123 (608)
T ss_pred             eEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCc
Confidence            489999999999999999995 78999999885    4789999999999999999999999887  66666655443

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

Probab=98.73  E-value=3.4e-08  Score=90.03  Aligned_cols=67  Identities=34%  Similarity=0.567  Sum_probs=59.6

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC---CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            4 VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR---PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         4 LfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~---~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      |||.||++.++.++|.++|+.||+|.+|++..+   ++|| ||+|+++++|++|++.|||..  +..|.+...
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~  150 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLF  150 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeec
Confidence            799999999999999999999999999999753   5889 999999999999999999997  555555544

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

Probab=98.73  E-value=1.4e-08  Score=87.38  Aligned_cols=72  Identities=33%  Similarity=0.551  Sum_probs=64.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC-------cEEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN-------GWRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~-------g~~V~v~~   70 (223)
                      .+||||.|...-.|||++.+|..||+|++|.+.+    .+||||||.|.+..+|++||..|+|..       .+.|+++.
T Consensus        20 rklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~AD   99 (371)
T KOG0146|consen   20 RKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKFAD   99 (371)
T ss_pred             hhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEecc
Confidence            4799999999999999999999999999999874    579999999999999999999999876       46777776


Q ss_pred             ccC
Q 041602           71 NSK   73 (223)
Q Consensus        71 ~~~   73 (223)
                      .++
T Consensus       100 Tdk  102 (371)
T KOG0146|consen  100 TDK  102 (371)
T ss_pred             chH
Confidence            544

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

Probab=98.70  E-value=3.1e-08  Score=92.23  Aligned_cols=72  Identities=21%  Similarity=0.374  Sum_probs=62.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      .||||++||+.++.++|.++|+..|+|..+.++.     .++|||||+|.-.+|++.|++..++..  |+.+.+..+..
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~   84 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKK   84 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccc
Confidence            5899999999999999999999999999998874     468999999999999999999998855  65555555443

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

Probab=98.63  E-value=4.6e-08  Score=84.34  Aligned_cols=72  Identities=25%  Similarity=0.420  Sum_probs=62.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe-----eCCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~-----~~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~~   72 (223)
                      |+|||=.||.+..+.+|..+|..||.|.+.++.     ..+|+|+||.|+++..+++||.+|||..    .++|.+.+++
T Consensus       286 CNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPk  365 (371)
T KOG0146|consen  286 CNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPK  365 (371)
T ss_pred             ceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCcc
Confidence            789999999999999999999999999888773     3579999999999999999999999987    3555555554


Q ss_pred             C
Q 041602           73 K   73 (223)
Q Consensus        73 ~   73 (223)
                      .
T Consensus       366 d  366 (371)
T KOG0146|consen  366 D  366 (371)
T ss_pred             c
Confidence            3

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

Probab=98.61  E-value=3.2e-08  Score=88.01  Aligned_cols=73  Identities=26%  Similarity=0.434  Sum_probs=62.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC-cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN-GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~-g~~V~v~~~~~~   74 (223)
                      ++||||+|+++++++.|++.|.+||+|.+|.+++     .++||+||+|++++.+.+++..-..+. +..|+...+.+.
T Consensus         7 ~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~r   85 (311)
T KOG4205|consen    7 GKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVSR   85 (311)
T ss_pred             cceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccCc
Confidence            6899999999999999999999999999999975     468999999999999999987655544 777777766543

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

Probab=98.61  E-value=1.3e-07  Score=79.55  Aligned_cols=70  Identities=29%  Similarity=0.559  Sum_probs=60.8

Q ss_pred             EEEEecCCCCCCHHHHHH----HHHcCCCeEEEEEee--CCCCEEEEEEcCHHHHHHHHHHhCCCC--c--EEEEEeecc
Q 041602            3 RVYVGNLDPRVSERDLED----EFRMFGVLRSVWVAR--RPPGYAFVEFDDRRDAVDAIRALDGKN--G--WRVELSHNS   72 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~----~F~~~G~I~~v~i~~--~~rGfaFV~F~~~e~A~~Al~~lng~~--g--~~V~v~~~~   72 (223)
                      ||||-||+..+..++|+.    +|++||+|.+|...+  +.+|-|||.|.+.+.|..|+.+|+|..  +  ++|++++.+
T Consensus        11 TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~   90 (221)
T KOG4206|consen   11 TLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSD   90 (221)
T ss_pred             eEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccCc
Confidence            899999999999998887    999999999998864  568999999999999999999999997  4  555555543

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

Probab=98.60  E-value=8.1e-08  Score=78.52  Aligned_cols=70  Identities=33%  Similarity=0.593  Sum_probs=58.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEE-EEe-----eCCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSV-WVA-----RRPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v-~i~-----~~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~   71 (223)
                      .+|||+||.++++|..|.+.|+.||.+... +++     ++++|||||.|++.+.+.+|++.||+..    .+.|.++..
T Consensus        97 anlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k  176 (203)
T KOG0131|consen   97 ANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFK  176 (203)
T ss_pred             ccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEe
Confidence            479999999999999999999999987652 332     4678999999999999999999999987    444555443

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.57  E-value=1.3e-07  Score=90.22  Aligned_cols=71  Identities=34%  Similarity=0.601  Sum_probs=61.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC--C------CCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR--P------PGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~--~------rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||.||++.+|.++|+.+|.+.|.|..+.|..+  +      .|||||+|.+.++|++|++.|+|+.  |..|++..+
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            45999999999999999999999999999988642  2      3999999999999999999999887  666666655


Q ss_pred             c
Q 041602           72 S   72 (223)
Q Consensus        72 ~   72 (223)
                      .
T Consensus       596 ~  596 (725)
T KOG0110|consen  596 E  596 (725)
T ss_pred             c
Confidence            4

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

Probab=98.55  E-value=1.9e-07  Score=87.53  Aligned_cols=70  Identities=20%  Similarity=0.383  Sum_probs=60.6

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      +|||.+|+..|...||+.+|++||+|...+|+.+     .++|+||++.+.++|.+||+.|+.++  |..|.|.++.
T Consensus       407 NlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  407 NLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             ceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            6999999999999999999999999999988742     36799999999999999999999887  6555555543

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.55  E-value=6.7e-08  Score=92.22  Aligned_cols=72  Identities=29%  Similarity=0.533  Sum_probs=64.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      +++|+|.|||+..+-.+++.+|..||.|..|.|+.+     ++|||||+|-++.+|.+|+++|..+.  |+++.+.|+.
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~  691 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAK  691 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhc
Confidence            579999999999999999999999999999999753     58999999999999999999999665  7666666654

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

Probab=98.48  E-value=4.6e-07  Score=82.65  Aligned_cols=69  Identities=33%  Similarity=0.527  Sum_probs=59.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC--CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR--PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~--~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      +..||||   +++||..|.++|+.+|+|..++++.+  +.|||||.|.++++|++||++||...  +..|.+.++.
T Consensus         1 ~~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~   73 (369)
T KOG0123|consen    1 MASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQ   73 (369)
T ss_pred             CCceecC---CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhc
Confidence            4689999   89999999999999999999988643  67899999999999999999999876  5556655553

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

Probab=98.44  E-value=1.3e-06  Score=73.78  Aligned_cols=74  Identities=23%  Similarity=0.359  Sum_probs=58.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEE--EEeeCC----CCEEEEEEcCHHHHHHHHHHhCCCC-------cEEEE
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSV--WVARRP----PGYAFVEFDDRRDAVDAIRALDGKN-------GWRVE   67 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v--~i~~~~----rGfaFV~F~~~e~A~~Al~~lng~~-------g~~V~   67 (223)
                      |.||||.+||.++...+|..+|..|---+..  ++..+.    +-+|||+|.+..+|++|+.+|||..       .++|+
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiE  113 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIE  113 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEee
Confidence            5699999999999999999999887533443  333222    3599999999999999999999985       47788


Q ss_pred             EeeccCC
Q 041602           68 LSHNSKG   74 (223)
Q Consensus        68 v~~~~~~   74 (223)
                      ++++..+
T Consensus       114 lAKSNtK  120 (284)
T KOG1457|consen  114 LAKSNTK  120 (284)
T ss_pred             ehhcCcc
Confidence            8776544

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

Probab=98.41  E-value=1.4e-06  Score=74.75  Aligned_cols=69  Identities=33%  Similarity=0.528  Sum_probs=58.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe-----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~-----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      +.+||+|+...+|.++++.+|+.||.|..+.|+     ++++|||||+|.+.+.+++|++ ||+..  +..+++...
T Consensus       102 ~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~  177 (231)
T KOG4209|consen  102 PSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLK  177 (231)
T ss_pred             ceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeee
Confidence            579999999999988899999999999887775     2579999999999999999998 99887  444444443

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

Probab=98.40  E-value=3.3e-07  Score=81.54  Aligned_cols=73  Identities=30%  Similarity=0.552  Sum_probs=60.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHh-CCCCcEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRAL-DGKNGWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~l-ng~~g~~V~v~~~~~~   74 (223)
                      .+|||++||.+++++++++.|++||.|..+.++.     +++||+||.|.+++.+++++..- +...+..|++..+.++
T Consensus        98 kkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~~f~~~~gk~vevkrA~pk  176 (311)
T KOG4205|consen   98 KKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQKFHDFNGKKVEVKRAIPK  176 (311)
T ss_pred             eEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecccceeeecCceeeEeeccch
Confidence            4899999999999999999999999998888763     56899999999999999997522 2222777888777654

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

Probab=98.38  E-value=5.7e-07  Score=86.04  Aligned_cols=70  Identities=37%  Similarity=0.570  Sum_probs=61.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee--------CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR--------RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~--------~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      |+|||+||++.++|+.|-..|..||+|..|+|+-        ..+.||||.|-+..||++|++.|+|..  ...+++.|+
T Consensus       175 TNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~gWg  254 (877)
T KOG0151|consen  175 TNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLGWG  254 (877)
T ss_pred             cceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeeccc
Confidence            6899999999999999999999999999999862        346799999999999999999999997  555555554

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.37  E-value=8.9e-07  Score=80.86  Aligned_cols=69  Identities=20%  Similarity=0.274  Sum_probs=59.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~   70 (223)
                      |+|||.|||.+.|++-|++.|..||.|+.++|+...+.-+.|.|.++++|+.|+..|++..  +..|+|..
T Consensus       537 ~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~GkskGVVrF~s~edAEra~a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  537 CQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSKGVVRFFSPEDAERACALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             cEEEEecCCccccHHHHHHHHHhccceehhhhhccCCccceEEecCHHHHHHHHHHhccCcccCceeeeee
Confidence            7899999999999999999999999999999954333344999999999999999999987  77776653

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

Probab=98.36  E-value=1e-06  Score=79.01  Aligned_cols=61  Identities=30%  Similarity=0.624  Sum_probs=56.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      .+|||..+.++.+|+||+..|+.||+|..|.+..     .++||+|++|++.....+|+..||-..
T Consensus       211 nRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFD  276 (544)
T KOG0124|consen  211 NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFD  276 (544)
T ss_pred             heEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhh
Confidence            5799999999999999999999999999999963     569999999999999999999998665

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

Probab=98.34  E-value=3.7e-07  Score=85.25  Aligned_cols=60  Identities=35%  Similarity=0.476  Sum_probs=56.9

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      +|+|-|||..+++++|..+|+.||+|+.|......+|..||+|-|.-+|+.|+++|++.+
T Consensus        77 ~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~  136 (549)
T KOG4660|consen   77 TLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRRE  136 (549)
T ss_pred             eEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHH
Confidence            799999999999999999999999999988877779999999999999999999999876

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.29  E-value=3.1e-06  Score=72.86  Aligned_cols=69  Identities=35%  Similarity=0.484  Sum_probs=59.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~   70 (223)
                      ++|+|.|||..++++||+++|+.||+++.+.|.    +.+.|.|-|.|...+||+.|++.+|+..  +..+++..
T Consensus        84 ~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   84 TKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             ceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            579999999999999999999999988888774    3567999999999999999999999975  44444443

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.24  E-value=4.4e-07  Score=76.26  Aligned_cols=59  Identities=24%  Similarity=0.276  Sum_probs=54.4

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ||||+|+...++|+-|.++|-+.|+|.+|.|..    +.+ ||||.|.++..+.-|++.|||..
T Consensus        11 tl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~   73 (267)
T KOG4454|consen   11 TLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDD   73 (267)
T ss_pred             HHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccch
Confidence            789999999999999999999999999999974    334 99999999999999999999886

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.23  E-value=4e-06  Score=69.84  Aligned_cols=60  Identities=28%  Similarity=0.455  Sum_probs=53.5

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcC-CCeEEEEEe-----eCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMF-GVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~-G~I~~v~i~-----~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      -++|..+|..+.+.++..+|.++ |.|..+++.     ++++|||||+|++++.|+-|-+.||+..
T Consensus        51 ~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYL  116 (214)
T KOG4208|consen   51 VVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYL  116 (214)
T ss_pred             ceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhh
Confidence            36889999999999999999988 688888773     4789999999999999999999999987

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

Probab=98.22  E-value=1e-06  Score=74.36  Aligned_cols=61  Identities=23%  Similarity=0.422  Sum_probs=51.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      .||||.||..++||++|+.+|+.|-....++|.. ..-..||++|++.+.|..|+..|+|..
T Consensus       211 stlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg~~  272 (284)
T KOG1457|consen  211 STLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQGNL  272 (284)
T ss_pred             hhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhcce
Confidence            5899999999999999999999997766666642 223489999999999999999998764

>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

Probab=98.11  E-value=2.1e-05  Score=56.89  Aligned_cols=66  Identities=26%  Similarity=0.354  Sum_probs=45.6

Q ss_pred             cEEEEecCCCCCCHHH----HHHHHHcCC-CeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERD----LEDEFRMFG-VLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~----L~~~F~~~G-~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      +.|+|.|||.+.+...    |++++..|| +|..|.     .+.|+|.|.+++.|..|.+.|+|..  |.+|.+....
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~-----~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS-----GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe-----CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence            5799999999988764    567777886 776662     6799999999999999999999887  7777777763

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.10  E-value=2.7e-05  Score=58.08  Aligned_cols=73  Identities=22%  Similarity=0.295  Sum_probs=58.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHc--CCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC------cEEEEE
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRM--FGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN------GWRVEL   68 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~--~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~------g~~V~v   68 (223)
                      |||.|.|+|...|.++|.+++..  .|....+.++-     -+.|||||.|.++++|.+-.+.++|..      ...+++
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            79999999999999999999865  36667777753     357999999999999999999999886      345566


Q ss_pred             eeccCC
Q 041602           69 SHNSKG   74 (223)
Q Consensus        69 ~~~~~~   74 (223)
                      ..|.-+
T Consensus        82 ~yAriQ   87 (97)
T PF04059_consen   82 SYARIQ   87 (97)
T ss_pred             ehhHhh
Confidence            665433

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

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

Probab=98.08  E-value=6e-06  Score=69.82  Aligned_cols=64  Identities=44%  Similarity=0.627  Sum_probs=56.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEE
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVEL   68 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v   68 (223)
                      +.+.|.|++..+.+.+|.++|.++|++....+   ..+++||+|.+.++|..|+..+++.+  +..|.+
T Consensus       100 ~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~---~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen  100 FRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA---RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             ceeeeccchhhhhHHHHhhhhcccCCCchhhh---hccccceeehhhhhhhhcchhccchhhcCceeee
Confidence            46788999999999999999999999966555   37899999999999999999999987  666666

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.03  E-value=1.6e-05  Score=70.76  Aligned_cols=76  Identities=20%  Similarity=0.291  Sum_probs=63.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEE--------EEEe----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEE
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRS--------VWVA----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVE   67 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~--------v~i~----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~   67 (223)
                      +.|||.|||.++|.+++.++|++||-|..        |++-    ++.+|-|.+.|-..++++-|++.|++..  |..|.
T Consensus       135 t~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~r  214 (382)
T KOG1548|consen  135 TSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKKLR  214 (382)
T ss_pred             ceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcEEE
Confidence            46999999999999999999999998764        3332    3568999999999999999999999998  77777


Q ss_pred             EeeccCCCCC
Q 041602           68 LSHNSKGGGG   77 (223)
Q Consensus        68 v~~~~~~~r~   77 (223)
                      |..+.-+.++
T Consensus       215 VerAkfq~Kg  224 (382)
T KOG1548|consen  215 VERAKFQMKG  224 (382)
T ss_pred             Eehhhhhhcc
Confidence            7777555443

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

Probab=97.91  E-value=4e-05  Score=57.95  Aligned_cols=59  Identities=22%  Similarity=0.322  Sum_probs=38.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK   61 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~   61 (223)
                      +-|.|.|++..++.++|++.|++||+|..|++... ..-|+|-|.++++|++|++++...
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G-~~~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG-DTEGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT--SEEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC-CCEEEEEECCcchHHHHHHHHHhc
Confidence            35788899999999999999999999999998732 338999999999999999876544

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

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

Probab=97.83  E-value=4.9e-05  Score=70.43  Aligned_cols=67  Identities=22%  Similarity=0.301  Sum_probs=52.3

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeEEEEEe---eCCCCEEEEEEcCHHHHHHHHHHhCCCC-cEEEEEeec
Q 041602            4 VYVGNLDPRVSERDLEDEFRMFGVLRSVWVA---RRPPGYAFVEFDDRRDAVDAIRALDGKN-GWRVELSHN   71 (223)
Q Consensus         4 LfVgnLp~~~te~~L~~~F~~~G~I~~v~i~---~~~rGfaFV~F~~~e~A~~Al~~lng~~-g~~V~v~~~   71 (223)
                      |-+.+||+++|++||.++|+.+ .|+.+.++   +++.|-|||+|.+++++++|+++-...+ ...|+|-.+
T Consensus        13 vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen   13 VRLRGLPWSATEKEILDFFSNC-GIENLEIPRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTA   83 (510)
T ss_pred             EEecCCCccccHHHHHHHHhcC-ceeEEEEeccCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEcc
Confidence            4457999999999999999999 56777665   3678999999999999999998433333 345555544

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=97.81  E-value=8.8e-05  Score=67.49  Aligned_cols=71  Identities=21%  Similarity=0.340  Sum_probs=62.9

Q ss_pred             cEEEEecCCCC-CCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPR-VSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~-~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      +.|.|.||..+ +|++.|..+|.-||+|..|+|..+++.-|.|+|.+...|+-|+++|+|..  +..+.+..++
T Consensus       298 ~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  298 VVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             eEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            46789999875 89999999999999999999988778899999999999999999999998  6666666653

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

Probab=97.73  E-value=0.00063  Score=56.23  Aligned_cols=58  Identities=36%  Similarity=0.432  Sum_probs=52.8

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      .|.|.+||+..+++||+++..+.|+|....+.+  .|++.|+|...|+.+-|+..|+...
T Consensus       117 RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~r--Dg~GvV~~~r~eDMkYAvr~ld~~~  174 (241)
T KOG0105|consen  117 RVVVSGLPPSGSWQDLKDHMREAGDVCFADVQR--DGVGVVEYLRKEDMKYAVRKLDDQK  174 (241)
T ss_pred             eEEEecCCCCCchHHHHHHHHhhCCeeeeeeec--ccceeeeeeehhhHHHHHHhhcccc
Confidence            578999999999999999999999998888865  4699999999999999999998765

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

Probab=97.61  E-value=0.0002  Score=47.43  Aligned_cols=52  Identities=21%  Similarity=0.586  Sum_probs=42.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHH
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAI   55 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al   55 (223)
                      +.|-|.|.++...+ ++..+|.+||+|..+.+. ....+.+|.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~-~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVP-ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcC-CCCcEEEEEECCHHHHHhhC
Confidence            46778898876654 455699999999999886 33569999999999999985

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.54  E-value=0.00025  Score=63.54  Aligned_cols=74  Identities=27%  Similarity=0.369  Sum_probs=61.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEE--------E-----eeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEE
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVW--------V-----ARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRV   66 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~--------i-----~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V   66 (223)
                      .+|||-+||..+++++|.++|.++|.|+.-+        |     ...+|+-|.|.|+++..|++|++.++++.  +..|
T Consensus        67 ~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn~i  146 (351)
T KOG1995|consen   67 ETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGNTI  146 (351)
T ss_pred             ccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCCCc
Confidence            5899999999999999999999999886522        1     12568999999999999999999999887  6677


Q ss_pred             EEeeccCCC
Q 041602           67 ELSHNSKGG   75 (223)
Q Consensus        67 ~v~~~~~~~   75 (223)
                      +|+.+....
T Consensus       147 kvs~a~~r~  155 (351)
T KOG1995|consen  147 KVSLAERRT  155 (351)
T ss_pred             hhhhhhhcc
Confidence            777765543

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

Probab=97.53  E-value=0.00036  Score=58.98  Aligned_cols=60  Identities=28%  Similarity=0.412  Sum_probs=55.1

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      .+|+.|||.+++.+.|..+|.+|.-.+.|.++....+.|||+|.+...|..|..++++..
T Consensus       148 ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~~lq~~~  207 (221)
T KOG4206|consen  148 ILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGFK  207 (221)
T ss_pred             EEEEecCCcchhHHHHHHHHhhCcccceeEeccCCCceeEEecchhhhhHHHhhhhccce
Confidence            689999999999999999999999989999886668899999999999999999998775

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=97.32  E-value=0.00033  Score=60.28  Aligned_cols=60  Identities=33%  Similarity=0.633  Sum_probs=52.6

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe-----eCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~-----~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      +||-|.|..+++.+.|-..|.+|-.....+++     ++++||+||.|.+++++..|+.+|||+.
T Consensus       192 RIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gky  256 (290)
T KOG0226|consen  192 RIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKY  256 (290)
T ss_pred             eeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccc
Confidence            68889999999999999999999765555554     3679999999999999999999999986

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

Probab=97.32  E-value=0.0012  Score=59.68  Aligned_cols=73  Identities=22%  Similarity=0.314  Sum_probs=64.2

Q ss_pred             cEEEEecCCCC-CCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPR-VSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~-~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      +.+.|-+|... ++-+-|..+|-.||.|+.|++++...|.|.|++.+..+++.|+..||+..  |.++++..+...
T Consensus       288 ~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~  363 (494)
T KOG1456|consen  288 CVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQN  363 (494)
T ss_pred             cEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHhccCccccceEEEeecccc
Confidence            35678899875 67788999999999999999999889999999999999999999999987  888888877543

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

Probab=97.32  E-value=0.00057  Score=63.51  Aligned_cols=69  Identities=22%  Similarity=0.303  Sum_probs=52.4

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEE-EEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC-cEEEEEeec
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRS-VWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN-GWRVELSHN   71 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~-v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~-g~~V~v~~~   71 (223)
                      .|-+.+||+.+|++||.++|+-.-.|.. +.++.    .+.|-|||.|++.++|++|+....... ...|+|-++
T Consensus       105 vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  105 VVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRS  179 (510)
T ss_pred             eEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHHHHHhhccceEEeehh
Confidence            3556899999999999999997644433 33432    457899999999999999998665555 456676655

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.06  E-value=0.00041  Score=63.55  Aligned_cols=60  Identities=22%  Similarity=0.320  Sum_probs=51.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC------------------CCCEEEEEEcCHHHHHHHHHHhCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR------------------PPGYAFVEFDDRRDAVDAIRALDGK   61 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~------------------~rGfaFV~F~~~e~A~~Al~~lng~   61 (223)
                      .+|.+-|||.+-.-+.|.++|..+|.|+.|+|++-                  .+-+|+|+|++.+.|.+|.+.|+..
T Consensus       232 rtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~e  309 (484)
T KOG1855|consen  232 RTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNPE  309 (484)
T ss_pred             ceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhchh
Confidence            37888999999888999999999999999999631                  2568999999999999999988544

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

Probab=96.99  E-value=0.00066  Score=63.94  Aligned_cols=71  Identities=24%  Similarity=0.496  Sum_probs=60.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC-c-EEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN-G-WRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~-g-~~V~v~~~~   72 (223)
                      .++||+|||...++..+.++...||+++...++.     .++||||.+|.++.....|+..|||.. + ..+.+..+.
T Consensus       290 ~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~  367 (500)
T KOG0120|consen  290 NKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAI  367 (500)
T ss_pred             chhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhh
Confidence            5789999999999999999999999998887764     568999999999999999999999998 3 444444443

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

Probab=96.99  E-value=0.0027  Score=59.47  Aligned_cols=59  Identities=29%  Similarity=0.528  Sum_probs=47.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee--------CCCC---EEEEEEcCHHHHHHHHHHhCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR--------RPPG---YAFVEFDDRRDAVDAIRALDGK   61 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~--------~~rG---faFV~F~~~e~A~~Al~~lng~   61 (223)
                      .+||||+||++++|+.|.+.|..||.+ .|+.++        .++|   |+|+.|+++..+.+-+.+....
T Consensus       260 ~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~  329 (520)
T KOG0129|consen  260 RKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEG  329 (520)
T ss_pred             cceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhc
Confidence            479999999999999999999999986 344441        2467   9999999999988877765433

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

Probab=96.80  E-value=0.0035  Score=58.68  Aligned_cols=69  Identities=29%  Similarity=0.458  Sum_probs=55.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHH-cCCCeEEEEEe-----eCCCCEEEEEEcCHHHHHHHHHH----hCCCC-cEEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFR-MFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRA----LDGKN-GWRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~-~~G~I~~v~i~-----~~~rGfaFV~F~~~e~A~~Al~~----lng~~-g~~V~v~~   70 (223)
                      .|||||+||.-++.++|-.+|+ -||.|..+-|-     +-++|-|=|+|.+..+-.+||.+    ++..+ ..+|||..
T Consensus       371 rTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsarFvql~h~d~~KRVEIkP  450 (520)
T KOG0129|consen  371 RTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISARFVQLDHTDIDKRVEIKP  450 (520)
T ss_pred             ceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhhheEEEeccccceeeeecc
Confidence            5899999999999999999998 69999988773     34799999999999999999873    33333 44566553

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

Probab=96.79  E-value=0.029  Score=51.04  Aligned_cols=65  Identities=22%  Similarity=0.209  Sum_probs=54.3

Q ss_pred             cCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC------cEEEEEeecc
Q 041602            8 NLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN------GWRVELSHNS   72 (223)
Q Consensus         8 nLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~------g~~V~v~~~~   72 (223)
                      |--+.+|.+-|..+-...|+|..|.|.+++---|.|+|++.+.|++|..+|||..      .++|+++++.
T Consensus       129 Np~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~  199 (494)
T KOG1456|consen  129 NPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPT  199 (494)
T ss_pred             cCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhcccccccccceeEEEEecCcc
Confidence            3334689999999999999999999987765689999999999999999999998      3566666543

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.75  E-value=0.004  Score=55.78  Aligned_cols=69  Identities=20%  Similarity=0.483  Sum_probs=54.3

Q ss_pred             EEEEecCCCCCCHHH------HHHHHHcCCCeEEEEEeeCC------CCE--EEEEEcCHHHHHHHHHHhCCCC--cEEE
Q 041602            3 RVYVGNLDPRVSERD------LEDEFRMFGVLRSVWVARRP------PGY--AFVEFDDRRDAVDAIRALDGKN--GWRV   66 (223)
Q Consensus         3 tLfVgnLp~~~te~~------L~~~F~~~G~I~~v~i~~~~------rGf--aFV~F~~~e~A~~Al~~lng~~--g~~V   66 (223)
                      -+||-+|++.+..++      -.++|.+||+|..|.|.++.      .+.  .||+|.+.|||..||.+.+|..  |..+
T Consensus       116 LvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~l  195 (480)
T COG5175         116 LVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRVL  195 (480)
T ss_pred             eeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCceE
Confidence            378999998865554      24789999999999886531      222  3999999999999999999987  7777


Q ss_pred             EEeec
Q 041602           67 ELSHN   71 (223)
Q Consensus        67 ~v~~~   71 (223)
                      +.+..
T Consensus       196 katYG  200 (480)
T COG5175         196 KATYG  200 (480)
T ss_pred             eeecC
Confidence            76664

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=96.70  E-value=0.0034  Score=57.42  Aligned_cols=69  Identities=23%  Similarity=0.381  Sum_probs=54.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCC-CeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC-----cEEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFG-VLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN-----GWRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G-~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~-----g~~V~v~~   70 (223)
                      ++|...|+|..++|++|+++|..-| .|+..+.-.+.+-+|++.+++.|+|..|+..++...     -++|.+++
T Consensus       415 atlHlsnip~svsee~lk~~f~~~g~~vkafkff~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSk  489 (492)
T KOG1190|consen  415 ATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSK  489 (492)
T ss_pred             hheeeccCCcccchhHHHHhhhcCCceEEeeeecCCCcceeecccCChhHhhhhccccccccCCCCceEEEEeec
Confidence            4789999999999999999999887 445555544456699999999999999998887665     34555543

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=96.62  E-value=0.0019  Score=57.10  Aligned_cols=68  Identities=25%  Similarity=0.498  Sum_probs=54.6

Q ss_pred             EEE-EecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            3 RVY-VGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         3 tLf-VgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++| |+||+..+++++|+.+|..+|.|..+.+..     ..+|||+|+|.+...+..|+.. +...  ++.+.+...
T Consensus       186 ~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  186 TIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEED  261 (285)
T ss_pred             cceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccC
Confidence            345 999999999999999999999999998863     4689999999999999999865 4443  444444444

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

Probab=96.47  E-value=0.018  Score=39.36  Aligned_cols=54  Identities=22%  Similarity=0.226  Sum_probs=43.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcC---CCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHh
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMF---GVLRSVWVARRPPGYAFVEFDDRRDAVDAIRAL   58 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~---G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~l   58 (223)
                      .+|+|.|+. +.+.++|+.+|..|   .....|.++.+.  -|-|.|.+.+.|.+||.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt--ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT--SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC--cEEEEECCHHHHHHHHHcC
Confidence            579999996 68889999999988   134567776543  5889999999999999865

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

Probab=96.44  E-value=0.0068  Score=57.49  Aligned_cols=60  Identities=28%  Similarity=0.436  Sum_probs=48.8

Q ss_pred             EEEEecCCCCCC------HHHHHHHHHcCCCeEEEEEe----eCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            3 RVYVGNLDPRVS------ERDLEDEFRMFGVLRSVWVA----RRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         3 tLfVgnLp~~~t------e~~L~~~F~~~G~I~~v~i~----~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      -|+|.|+|---.      ..-|..+|+++|+|..+.++    +..+||.|++|.+..+|+.|++.+||..
T Consensus        60 vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~  129 (698)
T KOG2314|consen   60 VVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKR  129 (698)
T ss_pred             EEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccce
Confidence            467788874322      12466889999999999886    3568999999999999999999999986

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

Probab=96.37  E-value=0.023  Score=42.60  Aligned_cols=58  Identities=17%  Similarity=0.292  Sum_probs=41.2

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEE------------EeeCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVW------------VARRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~------------i~~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      -|.|-|.|+. ....|.+.|++||+|.+..            -.........|.|+++.+|++||. -||..
T Consensus         8 wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i   77 (100)
T PF05172_consen    8 WVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTI   77 (100)
T ss_dssp             EEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEE
T ss_pred             EEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeE
Confidence            4677888877 5567788999999998774            111235699999999999999996 66665

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

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

Probab=96.33  E-value=0.0045  Score=56.92  Aligned_cols=69  Identities=39%  Similarity=0.596  Sum_probs=54.3

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcC--CCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC---cEEEEEeecc
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMF--GVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN---GWRVELSHNS   72 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~--G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~---g~~V~v~~~~   72 (223)
                      |+++|++||.+.++..||+.+|...  +--..+ ++  ..||+||++.+..-|.+|++.++++.   |.+.++...-
T Consensus         1 mnklyignL~p~~~psdl~svfg~ak~~~~g~f-l~--k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv   74 (584)
T KOG2193|consen    1 MNKLYIGNLSPQVTPSDLESVFGDAKIPGSGQF-LV--KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CCcccccccCCCCChHHHHHHhccccCCCCcce-ee--ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            6799999999999999999999754  211122 22  26899999999999999999999886   6666666543

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

Probab=96.31  E-value=0.0054  Score=52.91  Aligned_cols=47  Identities=23%  Similarity=0.413  Sum_probs=38.5

Q ss_pred             HHHHHHHH-cCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602           16 RDLEDEFR-MFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus        16 ~~L~~~F~-~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ++|...|+ +||+|+.++|..    +..|-++|.|...++|++|++.||+.-
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw  134 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRW  134 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCcc
Confidence            45555565 899999987753    347899999999999999999999875

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=96.30  E-value=0.0086  Score=56.48  Aligned_cols=55  Identities=22%  Similarity=0.373  Sum_probs=45.7

Q ss_pred             HHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEee
Q 041602           16 RDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSH   70 (223)
Q Consensus        16 ~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~   70 (223)
                      +|+.+...+||+|..|.|.+.+.|+.||.|.+.++|..|+.+|||.=  +..|..+.
T Consensus       468 edV~Eec~k~g~v~hi~vd~ns~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~  524 (549)
T KOG0147|consen  468 EDVIEECGKHGKVCHIFVDKNSAGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKY  524 (549)
T ss_pred             HHHHHHHHhcCCeeEEEEccCCCceEEEecCcHHHHHHHHHHHhhhhhccceeEEEE
Confidence            45666669999999999987777999999999999999999999875  55555443

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=96.23  E-value=0.013  Score=52.83  Aligned_cols=60  Identities=22%  Similarity=0.323  Sum_probs=48.0

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCC--CeEEEEE-----eeCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFG--VLRSVWV-----ARRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G--~I~~v~i-----~~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      -+|||||-+.||++||.+....-|  .+.++++     .+.+||||+|...+.+.+++-++.|..++
T Consensus        82 ~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~  148 (498)
T KOG4849|consen   82 CCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKT  148 (498)
T ss_pred             EEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccce
Confidence            489999999999999998887766  4444444     35789999999999999999888665443

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

Probab=96.05  E-value=0.017  Score=54.66  Aligned_cols=55  Identities=36%  Similarity=0.533  Sum_probs=43.7

Q ss_pred             HHHHHHHHcCCCeEEEEEeeC--------CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEee
Q 041602           16 RDLEDEFRMFGVLRSVWVARR--------PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSH   70 (223)
Q Consensus        16 ~~L~~~F~~~G~I~~v~i~~~--------~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~   70 (223)
                      ++++..+++||.|..|.++..        ..|..||+|.+.+++++|+++|+|.+  +..|..+.
T Consensus       424 Edvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsY  488 (500)
T KOG0120|consen  424 EDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASY  488 (500)
T ss_pred             HHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEe
Confidence            355666788999999998642        25688999999999999999999998  55555443

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=96.03  E-value=0.029  Score=50.44  Aligned_cols=56  Identities=34%  Similarity=0.532  Sum_probs=46.7

Q ss_pred             HHHHHHHHcCCCeEEEEEe-eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602           16 RDLEDEFRMFGVLRSVWVA-RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus        16 ~~L~~~F~~~G~I~~v~i~-~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|.+.-++||+|..|.|- .++.|.+-|.|.+.++|+.||+.|+|.-  ++.|.....
T Consensus       291 edl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~  349 (382)
T KOG1548|consen  291 EDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIW  349 (382)
T ss_pred             HHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEe
Confidence            4566778899999999886 4789999999999999999999999986  666655443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.71  E-value=0.051  Score=43.32  Aligned_cols=68  Identities=26%  Similarity=0.350  Sum_probs=51.2

Q ss_pred             CcEEEEecCCCCCC-HHH---HHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC-cEEEEEee
Q 041602            1 MSRVYVGNLDPRVS-ERD---LEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN-GWRVELSH   70 (223)
Q Consensus         1 ~ttLfVgnLp~~~t-e~~---L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~-g~~V~v~~   70 (223)
                      |.||.|.=|..++. .+|   +....+.||+|..|.+.+  +.-|.|.|.+..+|=+|+.+++... +-.+..++
T Consensus        86 MsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG--rqsavVvF~d~~SAC~Av~Af~s~~pgtm~qCsW  158 (166)
T PF15023_consen   86 MSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG--RQSAVVVFKDITSACKAVSAFQSRAPGTMFQCSW  158 (166)
T ss_pred             ceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC--CceEEEEehhhHHHHHHHHhhcCCCCCceEEeec
Confidence            57888877766643 244   445567899999999976  4589999999999999999988665 55555544

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

Probab=95.55  E-value=0.011  Score=58.35  Aligned_cols=70  Identities=19%  Similarity=0.246  Sum_probs=57.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe----eCCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA----RRPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~----~~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~   71 (223)
                      .+++|.|+|+..|.++|+.++.++|.++++.++    ++++|-|+|.|.++.++..++..++...    ...|.+..+
T Consensus       737 ~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  737 ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            368999999999999999999999999998775    4789999999999999999977665443    344555433

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

Probab=94.99  E-value=0.025  Score=51.55  Aligned_cols=68  Identities=24%  Similarity=0.266  Sum_probs=53.0

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCC-CeEE--EEEe----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            4 VYVGNLDPRVSERDLEDEFRMFG-VLRS--VWVA----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         4 LfVgnLp~~~te~~L~~~F~~~G-~I~~--v~i~----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      |-+.+||++.+.+||-++|..|. .|..  |.|+    +.+-|-|||+|.+.++|.+|..+.+.+.  .+.|++-..
T Consensus       283 vRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~  359 (508)
T KOG1365|consen  283 VRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPC  359 (508)
T ss_pred             eEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeec
Confidence            45689999999999999998886 3333  4443    3567899999999999999988776554  566776654

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

Probab=94.75  E-value=0.017  Score=52.76  Aligned_cols=58  Identities=16%  Similarity=0.140  Sum_probs=47.5

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-CCCCEEEEEEcCHHHHHHHHHHhCCC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-RPPGYAFVEFDDRRDAVDAIRALDGK   61 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-~~rGfaFV~F~~~e~A~~Al~~lng~   61 (223)
                      +++|++|+..+..+++-+.|..+|+|....+.. ...-+|-|+|........|+. ++|.
T Consensus       153 t~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~ask~~s~~c~~sf~~qts~~halr-~~gr  211 (479)
T KOG4676|consen  153 TREVQSLISAAILPESGESFERKGEVSYAHTASKSRSSSCSHSFRKQTSSKHALR-SHGR  211 (479)
T ss_pred             hhhhhcchhhhcchhhhhhhhhcchhhhhhhhccCCCcchhhhHhhhhhHHHHHH-hcch
Confidence            688999999999999999999999998877643 234477899999999999987 4444

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

Probab=94.62  E-value=0.022  Score=49.27  Aligned_cols=60  Identities=22%  Similarity=0.346  Sum_probs=51.3

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-------------CCC----CEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-------------RPP----GYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-------------~~r----GfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      .||+++||+.++..-|+++|++||+|-.|.+..             .+.    --|.|+|.+...|+.+.+.||+..
T Consensus        76 VvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   76 VVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             EEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            589999999999999999999999999998842             011    146899999999999999999876

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=94.59  E-value=0.1  Score=50.93  Aligned_cols=66  Identities=24%  Similarity=0.330  Sum_probs=52.4

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCe-EEEEEe----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEE
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVL-RSVWVA----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVEL   68 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I-~~v~i~----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v   68 (223)
                      .|-+-|+|++++-+||.++|.-|-.+ .+|.+.    +.+.|-|.|.|++.++|..|...++++.  ..+|.+
T Consensus       869 V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l  941 (944)
T KOG4307|consen  869 VLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSL  941 (944)
T ss_pred             EEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEE
Confidence            46678999999999999999999543 234332    2567899999999999999999999887  344444

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

Probab=94.49  E-value=0.11  Score=47.55  Aligned_cols=59  Identities=29%  Similarity=0.260  Sum_probs=44.8

Q ss_pred             EEEecCCCCCCHHHHHHHHHcC----CCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            4 VYVGNLDPRVSERDLEDEFRMF----GVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         4 LfVgnLp~~~te~~L~~~F~~~----G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      |-+.+||+++++.|+.++|..-    |..+.|.++.    ++.|-|||.|.++++|+.|+.+-.+..
T Consensus       164 vRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~khrq~i  230 (508)
T KOG1365|consen  164 VRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRKHRQNI  230 (508)
T ss_pred             EEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHHHHHHH
Confidence            4457999999999999999632    2444555543    457899999999999999997554433

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

Probab=94.42  E-value=0.049  Score=47.17  Aligned_cols=58  Identities=31%  Similarity=0.429  Sum_probs=49.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe----eCCCCEEEEEEcCHHHHHHHHHHhC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA----RRPPGYAFVEFDDRRDAVDAIRALD   59 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~----~~~rGfaFV~F~~~e~A~~Al~~ln   59 (223)
                      +.|||.||+..++.+.|...|..||+|....+.    .++.+-++|.|...-.|.+|+..+.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhc
Confidence            468999999999999999999999998775543    3556789999999999999998774

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=94.37  E-value=0.063  Score=53.52  Aligned_cols=68  Identities=26%  Similarity=0.463  Sum_probs=57.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC------cEEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN------GWRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~------g~~V~v~~   70 (223)
                      +.+||++|..++....|...|..||.|..|.+-. ..-||+|.|++...+++|+..|.+..      .+.|.++.
T Consensus       456 tr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h-gq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~  529 (975)
T KOG0112|consen  456 TRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH-GQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLAS  529 (975)
T ss_pred             eeeccCCCCCCChHHHHHHHhhccCcceeeeccc-CCcceeeecccCccchhhHHHHhcCcCCCCCccccccccc
Confidence            5789999999999999999999999999988752 24599999999999999999998775      34555554

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

Probab=94.24  E-value=0.24  Score=39.55  Aligned_cols=53  Identities=25%  Similarity=0.436  Sum_probs=41.2

Q ss_pred             HHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602           17 DLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus        17 ~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      +|-+.|.+||++.-++++   .+.-.|+|.+-..|.+|+. |+|.+  +..+++....+
T Consensus        52 ~ll~~~~~~GevvLvRfv---~~~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFV---GDTMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEE---TTCEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE---
T ss_pred             HHHHHHHhCCceEEEEEe---CCeEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCc
Confidence            677889999999888887   4578999999999999996 88887  66666665443

; PDB: 1UFW_A 2DNR_A.

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

Probab=94.09  E-value=0.42  Score=34.68  Aligned_cols=56  Identities=20%  Similarity=0.296  Sum_probs=40.5

Q ss_pred             cCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCCcEEE
Q 041602            8 NLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKNGWRV   66 (223)
Q Consensus         8 nLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~g~~V   66 (223)
                      .+|.++...||.++|+.||.|.- ..+.  ..-|||...+.+.|..|+..+.-....+|
T Consensus        15 tFPkeWK~~DI~qlFspfG~I~V-sWi~--dTSAfV~l~~r~~~~~v~~~~~~~~~y~i   70 (87)
T PF08675_consen   15 TFPKEWKTSDIYQLFSPFGQIYV-SWIN--DTSAFVALHNRDQAKVVMNTLKKNSSYRI   70 (87)
T ss_dssp             E--TT--HHHHHHHCCCCCCEEE-EEEC--TTEEEEEECCCHHHHHHHHHHTT-SSSEE
T ss_pred             eCchHhhhhhHHHHhccCCcEEE-EEEc--CCcEEEEeecHHHHHHHHHHhccCCceEE
Confidence            48999999999999999999743 3332  45899999999999999988864433333

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

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

Probab=93.42  E-value=0.071  Score=51.07  Aligned_cols=60  Identities=13%  Similarity=0.153  Sum_probs=51.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHc-CCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRM-FGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~-~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ..|+|.||-.-.|.-+|+.++.+ .|.|... +|.+-+-.|||.|.+.++|.+.+.+|||..
T Consensus       445 nvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-WmDkIKShCyV~yss~eEA~atr~AlhnV~  505 (718)
T KOG2416|consen  445 NVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WMDKIKSHCYVSYSSVEEAAATREALHNVQ  505 (718)
T ss_pred             ceEeeecccccchHHHHHHHHhhccCchHHH-HHHHhhcceeEecccHHHHHHHHHHHhccc
Confidence            36899999999999999999984 6677666 444447789999999999999999999986

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

Probab=93.42  E-value=0.0063  Score=60.02  Aligned_cols=61  Identities=33%  Similarity=0.488  Sum_probs=52.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe-----eCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~-----~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      +++||.||+..+.+.+|...|..+|.+..+.+.     ++.+|.|||+|..++++.+|+...+...
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~  733 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCF  733 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhh
Confidence            578999999999999999999999987776553     3668999999999999999998655444

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=92.69  E-value=2.2  Score=41.81  Aligned_cols=65  Identities=6%  Similarity=0.058  Sum_probs=40.7

Q ss_pred             cEEEEecCC--CCCCHHHHHHHHHcCCCeE-----EEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLD--PRVSERDLEDEFRMFGVLR-----SVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp--~~~te~~L~~~F~~~G~I~-----~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      +++|| |+.  ..++..+|-.+...-+.|.     .|+|.   ..|.||+-.. +.|.+.++.|++..  +..|.+..+
T Consensus       487 ~~~~~-~~g~~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~---~~~s~v~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  560 (629)
T PRK11634        487 QLYRI-EVGRDDGVEVRHIVGAIANEGDISSRYIGNIKLF---ASHSTIELPK-GMPGEVLQHFTRTRILNKPMNMQLL  560 (629)
T ss_pred             EEEEE-ecccccCCCHHHHHHHHHhhcCCChhhCCcEEEe---CCceEEEcCh-hhHHHHHHHhccccccCCceEEEEC
Confidence            34555 333  4578888888887655443     34444   5689999875 45777777887654  555555544

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

Probab=92.46  E-value=0.14  Score=46.90  Aligned_cols=58  Identities=17%  Similarity=0.299  Sum_probs=47.8

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee---C-----CCCEEEEEEcCHHHHHHHHHHhCCC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR---R-----PPGYAFVEFDDRRDAVDAIRALDGK   61 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~---~-----~rGfaFV~F~~~e~A~~Al~~lng~   61 (223)
                      .|.|.||.+++|.++++.+|...|+|..+.|..   +     ..-.|||.|.+...+..|.. |.++
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltnt   74 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNT   74 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccc
Confidence            578999999999999999999999999998843   1     13489999999988888864 4433

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=92.05  E-value=0.47  Score=42.11  Aligned_cols=53  Identities=26%  Similarity=0.446  Sum_probs=41.3

Q ss_pred             HHHHHHHHHcCCCeEEEEEee------CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEE
Q 041602           15 ERDLEDEFRMFGVLRSVWVAR------RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVE   67 (223)
Q Consensus        15 e~~L~~~F~~~G~I~~v~i~~------~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~   67 (223)
                      |+++.+..++||+|..|.|.-      +-.---||+|+..++|.+|+..|||..  |..|.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~  360 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVS  360 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeee
Confidence            356778889999999987742      112357999999999999999999987  55444

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=91.98  E-value=0.032  Score=55.54  Aligned_cols=60  Identities=23%  Similarity=0.375  Sum_probs=51.8

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      |||+|||+..+++.+|+..|..+|.|..|.|..    ..--||||.|.+.+.+-.|+..+.+..
T Consensus       374 TLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~  437 (975)
T KOG0112|consen  374 TLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPL  437 (975)
T ss_pred             hhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCc
Confidence            789999999999999999999999999998842    223499999999999999988777654

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=90.39  E-value=0.52  Score=46.21  Aligned_cols=67  Identities=22%  Similarity=0.169  Sum_probs=49.7

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCC-CeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC-cEEEEEee
Q 041602            4 VYVGNLDPRVSERDLEDEFRMFG-VLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN-GWRVELSH   70 (223)
Q Consensus         4 LfVgnLp~~~te~~L~~~F~~~G-~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~-g~~V~v~~   70 (223)
                      |-+-|||..+...||+.+|+-.- +--.|.|++.-.|-|||.|.+-|||.-|+-+-.++. +..|.+-.
T Consensus         5 IRLqnLP~tAga~DIR~FFSGL~IPdGgVHIIGGe~GeaFI~FsTDeDARlaM~kdr~~i~g~~VrLlL   73 (944)
T KOG4307|consen    5 IRLQNLPMTAGASDIRTFFSGLKIPDGGVHIIGGEEGEAFIGFSTDEDARLAMTKDRLMIHGAEVRLLL   73 (944)
T ss_pred             EEecCCcccccchHHHHhhcccccCCCceEEecccccceEEEecccchhhhhhhhcccceecceEEEEe
Confidence            44579999999999999998652 112367777668999999999999999985444443 55555443

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

Probab=89.77  E-value=1.6  Score=36.00  Aligned_cols=9  Identities=22%  Similarity=0.368  Sum_probs=4.2

Q ss_pred             HHHHHHHHH
Q 041602           48 RRDAVDAIR   56 (223)
Q Consensus        48 ~e~A~~Al~   56 (223)
                      ..+.+.+..
T Consensus        24 k~eLE~~F~   32 (195)
T KOG0107|consen   24 KRELERAFS   32 (195)
T ss_pred             hHHHHHHHH
Confidence            444455544

>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

Probab=88.06  E-value=0.82  Score=37.54  Aligned_cols=61  Identities=15%  Similarity=0.278  Sum_probs=41.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHc-CCCe---EEEE--Eee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRM-FGVL---RSVW--VAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~-~G~I---~~v~--i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ++|.|.+||+++||+++.+.++. +++-   ..+.  ...     ..-.-|||.|.+.+++..-...++|..
T Consensus         8 ~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~   79 (176)
T PF03467_consen    8 TKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHV   79 (176)
T ss_dssp             -EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEE
T ss_pred             ceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcE
Confidence            57999999999999998886665 5544   2332  111     113479999999999999999998864

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>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 []

Probab=87.36  E-value=5.6  Score=30.19  Aligned_cols=56  Identities=14%  Similarity=0.070  Sum_probs=41.9

Q ss_pred             ecCCCCCCHHHHHHHHHcCC-CeEEEEEeeCC---CCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            7 GNLDPRVSERDLEDEFRMFG-VLRSVWVARRP---PGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         7 gnLp~~~te~~L~~~F~~~G-~I~~v~i~~~~---rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ...|..++.++|..+.+.+- .|..++|+++.   +--+.+.|.+.++|++-.+.+||+.
T Consensus        19 ~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~   78 (110)
T PF07576_consen   19 AVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKP   78 (110)
T ss_pred             EeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCc
Confidence            34444566677766656654 67788887653   3478999999999999999999986

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

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

Probab=87.16  E-value=1.1  Score=42.76  Aligned_cols=39  Identities=18%  Similarity=0.302  Sum_probs=31.3

Q ss_pred             CCCCEEEEEEcCHHHHHHHHHHhCCCC------cEEEEEeeccCC
Q 041602           36 RPPGYAFVEFDDRRDAVDAIRALDGKN------GWRVELSHNSKG   74 (223)
Q Consensus        36 ~~rGfaFV~F~~~e~A~~Al~~lng~~------g~~V~v~~~~~~   74 (223)
                      .+.|||||.|.+++++..+.++.||+.      ....+++++.-+
T Consensus       429 cNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYArIQ  473 (549)
T KOG4660|consen  429 CNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYARIQ  473 (549)
T ss_pred             cccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhhhh
Confidence            357999999999999999999999997      445566666443

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=86.70  E-value=3  Score=37.18  Aligned_cols=54  Identities=15%  Similarity=0.175  Sum_probs=40.4

Q ss_pred             EecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            6 VGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         6 VgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      |-++++.. ..-|-.+|++||+|.+.... .+-.+-+|.|.+..+|++||. .||+.
T Consensus       202 VfGFppg~-~s~vL~~F~~cG~Vvkhv~~-~ngNwMhirYssr~~A~KALs-kng~i  255 (350)
T KOG4285|consen  202 VFGFPPGQ-VSIVLNLFSRCGEVVKHVTP-SNGNWMHIRYSSRTHAQKALS-KNGTI  255 (350)
T ss_pred             EeccCccc-hhHHHHHHHhhCeeeeeecC-CCCceEEEEecchhHHHHhhh-hcCee
Confidence            34555443 34566899999999887655 445699999999999999996 56665

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=86.33  E-value=0.44  Score=47.55  Aligned_cols=67  Identities=25%  Similarity=0.357  Sum_probs=53.6

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeec
Q 041602            4 VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHN   71 (223)
Q Consensus         4 LfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~   71 (223)
                      .++.|.+-..+-..|..+|.+||.|.+....++ ...|.|+|...+.|..|+++++|++    |..++|..+
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~-~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~a  371 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRD-LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFA  371 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheeccc-ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEec
Confidence            445566667788889999999999999887643 5689999999999999999999998    444444444

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=85.61  E-value=2  Score=38.03  Aligned_cols=46  Identities=24%  Similarity=0.337  Sum_probs=36.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCC-CeEEEEEeeCCCCEEEEEEcCH
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFG-VLRSVWVARRPPGYAFVEFDDR   48 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G-~I~~v~i~~~~rGfaFV~F~~~   48 (223)
                      +.|+|+||+.++.-.||+..+.+-+ ....+.+. .+.|-||++|.+.
T Consensus       331 ~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswk-g~~~k~flh~~~~  377 (396)
T KOG4410|consen  331 TDIKLTNLSRDIRVKDLKSELRKRECTPMSISWK-GHFGKCFLHFGNR  377 (396)
T ss_pred             cceeeccCccccchHHHHHHHHhcCCCceeEeee-cCCcceeEecCCc
Confidence            5689999999999999999998876 33455554 3478899999874

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=84.76  E-value=7.2  Score=27.05  Aligned_cols=64  Identities=20%  Similarity=0.363  Sum_probs=36.3

Q ss_pred             cEEEEe-cCCCCCCHHHHHHHHHcCC-----CeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEe
Q 041602            2 SRVYVG-NLDPRVSERDLEDEFRMFG-----VLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELS   69 (223)
Q Consensus         2 ttLfVg-nLp~~~te~~L~~~F~~~G-----~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~   69 (223)
                      +++||. |=-..++..+|-.++..-+     .|-.|.|.   ..|+||+-.. +.|+.+++.|++..  +.+|.+.
T Consensus         1 vrl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~---~~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve   72 (74)
T PF03880_consen    1 VRLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIF---DNFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             -EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE----SS-EEEEE-T-T-HHHHHHHHTT--SSS----EE
T ss_pred             CEEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEe---eeEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEE
Confidence            356662 2234688999999997764     45566665   5699999886 47888899998776  5555554

; PDB: 2G0C_A 3MOJ_B.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=84.72  E-value=2.9  Score=40.19  Aligned_cols=56  Identities=16%  Similarity=0.161  Sum_probs=44.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHc--CCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRM--FGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALD   59 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~--~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~ln   59 (223)
                      |-|.+.-||..+-+|+++.+|+.  +-++.+|.+..+  .-=||+|++.+||+.|.+.|.
T Consensus       176 cIvilREIpettp~e~Vk~lf~~encPk~iscefa~N--~nWyITfesd~DAQqAykylr  233 (684)
T KOG2591|consen  176 CIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN--DNWYITFESDTDAQQAYKYLR  233 (684)
T ss_pred             eEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec--CceEEEeecchhHHHHHHHHH
Confidence            45677899999999999999975  778888876432  246999999999999976554

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=82.33  E-value=0.97  Score=40.61  Aligned_cols=59  Identities=25%  Similarity=0.456  Sum_probs=45.0

Q ss_pred             EEEecCCCCC-CHHHHH--HHHHcCCCeEEEEEeeCC--------CCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            4 VYVGNLDPRV-SERDLE--DEFRMFGVLRSVWVARRP--------PGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         4 LfVgnLp~~~-te~~L~--~~F~~~G~I~~v~i~~~~--------rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      +||-+|+... .|..|+  +.|.+||.|..|.+.+++        -.-++|+|+..++|..||...+|..
T Consensus        80 vyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~  149 (327)
T KOG2068|consen   80 VYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFV  149 (327)
T ss_pred             hhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHH
Confidence            5677888765 455554  468899999999876422        1247999999999999999888876

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=80.93  E-value=0.8  Score=40.54  Aligned_cols=59  Identities=17%  Similarity=0.208  Sum_probs=48.8

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhC
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALD   59 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~ln   59 (223)
                      ++++|++++...+.+.+...++..+|.+....+..     ..++++.|+|...+.+..|+....
T Consensus        88 ~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~  151 (285)
T KOG4210|consen   88 SSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESG  151 (285)
T ss_pred             cccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhh
Confidence            36889999999999998999999999766655431     458999999999999999997544

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

Probab=80.88  E-value=5.6  Score=32.97  Aligned_cols=57  Identities=19%  Similarity=0.202  Sum_probs=39.3

Q ss_pred             CHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhC--CCC--cEEEEEeec
Q 041602           14 SERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALD--GKN--GWRVELSHN   71 (223)
Q Consensus        14 te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~ln--g~~--g~~V~v~~~   71 (223)
                      ..+.|+++|.+++++......+ +-+-..|.|.+.++|.+|...|+  +..  +..+.+..+
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~-sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~   68 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLK-SFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFG   68 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEET-TTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE--
T ss_pred             hHHHHHHHHHhcCCceEEEEcC-CCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEc
Confidence            4578999999999887776553 35578999999999999999988  554  555555544

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	223
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		9e-09
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		9e-09
2hvz_A	101	Solution Structure Of The Rrm Domain Of Sr Rich Fac		1e-07
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		3e-04
1x4a_A	109	Solution Structure Of Rrm Domain In Splicing Factor		4e-04

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 57.0 bits (136), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 33/75 (44%), Positives = 41/75 (54%), Gaps = 4/75 (5%)
Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFXXXXXXXXXXXXXXGKN 62
           +VYVGNL    ++ +LE  F  +G LRSVWVAR PPG+AFVEF              G+ 
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRT 134
Query: 63  ----GWRVELSHNSK 73
                 RVELS+  K
Sbjct: 135 LCGCRVRVELSNGEK 149

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 57.0 bits (136), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 33/75 (44%), Positives = 41/75 (54%), Gaps = 4/75 (5%)
Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFXXXXXXXXXXXXXXGKN 62
           +VYVGNL    ++ +LE  F  +G LRSVWVAR PPG+AFVEF              G+ 
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 134
Query: 63  ----GWRVELSHNSK 73
                 RVELS+  K
Sbjct: 135 LCGCRVRVELSNGEK 149

>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8 Length = 101

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/43 (55%), Positives = 31/43 (72%)
Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEF 45
          +VYVGNL     + +LE  F  +G LR+VW+AR PPG+AFVEF
Sbjct: 2  KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEF 44

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 30/50 (60%), Gaps = 6/50 (12%)
Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGV-LRSVWVARRP-----PGYAFVEF 45
          S +++GNLDP + E+ L D F  FGV L++  + R P      GYAF+ F
Sbjct: 6  SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINF 55

>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2 Length = 109

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 30/46 (65%), Gaps = 4/46 (8%)
Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR---PPGYAFVEF 45
          R+YVGNL P +  +D+ED F  +G +R + +  R   PP +AFVEF
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP-FAFVEF 68

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	223
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	6e-29
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-28
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-26
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-25
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-24
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-23
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-22
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	7e-22
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	9e-21
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-20
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-20
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-19
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-18
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	4e-18
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	7e-18
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-17
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-17
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	8e-17
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-16
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	4e-16
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-16
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	6e-16
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-15
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-15
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-15
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-15
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-15
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	5e-15
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	6e-15
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	7e-15
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	7e-15
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-14
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-14
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-14
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-14
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-14
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-14
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-14
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-14
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-14
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-14
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-12
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-14
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-14
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-14
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-14
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-14
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-14
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-14
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-14
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-12
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	5e-14
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	7e-14
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	8e-13
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	8e-14
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	8e-14
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	9e-14
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	9e-14
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-13
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-13
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-13
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-13
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-13
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-13
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-13
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-13
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-13
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-13
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-13
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-13
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-13
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-13
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-13
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-10
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-13
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	4e-13
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	4e-13
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-13
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	4e-13
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-13
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	5e-13
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	6e-13
2div_A	99	TRNA selenocysteine associated protein; structural	7e-13
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	7e-13
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	7e-13
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	8e-13
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	9e-13
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-10
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-12
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-12
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-12
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	9e-12
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-12
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-12
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-12
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-12
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-12
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-12
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-12
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-12
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-12
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-10
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-12
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-12
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-12
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-12
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	7e-12
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	7e-12
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	8e-12
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	8e-12
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-10
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	9e-12
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	9e-12
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	9e-12
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-11
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-11
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-11
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-11
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-11
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	3e-11
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-11
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-11
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-11
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-11
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	5e-11
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	6e-11
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	7e-11
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	9e-11
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-10
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-10
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-10
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-10
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-10
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-10
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	2e-10
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-10
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-10
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	7e-10
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	8e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-09
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-09
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-09
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	4e-09
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	8e-09
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-08
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-08
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-08
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-08
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-07
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	5e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	6e-08
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	9e-08
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-07
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-07
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-07
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-07
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-07
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-06
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	6e-07
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	9e-07
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-06
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	3e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	3e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	3e-06
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	7e-06
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	8e-06
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	8e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	9e-06
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	1e-05
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	8e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-05
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-05
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	2e-05
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-05
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	5e-05
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	5e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	5e-05
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	6e-05
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	6e-05
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	1e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	8e-05
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	1e-04
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-04
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-04
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	2e-04
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	6e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	7e-04
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	9e-04

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

 Score =  103 bits (259), Expect = 6e-29
 Identities = 45/101 (44%), Positives = 56/101 (55%), Gaps = 5/101 (4%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN 62
           +VYVGNL     + +LE  F  +G LR+VW+AR PPG+AFVEF+D RDA DA+R LDGK 
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 61

Query: 63  ----GWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGH 99
                 RVELS        R  R     + L+    G   H
Sbjct: 62  ICGSRVRVELSTG-MPRRSRFDRPPARRKLLEVLFNGPLEH 101

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score =  103 bits (258), Expect = 2e-28
 Identities = 42/77 (54%), Positives = 52/77 (67%), Gaps = 4/77 (5%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
             +VYVGNL    ++ +LE  F  +G LRSVWVAR PPG+AFVEF+D RDA DA+R LDG
Sbjct: 73  DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDG 132

Query: 61  KN----GWRVELSHNSK 73
           +       RVELS+  K
Sbjct: 133 RTLCGCRVRVELSNGEK 149

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 97.4 bits (243), Expect = 2e-26
 Identities = 34/88 (38%), Positives = 48/88 (54%), Gaps = 6/88 (6%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA--RRPPGYAFVEFDDRRDAVDAIRAL 58
             R+YVGNL P +  +D+ED F  +G +R + +   R  P +AFVEF+D RDA DA+   
Sbjct: 22  DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGR 81

Query: 59  DGKN----GWRVELSHNSKGGGGRGGRG 82
           DG +      RVE   + +G G     G
Sbjct: 82  DGYDYDGYRLRVEFPRSGRGTGSGPSSG 109

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

 Score = 93.8 bits (234), Expect = 3e-25
 Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 9/87 (10%)

Query: 2  SRVYVGNLDPR-VSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          SR+++GNL  + VS+ DL   F  +G +  + +      + F++FD+ +   DAI     
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN---AFGFIQFDNPQSVRDAIECESQ 67

Query: 61 KN----GWRVELSH-NSKGGGGRGGRG 82
          +        +E+S  N++     G  G
Sbjct: 68 EMNFGKKLILEVSSSNARPQFDHGDHG 94

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 91.1 bits (227), Expect = 3e-24
 Identities = 22/86 (25%), Positives = 36/86 (41%), Gaps = 7/86 (8%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          M ++++GNL    +E+++   F  +G +    + +    Y FV  +D+  A DAIR L  
Sbjct: 8  MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK---NYGFVHIEDKTAAEDAIRNLHH 64

Query: 61 KN----GWRVELSHNSKGGGGRGGRG 82
                   VE S N          G
Sbjct: 65 YKLHGVNINVEASKNKSKASSGPSSG 90

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 88.4 bits (220), Expect = 3e-23
 Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 11/89 (12%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          ++++VGN+ P  + ++L  +F  +G +    + +    YAFV  +   DAV+AIR LD  
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK---DYAFVHMERAEDAVEAIRGLDNT 67

Query: 62 N----GWRVELSHNSKGGGGRGGRGRGGG 86
                  V+LS        R   G   G
Sbjct: 68 EFQGKRMHVQLST----SRLRTASGPSSG 92

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 87.0 bits (216), Expect = 2e-22
 Identities = 25/86 (29%), Positives = 44/86 (51%), Gaps = 6/86 (6%)

Query: 2   SRVYVGNLDP-RVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           SRV++GNL+   V + D+E  F  +G +    V +   GYAFV++ + R A  A+   +G
Sbjct: 28  SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK---GYAFVQYSNERHARAAVLGENG 84

Query: 61  K--NGWRVELSHNSKGGGGRGGRGRG 84
           +   G  ++++   +    R G   G
Sbjct: 85  RVLAGQTLDINMAGEPKPDRSGPSSG 110

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 85.0 bits (211), Expect = 7e-22
 Identities = 24/86 (27%), Positives = 38/86 (44%), Gaps = 6/86 (6%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
            +++VGN+    + ++L   F   G +    V +    YAFV  +   DA  AI  L+G
Sbjct: 9  TWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK---DYAFVHMEKEADAKAAIAQLNG 65

Query: 61 K--NGWRVELSHNSKGGGGRGGRGRG 84
          K   G R+ +   S  G  + G   G
Sbjct: 66 KEVKGKRINVEL-STKGQKKSGPSSG 90

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 82.4 bits (204), Expect = 9e-21
 Identities = 20/77 (25%), Positives = 40/77 (51%), Gaps = 8/77 (10%)

Query: 2  SRVYVGNLDPR-VSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          SR+++GNL  + VS+ DL   F  +G +  + +      + F++FD+ +   DAI     
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN---AFGFIQFDNPQSVRDAIEXESQ 79

Query: 61 K--NGWR--VELSHNSK 73
          +   G +  +E+S ++ 
Sbjct: 80 EMNFGKKLILEVSSSNA 96

>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 Length = 93

 Score = 81.9 bits (203), Expect = 1e-20
 Identities = 28/88 (31%), Positives = 43/88 (48%), Gaps = 5/88 (5%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          M+++Y+GNL P V+  DL   F    +  +  V     GYAFV++ D+  A+ AI  L G
Sbjct: 8  MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-LLKSGYAFVDYPDQNWAIRAIETLSG 66

Query: 61 K---NGWRVELSHNSKGGGGRGGRGRGG 85
          K   +G  +E+ + S     R      G
Sbjct: 67 KVELHGKIMEVDY-SVSKKLRSSGPSSG 93

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

 Score = 82.0 bits (203), Expect = 2e-20
 Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 3/60 (5%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          +R++V      V E +L + F  FG ++ V +     G+AFVEF++   A  AI  + GK
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN---GFAFVEFEEAESAAKAIEEVHGK 88

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 77.9 bits (192), Expect = 5e-19
 Identities = 21/75 (28%), Positives = 30/75 (40%), Gaps = 4/75 (5%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK- 61
           VYVGNL       DL+   R  G +      + P   AF+ + D   A  A+  L G  
Sbjct: 21 DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLR 80

Query: 62 ---NGWRVELSHNSK 73
             +  RV L+   +
Sbjct: 81 LGTDTLRVALARQQR 95

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 75.8 bits (187), Expect = 3e-18
 Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 5/69 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK- 61
           ++V NL   V+E  LE  F  FG L  V   +    YAF+ FD+R  AV A+  ++GK 
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVKKLK---DYAFIHFDERDGAVKAMEEMNGKD 69

Query: 62 -NGWRVELS 69
            G  +E+ 
Sbjct: 70 LEGENIEIV 78

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 75.4 bits (186), Expect = 4e-18
 Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          R++VG L P  S   L  EF  FG +R++    +   +A+++++    A  A   + G 
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDH-VKGDSFAYIQYESLDAAQAACAKMRGF 76

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 74.6 bits (184), Expect = 7e-18
 Identities = 28/83 (33%), Positives = 42/83 (50%), Gaps = 7/83 (8%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK-- 61
          +YV NL    SE  +E EF          V ++   YAFV F +R DAV+A++AL+GK  
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERV-KKIRDYAFVHFSNREDAVEAMKALNGKVL 76

Query: 62 NGWRVELSH----NSKGGGGRGG 80
          +G  +E++     +    G   G
Sbjct: 77 DGSPIEVTLAKPVDKDSSGPSSG 99

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 73.4 bits (181), Expect = 2e-17
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           SR++VGNL P ++E ++   F  +G    V++ +   G+ F+  + R  A  A   LD 
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK-DKGFGFIRLETRTLAEIAKVELDN 73

Query: 61 K 61
           
Sbjct: 74 M 74

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 73.2 bits (180), Expect = 4e-17
 Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 6/77 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR--RPPGYAFVEFDDRRDAVDAIRALDGK 61
          +Y+ NL  +++  ++ D F  +G +R + V       G A+V ++D  DA +A+  L G 
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGF 70

Query: 62 N----GWRVELSHNSKG 74
          N       V   + ++ 
Sbjct: 71 NVSNRYLVVLYYNANRA 87

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 72.4 bits (178), Expect = 8e-17
 Identities = 22/105 (20%), Positives = 48/105 (45%), Gaps = 14/105 (13%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRA 57
            ++++G L+   +E+ L+  F   G +  V + +    +  G+AF+ F++  DA +A + 
Sbjct: 8   GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKD 67

Query: 58  LDGK--NG--WRVELSH------NSKGGGGRGGRGRGGGEDLKCY 92
           ++GK  +G   +VE +         +       R R     L+ +
Sbjct: 68  MNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEHH 112

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 71.8 bits (176), Expect = 4e-16
 Identities = 25/66 (37%), Positives = 35/66 (53%), Gaps = 5/66 (7%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
           M+ + V NL  R S   L   F  +G +  V++ R        G+AFV F D+RDA DA+
Sbjct: 70  MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 129

Query: 56  RALDGK 61
            A+DG 
Sbjct: 130 DAMDGA 135

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 70.5 bits (173), Expect = 4e-16
 Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 5/66 (7%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP-----GYAFVEFDDRRDAVDAI 55
          +  V    L+  V E  L+D  R +G +  V +   P      G A V F   R A + +
Sbjct: 6  LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65

Query: 56 RALDGK 61
          + L   
Sbjct: 66 KNLHLT 71

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 69.6 bits (171), Expect = 6e-16
 Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 1/61 (1%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          +  Y+GN+    +E DL   F+ FG +          G  F+++D    A   I AL   
Sbjct: 28 TTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-KGCCFIKYDTHEQAAVCIVALANF 86

Query: 62 N 62
           
Sbjct: 87 P 87

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 69.6 bits (171), Expect = 6e-16
 Identities = 30/91 (32%), Positives = 41/91 (45%), Gaps = 9/91 (9%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
           M  + V NL  R S   L   F  +G +  V++ R      P G+AFV F DRRDA DA 
Sbjct: 13  MITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAE 72

Query: 56  RALDGKN----GWRVELSHNSKGGGGRGGRG 82
            A+DG        RV+++   +        G
Sbjct: 73  AAMDGAELDGRELRVQVARYGRRDLSGPSSG 103

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 68.9 bits (169), Expect = 1e-15
 Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
            VY G +   ++++ +   F  FG +  + V     GY+FV F     A  AI +++G 
Sbjct: 26 CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-KGYSFVRFSTHESAAHAIVSVNGT 84

Query: 62 --NGWRVELS 69
             G  V+  
Sbjct: 85 TIEGHVVKCY 94

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 68.4 bits (168), Expect = 2e-15
 Identities = 27/90 (30%), Positives = 42/90 (46%), Gaps = 11/90 (12%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
            + + V NL     E DL++ FR FG +  +++A+     +  G+AF+ F  R DA  AI
Sbjct: 15  NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74

Query: 56  RALDGKNGW-----RVELSHNSKGGGGRGG 80
             + G  G+      VE +  S   G   G
Sbjct: 75  AGVSGF-GYDHLILNVEWAKPSTNSGPSSG 103

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 68.0 bits (167), Expect = 2e-15
 Identities = 16/66 (24%), Positives = 36/66 (54%), Gaps = 6/66 (9%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR------RPPGYAFVEFDDRRDAVDAI 55
          ++V++G L   V++  + + F  +G ++ + +           GYA+VEF++  +A  A+
Sbjct: 5  TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64

Query: 56 RALDGK 61
          + +DG 
Sbjct: 65 KHMDGG 70

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

 Score = 69.0 bits (169), Expect = 3e-15
 Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 5/65 (7%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
             +YVG L   V ++ L   F  FG +  + +       +  G+AFVEF+   DA  AI 
Sbjct: 64  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123

Query: 57  ALDGK 61
            ++  
Sbjct: 124 NMNES 128

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

 Score = 66.8 bits (164), Expect = 4e-15
 Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
            +YVG L   V ++ L   F  FG +  + +       +  G+AFVEF+   DA  AI 
Sbjct: 8  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67

Query: 57 ALDGK 61
           ++  
Sbjct: 68 NMNES 72

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 66.9 bits (164), Expect = 5e-15
 Identities = 21/64 (32%), Positives = 29/64 (45%), Gaps = 4/64 (6%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRA 57
            V+VGNL+ RV E  L + F   G L  V + +    +P  + FV F        AI  
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIAL 76

Query: 58 LDGK 61
          L+G 
Sbjct: 77 LNGI 80

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 66.9 bits (164), Expect = 6e-15
 Identities = 22/91 (24%), Positives = 36/91 (39%), Gaps = 9/91 (9%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
             VY+G++    +E  + D     G + ++ +       R  GYAF+EF D   +  A+
Sbjct: 2  SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61

Query: 56 RALDGKN----GWRVELSHNSKGGGGRGGRG 82
          R L+G        +   S NS   G      
Sbjct: 62 RNLNGYQLGSRFLKCGYSSNSDISGVSLEHH 92

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 67.8 bits (166), Expect = 7e-15
 Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 4/65 (6%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRA 57
           +++ V NLD  VS+ D+++ F  FG L+   V      R  G A V F+ R DA+ A++ 
Sbjct: 36  AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 95

Query: 58  LDGKN 62
             G  
Sbjct: 96  YKGVP 100

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 66.9 bits (164), Expect = 7e-15
 Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 4/65 (6%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRA 57
           ++ V NLD  VS+ D+++ F  FG L+   V      R  G A V F+ + DA+ A++ 
Sbjct: 30 GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 89

Query: 58 LDGKN 62
           +G  
Sbjct: 90 YNGVP 94

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 66.3 bits (162), Expect = 1e-14
 Identities = 17/89 (19%), Positives = 29/89 (32%), Gaps = 10/89 (11%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          S + V NL    + +++ D  + + +        R    AFV   +   A +AI+     
Sbjct: 6  SGILVKNLPQDSNCQEVHDLLKDYDL--KYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQY 63

Query: 62 --NGW--RVELSHNSKGGGGRGGRGRGGG 86
             G    V+L             G   G
Sbjct: 64 SFRGKDLIVQLQPTDA----LLCSGPSSG 88

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 66.5 bits (163), Expect = 1e-14
 Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 5/68 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDAVDAIRALDG 60
          +++ NLD  +  + L D F  FG + S  V        GY FV F+ +  A  AI  ++G
Sbjct: 8  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67

Query: 61 K--NGWRV 66
             N  +V
Sbjct: 68 MLLNDRKV 75

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 66.3 bits (162), Expect = 2e-14
 Identities = 27/106 (25%), Positives = 42/106 (39%), Gaps = 22/106 (20%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRS--------VWVAR-----RPPGYAFVEFDDR 48
           + ++V  L   V+   + D F+  G++++        + +       +  G A V FDD 
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 49  RDAVDAIRALDGK----NGWRVELSH-----NSKGGGGRGGRGRGG 85
             A  AI   DGK    N  +V  +      N  GG GRGG     
Sbjct: 68  PSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGLEHHH 113

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 65.7 bits (161), Expect = 2e-14
 Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 3/61 (4%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP---GYAFVEFDDRRDAVDAIRALDG 60
          +YVGNL   V+E  +   F   G  +S  +         Y FVEF + RDA  A+ A++G
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNG 77

Query: 61 K 61
          +
Sbjct: 78 R 78

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 66.2 bits (162), Expect = 2e-14
 Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
            +Y+ NL PRV+ERDL   F  F   +   +       R  G AF+ F ++  A  A+ 
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 57 ALDGK 61
           ++G 
Sbjct: 86 LVNGY 90

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 65.7 bits (161), Expect = 2e-14
 Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
          S VYV NL   ++  DL   F  +G +  V + +     +  G AF+ F D+  A +  R
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76

Query: 57 ALDGK 61
          A++ K
Sbjct: 77 AINNK 81

>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 Length = 109

 Score = 66.0 bits (161), Expect = 2e-14
 Identities = 15/67 (22%), Positives = 26/67 (38%), Gaps = 7/67 (10%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFG-------VLRSVWVARRPPGYAFVEFDDRRDAVDAI 55
          R+++G +       ++ +E            V  S     +  G+AFVE++  R A  A 
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69

Query: 56 RALDGKN 62
          R L    
Sbjct: 70 RKLMPGR 76

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 65.3 bits (160), Expect = 2e-14
 Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 5/66 (7%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAI 55
            R++V NL    SE DLE  F  +G L  +        ++P G+AFV F     AV A 
Sbjct: 8  SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAY 67

Query: 56 RALDGK 61
            +DG+
Sbjct: 68 AEVDGQ 73

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 67.2 bits (165), Expect = 2e-14
 Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 5/65 (7%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
           + +YV NL   +++  L+  F  +G +    + R     RP G AFV ++ R +A +AI 
Sbjct: 90  TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149

Query: 57  ALDGK 61
           AL+  
Sbjct: 150 ALNNV 154

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 66.4 bits (163), Expect = 4e-14
 Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRAL 58
          + V  L   +++R+L   FR  G + +  + R        GYAFV+F    D+  AI+ L
Sbjct: 6  LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 59 DGK 61
          +G 
Sbjct: 66 NGI 68

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 69.2 bits (170), Expect = 2e-14
 Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 5/65 (7%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
           + + V NL P ++++  E+  R FG L   ++       +  GY F E+  +  A  A  
Sbjct: 96  ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKS 155

Query: 57  ALDGK 61
            L GK
Sbjct: 156 DLLGK 160

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 65.4 bits (160), Expect = 6e-13
 Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 2/60 (3%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
           ++ +  L   V+ +++ D    + +    +V  +  G AFV   +   A  AI A    
Sbjct: 23 RKILIRGLPGDVTNQEVHDLLSDYELK-YCFV-DKYKGTAFVTLLNGEQAEAAINAFHQS 80

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 62.7 bits (153), Expect = 5e-12
 Identities = 13/64 (20%), Positives = 24/64 (37%), Gaps = 5/64 (7%)

Query: 3   RVYVGNLDPRVSERD-LEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRA 57
            + V  L P  ++ D L              +A     +  G+A +E++    A +A + 
Sbjct: 186 CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQ 245

Query: 58  LDGK 61
            DG 
Sbjct: 246 ADGL 249

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 64.8 bits (159), Expect = 2e-14
 Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 5/64 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
           ++VG+L+  V +  L + F+ F    S  V          GY FV F  + DA +A+ +
Sbjct: 3  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 58 LDGK 61
          + G+
Sbjct: 63 MQGQ 66

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 65.4 bits (160), Expect = 2e-14
 Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 3/63 (4%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWV---ARRPPGYAFVEFDDRRDAVDAIRAL 58
           R++V N+  R  + DL   F  FG +  V +    R   G+ FV F++  DA  A   L
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 75

Query: 59 DGK 61
           G 
Sbjct: 76 HGT 78

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

 Score = 65.4 bits (160), Expect = 2e-14
 Identities = 13/65 (20%), Positives = 33/65 (50%), Gaps = 4/65 (6%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRA 57
           ++++  L    ++ +LE+  +  G ++ + +      +P G A+VE+++   A  A+  
Sbjct: 18 HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMK 77

Query: 58 LDGKN 62
          +DG  
Sbjct: 78 MDGMT 82

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 65.8 bits (161), Expect = 3e-14
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 4/64 (6%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRA 57
          S V+V NLD +V  + L++ F M GV+    +      +  G   V F+   +AV AI  
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75

Query: 58 LDGK 61
           +G+
Sbjct: 76 FNGQ 79

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 68.1 bits (167), Expect = 3e-14
 Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 5/66 (7%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
          MSRVYVG++   + E  +   F  FG ++S+ ++      +  G+AFVE++    A  A+
Sbjct: 28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87

Query: 56 RALDGK 61
            ++  
Sbjct: 88 EQMNSV 93

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 65.8 bits (161), Expect = 2e-13
 Identities = 17/64 (26%), Positives = 37/64 (57%), Gaps = 5/64 (7%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
           R+YV ++   +S+ D++  F  FG ++S  +AR     +  GY F+E++  + + DA+ +
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186

Query: 58  LDGK 61
           ++  
Sbjct: 187 MNLF 190

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 64.9 bits (159), Expect = 3e-14
 Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 5/66 (7%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
             + V  L    +ERDL + F  +G +  V +       R  G+AFV F++  DA +A 
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74

Query: 56 RALDGK 61
             +G 
Sbjct: 75 ERANGM 80

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

 Score = 64.5 bits (158), Expect = 5e-14
 Identities = 17/83 (20%), Positives = 36/83 (43%), Gaps = 5/83 (6%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDAVDAIRALD 59
          +++V NL    + + L+D+F   G +    +     +  G   V+F+    A  A R ++
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMN 69

Query: 60 GK--NGWRVELSHNSKGGGGRGG 80
          G   +G  +++  +    G   G
Sbjct: 70 GMKLSGREIDVRIDRNASGPSSG 92

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 67.3 bits (165), Expect = 5e-14
 Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 3/62 (4%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDAVDAIRALD 59
            +++ NLD  +  + L D F  FG + S  V        GY FV F+ +  A  AI  ++
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 164

Query: 60  GK 61
           G 
Sbjct: 165 GM 166

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 63.5 bits (155), Expect = 1e-12
 Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 5/66 (7%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
          M+ +YVG+L P V+E  L ++F   G + S+ V R     R  GYA+V F    DA  A+
Sbjct: 15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74

Query: 56 RALDGK 61
            ++  
Sbjct: 75 DTMNFD 80

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 66.0 bits (161), Expect = 5e-14
 Identities = 26/96 (27%), Positives = 45/96 (46%), Gaps = 10/96 (10%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAI 55
              +YVGNL    +E  + + F   G ++ + +      +   G+ FVE+  R DA +A+
Sbjct: 39  SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98

Query: 56  RALDGK--NGW--RVELSHNSKGGGGRGGRGRGGGE 87
           R ++G   +    R +        G + GRGR GG+
Sbjct: 99  RYINGTRLDDRIIRTDWD-AGFKEGRQYGRGRSGGQ 133

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 66.1 bits (162), Expect = 7e-14
 Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 5/65 (7%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
           + +YV  L   +++++LE  F  +G + +  +          G  F+ FD R +A +AI+
Sbjct: 89  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148

Query: 57  ALDGK 61
            L+G+
Sbjct: 149 GLNGQ 153

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 63.0 bits (154), Expect = 8e-13
 Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 5/63 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRAL 58
          + V  L   +++ +    F   G + S  + R     +  GY FV + D +DA  AI  L
Sbjct: 5  LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 59 DGK 61
          +G 
Sbjct: 65 NGL 67

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 66.1 bits (162), Expect = 8e-14
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 4/64 (6%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRAL 58
           ++++G +  + +E D+   F  FG +    + R       G AFV F  R  A  AI+A+
Sbjct: 97  KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM 156

Query: 59  DGKN 62
               
Sbjct: 157 HQAQ 160

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 66.1 bits (162), Expect = 8e-14
 Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 7/65 (10%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-------RPPGYAFVEFDDRRDAVDAIR 56
          ++VG +    SE+DL + F  +G +  + V R       +  G  FV F  R+ A++A  
Sbjct: 6  MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65

Query: 57 ALDGK 61
          AL   
Sbjct: 66 ALHNM 70

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 64.2 bits (157), Expect = 9e-14
 Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 4/64 (6%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRA 57
           +++VG L+ + SE D+   F+ FGV+    V R       G AFV+F    +A  AI A
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHA 75

Query: 58 LDGK 61
          L G 
Sbjct: 76 LHGS 79

>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 Length = 105

 Score = 64.2 bits (157), Expect = 9e-14
 Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
          + VYVG LD +VSE  L + F   G + +  + +     +  GY FVEF    DA  AI+
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75

Query: 57 ALDGK 61
           +D  
Sbjct: 76 IMDMI 80

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 63.4 bits (155), Expect = 1e-13
 Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
            +YVG L   V ++ L   F  FG +  + +       +  G+AFVEF+   DA  AI 
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72

Query: 57 ALDGK 61
           ++  
Sbjct: 73 NMNES 77

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 66.6 bits (163), Expect = 1e-13
 Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          R++VGNL   ++E D +  F  +G    V++ R   G+ F+  + R  A  A   LDG 
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-RGFGFIRLESRTLAEIAKAELDGT 81

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 66.3 bits (162), Expect = 2e-13
 Identities = 20/64 (31%), Positives = 25/64 (39%), Gaps = 4/64 (6%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRA 57
           + + V NL P VS   LE  F  FG +    V      R  G  FVEF  +  A  A+  
Sbjct: 97  AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALER 156

Query: 58  LDGK 61
               
Sbjct: 157 CGDG 160

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 63.5 bits (155), Expect = 1e-13
 Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 3/63 (4%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWV---ARRPPGYAFVEFDDRRDAVDAIRAL 58
           R++V N+  R  + DL   F  FG +  V +    R   G+ FV F++  DA  A   L
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 89

Query: 59 DGK 61
           G 
Sbjct: 90 HGT 92

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 65.3 bits (159), Expect = 2e-13
 Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 4/65 (6%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRA 57
           +++ V NLD  VS+ D+++ F  FG L+   V      R  G A V F+ R DA+ A++ 
Sbjct: 89  AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 148

Query: 58  LDGKN 62
             G  
Sbjct: 149 YKGVP 153

>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 Length = 104

 Score = 63.4 bits (155), Expect = 2e-13
 Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 9/94 (9%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
           +  V+VGN+    +E  L+D F   G + S  +       +P GY F E+ D+  A+ A+
Sbjct: 8   LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67

Query: 56  RALDGK--NG--WRVELSHNSKGGGGRGGRGRGG 85
           R L+G+  +G   RV+ + + K        G G 
Sbjct: 68  RNLNGREFSGRALRVDNAASEKNKEELKSLGTGA 101

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 63.4 bits (155), Expect = 2e-13
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 3/64 (4%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDAVDAIRA 57
          +  +YV NLD  + +  L   F  FG + S  V     R  G+ FV F    +A  A+  
Sbjct: 15 VVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTE 74

Query: 58 LDGK 61
          ++G+
Sbjct: 75 MNGR 78

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 64.0 bits (156), Expect = 2e-13
 Identities = 25/66 (37%), Positives = 35/66 (53%), Gaps = 5/66 (7%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
           M+ + V NL  R S   L   F  +G +  V++ R        G+AFV F D+RDA DA+
Sbjct: 47  MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106

Query: 56  RALDGK 61
            A+DG 
Sbjct: 107 DAMDGA 112

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 62.7 bits (153), Expect = 2e-13
 Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 4/69 (5%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK-- 61
          +YVG L   ++E DL + F  FG +R++ V +R    AF++F  R+ A  A      K  
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-QQCAFIQFATRQAAEVAAEKSFNKLI 73

Query: 62 -NGWRVELS 69
           NG R+ + 
Sbjct: 74 VNGRRLNVK 82

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 64.5 bits (158), Expect = 2e-13
 Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 5/64 (7%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
            ++VG+L+  V +  L + F+ F    S  V          GY FV F  + DA +A+ +
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148

Query: 58  LDGK 61
           + G+
Sbjct: 149 MQGQ 152

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 63.7 bits (156), Expect = 5e-13
 Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 4/62 (6%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALD 59
          +YVGNLD  ++E  L+  F++ G + ++ +      +   YAFVE+    DA  A++ L+
Sbjct: 3  LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62

Query: 60 GK 61
          GK
Sbjct: 63 GK 64

>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} Length = 87

 Score = 62.2 bits (152), Expect = 3e-13
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
           V+VG+L P ++   +   F  FG +    V +     +  GY FV F ++ DA +AI+ 
Sbjct: 8  HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 58 LDGK 61
          + G+
Sbjct: 68 MGGQ 71

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 62.7 bits (153), Expect = 3e-13
 Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 5/66 (7%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
            R+YVG+L   ++E  L   F  FG + S+ +       R  GY F+ F D   A  A+
Sbjct: 26 PMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 85

Query: 56 RALDGK 61
            L+G 
Sbjct: 86 EQLNGF 91

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 63.0 bits (154), Expect = 3e-13
 Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 4/62 (6%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALD 59
          +Y+ NL   + E++LE+  + FG + S  + R       G  F   +        I   +
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFN 87

Query: 60 GK 61
          GK
Sbjct: 88 GK 89

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 66.2 bits (162), Expect = 3e-13
 Identities = 13/77 (16%), Positives = 32/77 (41%), Gaps = 9/77 (11%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFG-VLRSVWVARRPP----GYAFVEFDDRRDAVDAIR 56
             +++ N  P  ++R++ D  +    V  S+ +          +A+++   + DA   + 
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177

Query: 57  ALDGK--NG--WRVELS 69
            L+G    G     ++S
Sbjct: 178 KLNGLKIEGYTLVTKVS 194

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 66.2 bits (162), Expect = 3e-13
 Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 4/74 (5%)

Query: 4   VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDAVDAIRALDG 60
           V V NL    ++  +   F+  G +  V VA    +   +A +EF     A+ AI     
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK 103

Query: 61  K-NGWRVELSHNSK 73
                 + +SH ++
Sbjct: 104 VVGQNEIIVSHLTE 117

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 58.1 bits (141), Expect = 2e-10
 Identities = 12/65 (18%), Positives = 26/65 (40%), Gaps = 8/65 (12%)

Query: 4   VYVGNLDPRVS-ERDLEDEFRMFGVLRSVWVARRPP------GYAFVEFDDRRDAVDAIR 56
           + + NL   +  E  L + F  FG +  + +             AF+ F+++  A  A+ 
Sbjct: 213 IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL- 271

Query: 57  ALDGK 61
            ++  
Sbjct: 272 QMNRS 276

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 62.1 bits (151), Expect = 4e-13
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 2/63 (3%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWV--ARRPPGYAFVEFDDRRDAVDAIRALD 59
           ++ + N+ P +    L+     +GV+ S              V +  +  A  A+  L+
Sbjct: 16 RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLN 75

Query: 60 GKN 62
          G  
Sbjct: 76 GFQ 78

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 62.3 bits (152), Expect = 4e-13
 Identities = 20/93 (21%), Positives = 41/93 (44%), Gaps = 10/93 (10%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR--------RPPGYAFVEFDDRRDAVD 53
          S +++ NL+   +E  L+  F   G ++S  +++           G+ FVE+     A  
Sbjct: 6  SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 54 AIRALDGK--NGWRVELSHNSKGGGGRGGRGRG 84
          A++ L G   +G ++E+  + +      G   G
Sbjct: 66 ALKQLQGHTVDGHKLEVRISERATKPASGPSSG 98

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 62.3 bits (152), Expect = 4e-13
 Identities = 27/90 (30%), Positives = 45/90 (50%), Gaps = 7/90 (7%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
            +++VG L    +E+ LE  F  +G +  V V +     R  G+ FV F++  DA DA+ 
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72

Query: 57  ALDGK--NGWRVELSHNSKGGGGRGGRGRG 84
           A++GK  +G ++ +    K    R G   G
Sbjct: 73  AMNGKSVDGRQIRVDQAGKSSDNRSGPSSG 102

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

 Score = 62.0 bits (151), Expect = 4e-13
 Identities = 20/89 (22%), Positives = 32/89 (35%), Gaps = 7/89 (7%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRA--- 57
          +  V+V      V    L + F  FG + SV + +    +A VE  D   A +A+ +   
Sbjct: 8  LRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGD-VGAREAVLSQSQ 66

Query: 58 --LDGKNGWRVELSHNSKGGGGRGGRGRG 84
            L G    RV      +         +G
Sbjct: 67 HSLGGHR-LRVRPREQKEFQSPASKSPKG 94

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 63.0 bits (153), Expect = 4e-13
 Identities = 13/67 (19%), Positives = 23/67 (34%), Gaps = 6/67 (8%)

Query: 2  SRVYVGNLDPRVSERDL----EDEFRMFGVLRSVWVAR--RPPGYAFVEFDDRRDAVDAI 55
            V + N++P V +  L           G +  + V       G A++ F  +  A   +
Sbjct: 30 QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFV 89

Query: 56 RALDGKN 62
           A  G  
Sbjct: 90 EAFQGYP 96

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 61.4 bits (150), Expect = 5e-13
 Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
          S +Y+  L P  +++DL    + +G + S          +  GY FV+FD    A  A+ 
Sbjct: 6  SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65

Query: 57 ALDGK 61
          AL   
Sbjct: 66 ALKAS 70

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 61.8 bits (151), Expect = 5e-13
 Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 6/66 (9%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFG-VLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
          S +++GNLDP + E+ L D F  FG +L++  + R        GYAF+ F     +  AI
Sbjct: 6  SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65

Query: 56 RALDGK 61
           A++G+
Sbjct: 66 EAMNGQ 71

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 63.3 bits (154), Expect = 6e-13
 Identities = 17/91 (18%), Positives = 40/91 (43%), Gaps = 9/91 (9%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
             ++V ++     E +++++F  +G ++++ +          GYA VE++  + A+ A  
Sbjct: 73  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 132

Query: 57  ALDGK--NGW--RVELSHNSKGGGGRGGRGR 83
           AL+G    G   +V+          +    R
Sbjct: 133 ALNGAEIMGQTIQVDWCFVKGPKRVKKSEKR 163

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 61.6 bits (150), Expect = 7e-13
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 6/64 (9%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFG-VLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
          +++G+L+P + E  +   F   G  + SV + R      P GY FVEF D   A   +  
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71

Query: 58 LDGK 61
          ++GK
Sbjct: 72 INGK 75

>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 Length = 108

 Score = 61.7 bits (150), Expect = 7e-13
 Identities = 27/90 (30%), Positives = 34/90 (37%), Gaps = 8/90 (8%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK- 61
           RV V  L P  S +DL+D  R  G +    V R   G   VEF  + D   A+R LD   
Sbjct: 17  RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTK 74

Query: 62  -NGWRVELSH----NSKGGGGRGGRGRGGG 86
                 E ++             GR R  G
Sbjct: 75  FRSHEGETAYIRVKVDGPRSPSYGRSRSSG 104

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 61.5 bits (150), Expect = 7e-13
 Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 6/67 (8%)

Query: 2  SRVYVGNLDPRVSERDLEDE----FRMFGVLRSVWVAR--RPPGYAFVEFDDRRDAVDAI 55
            +Y+ NL+ ++ + +L+      F  FG +  + V+R  +  G AFV F +   A +A+
Sbjct: 9  HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 68

Query: 56 RALDGKN 62
          R++ G  
Sbjct: 69 RSMQGFP 75

>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 Length = 229

 Score = 64.4 bits (156), Expect = 8e-13
 Identities = 25/139 (17%), Positives = 45/139 (32%), Gaps = 10/139 (7%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGV--LRSVWVAR-----RPPGYAFVEFDDRRDAVD 53
              +Y+GNL    ++ DL +     GV  +  +         +  G+A V       +  
Sbjct: 68  RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 127

Query: 54  AIRALDGK--NGWRVELSH-NSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRIGS 110
            +  L  +  +G    ++  N +       + R   +  +    G+ G      R     
Sbjct: 128 LMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQ 187

Query: 111 RGLGSGRRRSPSPRRRRSP 129
            G G GR     P   R P
Sbjct: 188 GGRGRGRFPGAVPGGDRFP 206

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 63.8 bits (155), Expect = 9e-13
 Identities = 22/102 (21%), Positives = 41/102 (40%), Gaps = 3/102 (2%)

Query: 4   VYVGNLDP-RVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK- 61
           + V NL+P RV+ + L   F ++G ++ V +       A V+  D   A  A+  L+G  
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHK 65

Query: 62  -NGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFAR 102
            +G  + ++ +          G+      K Y       F +
Sbjct: 66  LHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKK 107

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 58.0 bits (140), Expect = 1e-10
 Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFG-VLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
           + +++ N+ P VSE DL+  F   G V++     ++    A ++     +AV A+  L  
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHN 180

Query: 61  KN 62
            +
Sbjct: 181 HD 182

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 63.5 bits (155), Expect = 1e-12
 Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 5/64 (7%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
           ++++G L   +++  +++    FG L++  + +        GYAF E+ D      AI  
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175

Query: 58  LDGK 61
           L+G 
Sbjct: 176 LNGM 179

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 63.1 bits (154), Expect = 1e-12
 Identities = 22/113 (19%), Positives = 38/113 (33%), Gaps = 15/113 (13%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP----------GYAFVEFDDRRD 50
             R+YVGN+   ++E  + D F     L  +  A   P           +AF+EF    +
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 51  AVDAIRALDGKN----GWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGH 99
              A+ A DG        ++   H+ +   G           +      +  H
Sbjct: 64  TTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAH 115

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 62.1 bits (151), Expect = 1e-12
 Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 5/66 (7%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
              + V  L    +ERDL + F  +G +  V +       R  G+AFV F++  DA +A 
Sbjct: 46  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105

Query: 56  RALDGK 61
              +G 
Sbjct: 106 ERANGM 111

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 61.6 bits (150), Expect = 1e-12
 Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 5/64 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
           V+VG+L P ++  D++  F  FG +    V +     +  GY FV F ++ DA +AI+ 
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76

Query: 58 LDGK 61
          + G+
Sbjct: 77 MGGQ 80

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 62.6 bits (153), Expect = 1e-12
 Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 5/64 (7%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
           ++++G L   +++  +++    FG L++  + +        GYAF E+ D      AI  
Sbjct: 96  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155

Query: 58  LDGK 61
           L+G 
Sbjct: 156 LNGM 159

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 60.3 bits (147), Expect = 9e-12
 Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 11/68 (16%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP----------GYAFVEFDDRRDAV 52
          R+YVGN+   ++E  + D F     L  +  A   P           +AF+EF    +  
Sbjct: 6  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 53 DAIRALDG 60
           A+ A DG
Sbjct: 66 QAM-AFDG 72

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 61.6 bits (150), Expect = 1e-12
 Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 5/65 (7%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
             +++ +L    ++ DL   F  FG + S  V           + FV FD+   A  AI+
Sbjct: 41  CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100

Query: 57  ALDGK 61
           A++G 
Sbjct: 101 AMNGF 105

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 61.2 bits (149), Expect = 1e-12
 Identities = 14/64 (21%), Positives = 34/64 (53%), Gaps = 5/64 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
           ++V ++     E +++++F  +G ++++ +          GYA VE++  + A+ A  A
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 58 LDGK 61
          L+G 
Sbjct: 88 LNGA 91

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 60.6 bits (148), Expect = 1e-12
 Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
          S +YVG+L   ++E  L   F  FG + ++ + +     R  GY F+ F D   A  A+ 
Sbjct: 6  SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65

Query: 57 ALDGK 61
           L+G 
Sbjct: 66 QLNGF 70

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 62.6 bits (153), Expect = 1e-12
 Identities = 15/86 (17%), Positives = 30/86 (34%), Gaps = 9/86 (10%)

Query: 4   VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP----GYAFVEFDDRRDAVDAI---- 55
           +++GNL+P  S  +L+           + V          + +V+F+   D   A+    
Sbjct: 16  LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTG 75

Query: 56  RALDGKNGWRVELSHNSKGGGGRGGR 81
             + G    ++E          R  R
Sbjct: 76  LKVFGNE-IKLEKPKGRDSKKVRAAR 100

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 62.2 bits (152), Expect = 2e-12
 Identities = 14/59 (23%), Positives = 25/59 (42%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
            +   NL   ++E +L++ F     +R V    +  G A++EF    DA   +    G 
Sbjct: 101 TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGA 159

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

 Score = 60.7 bits (148), Expect = 2e-12
 Identities = 14/65 (21%), Positives = 33/65 (50%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
            ++V  +    +E D+ D+F  +G ++++ +          GY  VE++  ++A  A+ 
Sbjct: 24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83

Query: 57 ALDGK 61
           L+G+
Sbjct: 84 GLNGQ 88

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 60.8 bits (148), Expect = 2e-12
 Identities = 19/90 (21%), Positives = 34/90 (37%), Gaps = 10/90 (11%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRA 57
             + + NL    +E  L++ F        + V +    +  GYAF+EF    DA +A+ +
Sbjct: 16  KTLVLSNLSYSATEETLQEVFEKAT---FIKVPQNQNGKSKGYAFIEFASFEDAKEALNS 72

Query: 58  LDGK--NGWRVELSHNSKGGGGRGGRGRGG 85
            + +   G  + L       G        G
Sbjct: 73  CNKREIEGRAIRLEL-QGPRGSPNSGPSSG 101

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 60.4 bits (147), Expect = 2e-12
 Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
            +   NL   ++E +L++ F     +R V    +  G A++EF    DA   +    G 
Sbjct: 17 RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGA 76

Query: 62 --NGWRVELSHNSKGGGGRG 79
            +G  V L +  + GG RG
Sbjct: 77 EIDGRSVSLYYTGEKGGTRG 96

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 60.8 bits (148), Expect = 2e-12
 Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 5/63 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRAL 58
          +++ +L     ++DL   F  FG + S  V           + FV +D+   A  AI+++
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 59 DGK 61
          +G 
Sbjct: 88 NGF 90

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 63.7 bits (154), Expect = 2e-12
 Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 6/65 (9%)

Query: 3  RVYVGNLDPRVSERDLEDE----FRMFGVLRSVWVAR--RPPGYAFVEFDDRRDAVDAIR 56
           +Y+ NL+ ++ + +L+      F  FG +  + V+R  +  G AFV F +   A +A+R
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 70

Query: 57 ALDGK 61
          ++ G 
Sbjct: 71 SMQGF 75

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 54.9 bits (131), Expect = 3e-09
 Identities = 18/58 (31%), Positives = 24/58 (41%)

Query: 5   YVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN 62
           ++ NL    +E  L   F  F   + V +       AFVEFD+   A  A  AL G  
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFK 268

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 63.1 bits (153), Expect = 2e-12
 Identities = 22/102 (21%), Positives = 41/102 (40%), Gaps = 3/102 (2%)

Query: 4   VYVGNLDP-RVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK- 61
           + V NL+P RV+ + L   F ++G ++ V +       A V+  D   A  A+  L+G  
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHK 96

Query: 62  -NGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFAR 102
            +G  + ++ +          G+      K Y       F +
Sbjct: 97  LHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKK 138

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 56.9 bits (137), Expect = 4e-10
 Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 4   VYVGNLDPRVSERDLEDEFRMFG-VLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN 62
           +++ N+ P VSE DL+  F   G V++     ++    A ++     +AV A+  L   +
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHD 213

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 60.9 bits (148), Expect = 3e-12
 Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 6/64 (9%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
            VYVGN+D   + +DLE  F   G +  + +        P GYA++EF + R++VDA  A
Sbjct: 38  SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-RNSVDAAVA 96

Query: 58  LDGK 61
           +D  
Sbjct: 97  MDET 100

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 60.0 bits (146), Expect = 3e-12
 Identities = 15/69 (21%), Positives = 30/69 (43%), Gaps = 5/69 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK-- 61
          +YV   D  ++   L   F  FG +  + +   P   AFV ++    A  A+  L+G   
Sbjct: 18 LYVYGED--MTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQV 74

Query: 62 NGWRVELSH 70
             +++++ 
Sbjct: 75 ESVQLKVNI 83

>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* Length = 126

 Score = 60.5 bits (147), Expect = 3e-12
 Identities = 22/98 (22%), Positives = 43/98 (43%), Gaps = 11/98 (11%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
             ++V  +    +E D+ D+F  +G ++++ +          GY  VE++  ++A  A+ 
Sbjct: 23  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82

Query: 57  ALDGK--NGWRVELSH----NSKGGGGRGGRGRGGGED 88
            L+G+   G  + +          G  RGGR R    D
Sbjct: 83  GLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSPD 120

>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 Length = 111

 Score = 59.4 bits (144), Expect = 7e-12
 Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 1/58 (1%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          +   NL       ++++ F  FG L  V +       A VEF +  +A  A R L   
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-GGITAIVEFLEPLEARKAFRHLAYS 69

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 58.9 bits (143), Expect = 7e-12
 Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 13/73 (17%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRS--------VWVAR-----RPPGYAFVEFDDR 48
          + ++V  L   V+   + D F+  G++++        + +       +  G A V FDD 
Sbjct: 14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 49 RDAVDAIRALDGK 61
            A  AI   DGK
Sbjct: 74 PSAKAAIDWFDGK 86

>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 Length = 114

 Score = 59.3 bits (144), Expect = 7e-12
 Identities = 26/88 (29%), Positives = 35/88 (39%), Gaps = 10/88 (11%)

Query: 4   VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRAL 58
           V+   L  R+  RDLED F   G +R V +       R  G A+VEF +   +V     L
Sbjct: 28  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE-IQSVPLAIGL 86

Query: 59  DGK--NGW--RVELSHNSKGGGGRGGRG 82
            G+   G    V+ S   K        G
Sbjct: 87  TGQRLLGVPIIVQASQAEKNRLSGPSSG 114

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 59.8 bits (145), Expect = 8e-12
 Identities = 18/66 (27%), Positives = 27/66 (40%), Gaps = 5/66 (7%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
           +  + V  +   V E  L   F  +G + SV +       +  GY FV+F     A  AI
Sbjct: 42  LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101

Query: 56  RALDGK 61
             L+G 
Sbjct: 102 AGLNGF 107

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 61.3 bits (148), Expect = 8e-12
 Identities = 21/104 (20%), Positives = 36/104 (34%), Gaps = 5/104 (4%)

Query: 4   VYVGNLDP-RVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK- 61
           + V  LD  +++   + + F ++G +  V   +  PG A VE  D      AI  L+   
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNF 66

Query: 62  ---NGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFAR 102
                  V +S       G+      G    K +       F+ 
Sbjct: 67  MFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFST 110

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 56.3 bits (135), Expect = 5e-10
 Identities = 12/63 (19%), Positives = 24/63 (38%), Gaps = 5/63 (7%)

Query: 4   VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP-----GYAFVEFDDRRDAVDAIRAL 58
           ++  N    V+E +  +     GV R   V              +E+D + DA++ +  L
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFL 185

Query: 59  DGK 61
           +  
Sbjct: 186 NHY 188

>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 Length = 89

 Score = 58.3 bits (142), Expect = 9e-12
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 6/64 (9%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
           +YVGN+D   +  +LE  F   G +  V +        P G+A++EF D +++V    A
Sbjct: 8  SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTSLA 66

Query: 58 LDGK 61
          LD  
Sbjct: 67 LDES 70

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 58.8 bits (143), Expect = 9e-12
 Identities = 22/88 (25%), Positives = 35/88 (39%), Gaps = 5/88 (5%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVW--VARRPPGYAFVEFDDRRDAVDAIRALD 59
             ++V  L    +E  L++ F      R V         G+ FV+F+   DA  A  A++
Sbjct: 16  KTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75

Query: 60  GK--NGWRVELSHNSKGGGGRGGRGRGG 85
               +G +V L   +K  G  G     G
Sbjct: 76  DGEIDGNKVTLDW-AKPKGEGGSGPSSG 102

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 58.9 bits (143), Expect = 9e-12
 Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 6/63 (9%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR------RPPGYAFVEFDDRRDAVDAI 55
          S++ V N+  + ++R++ + F  FG L++V + +         G+ FV+F  ++DA  A 
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75

Query: 56 RAL 58
           AL
Sbjct: 76 NAL 78

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 58.6 bits (142), Expect = 1e-11
 Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 11/70 (15%)

Query: 2  SRVYVGNLDPRVSE-------RDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDA 51
          S + V N+ P+V           +   F  FG + + +      +  GY F+E+     A
Sbjct: 16 SVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHA 74

Query: 52 VDAIRALDGK 61
          VDA++  DG 
Sbjct: 75 VDAVKNADGY 84

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 59.5 bits (144), Expect = 1e-11
 Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 10/70 (14%)

Query: 2   SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----------RPPGYAFVEFDDRRDA 51
            R+YV NL   V E+DL+  F  +    S               R  G AF+   + + A
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105

Query: 52  VDAIRALDGK 61
             A++  +G 
Sbjct: 106 AKALKEANGY 115

>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 Length = 106

 Score = 58.5 bits (142), Expect = 1e-11
 Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 5/66 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
           ++++G +   + E+DL+  F  FG +  + V +        G AF+ + +R  A+ A  
Sbjct: 14 IKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQS 73

Query: 57 ALDGKN 62
          AL  + 
Sbjct: 74 ALHEQK 79

>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 Length = 95

 Score = 58.1 bits (141), Expect = 1e-11
 Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 7/80 (8%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLR-SVWVAR----RPPGYAFVEFDDRRDAVDAIR 56
          + + V N+   VS  ++ D F  + V+  SV +       P G A V F+ R +A  A+ 
Sbjct: 16 TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 57 ALDGKN--GWRVELSHNSKG 74
           L+ +     +V+LS  S G
Sbjct: 76 DLNDRPIGSRKVKLSGPSSG 95

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 58.3 bits (141), Expect = 2e-11
 Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 2/61 (3%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFG--VLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          R+ + NL    S +DL+D  R        S    R   G   +EF      V+A+  L+ 
Sbjct: 30 RITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNN 89

Query: 61 K 61
           
Sbjct: 90 I 90

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 57.3 bits (139), Expect = 3e-11
 Identities = 11/68 (16%), Positives = 25/68 (36%), Gaps = 7/68 (10%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVL--RSVWVAR-----RPPGYAFVEFDDRRDAVD 53
          M  + + N+ P      +      +  L   ++ + +     +  G+AFV+     DA  
Sbjct: 9  MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQ 68

Query: 54 AIRALDGK 61
           ++ L   
Sbjct: 69 LLQILQSL 76

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 57.2 bits (139), Expect = 3e-11
 Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 6/66 (9%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
          M  +YVGNL    +   +++ F  FG + +V +       +P G+ FVE  +     +AI
Sbjct: 1  MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAI 59

Query: 56 RALDGK 61
            LD  
Sbjct: 60 AKLDNT 65

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 57.2 bits (139), Expect = 3e-11
 Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 7/68 (10%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRA 57
          + V+VG +D R+ E ++   F  +G ++ V +         GY FV F +  D    + +
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69

Query: 58 ---LDGKN 62
               GK 
Sbjct: 70 QINFHGKK 77

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 56.9 bits (138), Expect = 3e-11
 Identities = 13/63 (20%), Positives = 25/63 (39%), Gaps = 5/63 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRAL 58
           +++GNL+P  S  +L+           + V          + +V+F+   D   A+  L
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-EL 77

Query: 59 DGK 61
           G 
Sbjct: 78 TGL 80

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 57.1 bits (138), Expect = 4e-11
 Identities = 16/62 (25%), Positives = 24/62 (38%), Gaps = 2/62 (3%)

Query: 2  SRV-YVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          S V +V  L   V E DL +    FG +  V +       A VEF++   A + +     
Sbjct: 15 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-KRQALVEFENIDSAKECVTFAAD 73

Query: 61 KN 62
            
Sbjct: 74 VP 75

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

 Score = 57.2 bits (138), Expect = 5e-11
 Identities = 17/80 (21%), Positives = 35/80 (43%), Gaps = 13/80 (16%)

Query: 4  VYVGNLDPRVSERDL---EDEFRMFGVLRSVWVARR--------PPGYAFVEFDDRRDAV 52
          V+V  L  R+++ ++    + F  FG +  V +           P   A+V +    DA+
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 53 DAIRALDGK--NGWRVELSH 70
           AI+ ++    +G  ++ S 
Sbjct: 78 RAIQCVNNVVVDGRTLKASL 97

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 57.0 bits (138), Expect = 5e-11
 Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 13/73 (17%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRS--------VWVAR-----RPPGYAFVEFDDR 48
          S +YV  L+  V+  DL D F+  GV++         + +       +P G A V ++D 
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75

Query: 49 RDAVDAIRALDGK 61
            A  A+   DGK
Sbjct: 76 PTAKAAVEWFDGK 88

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 56.6 bits (137), Expect = 6e-11
 Identities = 16/66 (24%), Positives = 25/66 (37%), Gaps = 5/66 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
            V++ NL     E  L +  + FG L+ V V          G AF +F  +  A   + 
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75

Query: 57 ALDGKN 62
          A   + 
Sbjct: 76 AASLEA 81

>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 Length = 115

 Score = 56.8 bits (137), Expect = 7e-11
 Identities = 34/130 (26%), Positives = 41/130 (31%), Gaps = 34/130 (26%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK- 61
           RV V  L P  S +DL+D  R  G +    V R   G   VEF  + D   A+R LD   
Sbjct: 18  RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTK 75

Query: 62  -NGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRIGSRGLGSGRRRS 120
                 E +                              + R       S   G  R RS
Sbjct: 76  FRSHEGETA------------------------------YIRVKVDGPRSPSYGRSRSRS 105

Query: 121 PSPRRRRSPS 130
            S  R RS S
Sbjct: 106 RSRSRSRSRS 115

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 55.5 bits (134), Expect = 9e-11
 Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 11/70 (15%)

Query: 2  SRVYVGNLDPRVSE-------RDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDA 51
          S + V N+ P+V           +   F  FG + + +      +  GY F+E+     A
Sbjct: 2  SVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHA 60

Query: 52 VDAIRALDGK 61
          VDA++  DG 
Sbjct: 61 VDAVKNADGY 70

>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 Length = 90

 Score = 55.7 bits (135), Expect = 1e-10
 Identities = 12/66 (18%), Positives = 24/66 (36%), Gaps = 7/66 (10%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGV--LRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
           +Y+GNL    ++ DL +     GV  +  +         +  G+A V       +   +
Sbjct: 3  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 56 RALDGK 61
            L  +
Sbjct: 63 DLLPKR 68

>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* Length = 437

 Score = 59.5 bits (143), Expect = 1e-10
 Identities = 31/140 (22%), Positives = 50/140 (35%), Gaps = 7/140 (5%)

Query: 4   VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRAL 58
           ++V  ++   +E  L  EF ++G ++ + +       +P GYAF+E++  RD   A +  
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 59  DGK--NGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRIGSRGLGSG 116
           DGK  +G RV +              R GG        G   +     R          G
Sbjct: 165 DGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPG 224

Query: 117 RRRSPSPRRRRSPSYGYGRR 136
               P   R R        R
Sbjct: 225 PSPLPHRDRDRDRERERRER 244

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 56.9 bits (137), Expect = 1e-10
 Identities = 20/97 (20%), Positives = 34/97 (35%), Gaps = 9/97 (9%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLR--SVWVAR-----RPPGYAFVEFDDRRDAVD 53
            + VYVG+     +++ L    R  GV     +  A      +  GYA V          
Sbjct: 55  RAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHK 114

Query: 54  AIRALDGK--NGWRVELSHNSKGGGGRGGRGRGGGED 88
            +  L GK  NG +V++   ++    +        E 
Sbjct: 115 LLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKREC 151

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 57.0 bits (137), Expect = 1e-10
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGY-AFVEFDDRRDAVDAIRALDGK 61
           R+ V NL   V+   L   F  FG +  +    +   + A +++ D   A  A  +LDG+
Sbjct: 48  RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 107

Query: 62  N 62
           N
Sbjct: 108 N 108

>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 Length = 98

 Score = 55.4 bits (134), Expect = 1e-10
 Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 7/83 (8%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLR-SVWVAR----RPPGYAFVEFDDRRDAVDAIR 56
          + + V N+   VS  ++ D F  + V+  SV +       P G A V F+ R +A  A+ 
Sbjct: 16 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 57 ALDGKN--GWRVELSHNSKGGGG 77
           L+ +     +V+L   S    G
Sbjct: 76 DLNDRPIGSRKVKLVLGSGPSSG 98

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 55.4 bits (134), Expect = 2e-10
 Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 5/64 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEF-RMFGVLRSVWVARRPP----GYAFVEFDDRRDAVDAIRA 57
           ++VG+L P V +  L + F +++   R   V         GY FV+F D  +   A+  
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70

Query: 58 LDGK 61
            G 
Sbjct: 71 CQGA 74

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 55.8 bits (134), Expect = 2e-10
 Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFG-VLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          R+ V NL   V+   L   F  FG VL+ +   +     A +++ D   A  A  +LDG+
Sbjct: 30 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 89

Query: 62 N 62
          N
Sbjct: 90 N 90

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 55.0 bits (133), Expect = 2e-10
 Identities = 23/89 (25%), Positives = 38/89 (42%), Gaps = 11/89 (12%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
             YVGNL     + D++  F+   + RSV + R     +  G+ +VEFD+     +A+  
Sbjct: 17  TAYVGNLPFNTVQGDIDAIFKDLSI-RSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-T 74

Query: 58  LDGKN----GWRVELSHNSKGGGGRGGRG 82
            DG        RV+++   K        G
Sbjct: 75  YDGALLGDRSLRVDIAEGRKQDKSGPSSG 103

>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 Length = 104

 Score = 54.6 bits (132), Expect = 3e-10
 Identities = 19/90 (21%), Positives = 41/90 (45%), Gaps = 12/90 (13%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR------RPPGYAFVEFDDRRDAVDAIR 56
             ++GNL   V+E  +++ FR   +  +V + R      R  G+ + EF+D    + A+ 
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNI-SAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL- 74

Query: 57  ALDGK--NG--WRVELSHNSKGGGGRGGRG 82
           +L+ +       RV+++  ++        G
Sbjct: 75  SLNEESLGNKRIRVDVADQAQDKDSGPSSG 104

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

 Score = 53.6 bits (129), Expect = 7e-10
 Identities = 12/62 (19%), Positives = 22/62 (35%), Gaps = 4/62 (6%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALD 59
          VY+       +  D+++     G + ++ + R       G  FV FD    A   +    
Sbjct: 14 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG 73

Query: 60 GK 61
           K
Sbjct: 74 QK 75

>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 Length = 87

 Score = 52.8 bits (127), Expect = 8e-10
 Identities = 19/70 (27%), Positives = 29/70 (41%), Gaps = 11/70 (15%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP----------GYAFVEFDDRRDAV 52
          R+YVGN+   ++E  + D F     L  +  A   P           +AF+EF    +  
Sbjct: 8  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 53 DAIRALDGKN 62
           A+ A DG  
Sbjct: 68 QAM-AFDGII 76

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 52.8 bits (127), Expect = 1e-09
 Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN 62
          V++  L   V E DL +  + FG +  V V  +    A VEF+D   A +A+       
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMPK-KRQALVEFEDVLGACNAVNYAADNQ 81

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

 Score = 53.0 bits (127), Expect = 1e-09
 Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 5/60 (8%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP--GYAFVEFDDRRDAVDAIRALDGK 61
          V  G L   VS   L       G++ ++ +   PP   Y+F  +    ++  A   L+GK
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLM---PPNKPYSFARYRTTEESKRAYVTLNGK 86

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

 Score = 52.4 bits (126), Expect = 2e-09
 Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 5/62 (8%)

Query: 5  YVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALD 59
           + +    V ++ L   F   G + ++         +  G+ FVE     DA   I++  
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 60 GK 61
          GK
Sbjct: 76 GK 77

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 51.8 bits (124), Expect = 4e-09
 Identities = 12/64 (18%), Positives = 25/64 (39%), Gaps = 2/64 (3%)

Query: 2  SRV-YVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          SRV ++  L   V+E ++      FG + ++ +  +    AF+E +    A   +     
Sbjct: 16 SRVIHIRKLPIDVTEGEVISLGLPFGKVTNL-LMLKGKNQAFIEMNTEEAANTMVNYYTS 74

Query: 61 KNGW 64
              
Sbjct: 75 VTPV 78

>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 Length = 101

 Score = 50.6 bits (121), Expect = 8e-09
 Identities = 12/62 (19%), Positives = 25/62 (40%), Gaps = 2/62 (3%)

Query: 2  SRV-YVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          SRV ++  L   V+E ++      FG + ++ + +     AF+E      A+  +     
Sbjct: 15 SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-KNQAFLELATEEAAITMVNYYSA 73

Query: 61 KN 62
            
Sbjct: 74 VT 75

>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 Length = 119

 Score = 50.7 bits (121), Expect = 1e-08
 Identities = 12/62 (19%), Positives = 25/62 (40%), Gaps = 2/62 (3%)

Query: 2  SRV-YVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          SRV ++  L   V+E ++      FG + ++ +  +    AF+E +    A   +     
Sbjct: 31 SRVIHIRKLPIDVTEGEVISLGLPFGKVTNL-LMLKGKNQAFIEMNTEEAANTMVNYYTS 89

Query: 61 KN 62
            
Sbjct: 90 VT 91

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 49.5 bits (119), Expect = 2e-08
 Identities = 14/65 (21%), Positives = 30/65 (46%), Gaps = 6/65 (9%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWV-----ARRPPGYAFVEFDDRRDAVDAIRA 57
            ++GNL   V+E  +++ FR   +             R  G+ + EF+D    + A+ +
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 79

Query: 58 LDGKN 62
          L+ ++
Sbjct: 80 LNEES 84

>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 Length = 102

 Score = 49.3 bits (118), Expect = 3e-08
 Identities = 29/87 (33%), Positives = 37/87 (42%), Gaps = 8/87 (9%)

Query: 4   VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALD 59
           V++  L  R +E D+ + F     +R V +      R  G A VEF    DAV A+ A D
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGPDGRVTGEADVEFATHEDAVAAM-AKD 75

Query: 60  GKN--GWRVELSHNSKGGGGRGGRGRG 84
             N     VEL  NS  G    G   G
Sbjct: 76  KANMQHRYVELFLNSTAGTSGSGPSSG 102

>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 Length = 167

 Score = 50.2 bits (121), Expect = 3e-08
 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 8/74 (10%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
           +++VG + P V  ++ E+ F  +G +    +       +  G+ FV +D   DAVD +  
Sbjct: 89  KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS-ADAVDRVCQ 147

Query: 58  LDGK--NGWRVELS 69
                    ++E+ 
Sbjct: 148 NKFIDFKDRKIEIK 161

>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 Length = 167

 Score = 48.7 bits (117), Expect = 1e-07
 Identities = 14/68 (20%), Positives = 33/68 (48%), Gaps = 8/68 (11%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
           ++++G L+   +E +L + F  +G +  + + +     R  G+ F+ F+      + ++
Sbjct: 4  CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63

Query: 57 A---LDGK 61
              LDGK
Sbjct: 64 TQHILDGK 71

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 49.3 bits (117), Expect = 5e-08
 Identities = 13/60 (21%), Positives = 25/60 (41%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN 62
           + + N    ++   L       G ++ + + +R    A VEF+    A  A  AL+G +
Sbjct: 27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGAD 86

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 49.1 bits (117), Expect = 6e-08
 Identities = 25/91 (27%), Positives = 38/91 (41%), Gaps = 11/91 (12%)

Query: 4   VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALD 59
           V++  L  + +E D+ + F     +R V +      R  G A VEF    +AV A+ + D
Sbjct: 49  VHMRGLPYKATENDIYNFFSPLNPVR-VHIEIGPDGRVTGEADVEFATHEEAVAAM-SKD 106

Query: 60  GKN--GWRVELSHNSKGG---GGRGGRGRGG 85
             N     +EL  NS  G   G    +   G
Sbjct: 107 RANMQHRYIELFLNSTTGASNGAYSSQVMQG 137

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 47.6 bits (114), Expect = 9e-08
 Identities = 22/87 (25%), Positives = 37/87 (42%), Gaps = 13/87 (14%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRA---- 57
          S V+VG     ++E +L + F  +G +  V++ +    +AFV F D      ++      
Sbjct: 6  SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFAD-DQIAQSLCGEDLI 64

Query: 58 LDGKNGWRVELS-----HNSKGGGGRG 79
          + G     V +S     HNS  G   G
Sbjct: 65 IKGI---SVHISNAEPKHNSNSGPSSG 88

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 47.6 bits (114), Expect = 1e-07
 Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 12/90 (13%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
          ++++VG +     E +L + F+ FGV+  V +       RP G+ F+ F+D   +VD   
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFED-EQSVDQAV 69

Query: 57 ALDGK--NGWRVE----LSHNSKGGGGRGG 80
           +      G +VE       +SK  G   G
Sbjct: 70 NMHFHDIMGKKVEVKRAEPRDSKSSGPSSG 99

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 49.8 bits (118), Expect = 1e-07
 Identities = 16/97 (16%), Positives = 29/97 (29%), Gaps = 19/97 (19%)

Query: 4   VYVGNLDPRVS---------ERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDA 54
           +YVG +D  ++         E  +   F   G +  +          FV+F  + +A  A
Sbjct: 137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK-NCGFVKFKYQANAEFA 195

Query: 55  IRALDGKNGWRVELSHNSKGGGGRGGRGRGGGEDLKC 91
             A+  +                +    R  G  L  
Sbjct: 196 KEAMSNQ---------TLLLPSDKEWDDRREGTGLLV 223

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 9/71 (12%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
           ++++VG L    ++  L   F  FG +    V       +  GY FV   DR  A  A 
Sbjct: 17 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 76

Query: 56 RA----LDGKN 62
          +     +DG+ 
Sbjct: 77 KDPNPIIDGRK 87

>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 Length = 114

 Score = 47.4 bits (113), Expect = 2e-07
 Identities = 13/64 (20%), Positives = 25/64 (39%), Gaps = 6/64 (9%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFG-VLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRAL 58
           ++ N+   +++ D+            +V V      +  G A V+F +  DA  + R L
Sbjct: 18 AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-L 76

Query: 59 DGKN 62
            K 
Sbjct: 77 HRKK 80

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

 Score = 46.4 bits (111), Expect = 2e-07
 Identities = 14/65 (21%), Positives = 30/65 (46%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRA---- 57
          S+V+VG     ++  +L+  F  +G +  V++ +    +AFV F D      ++      
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFAD-DKVAQSLCGEDLI 70

Query: 58 LDGKN 62
          + G +
Sbjct: 71 IKGIS 75

>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 Length = 196

 Score = 48.1 bits (115), Expect = 4e-07
 Identities = 26/92 (28%), Positives = 37/92 (40%), Gaps = 12/92 (13%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
           +++VG +     E  L D F  +G +  + +       +  G+AFV FDD  D+VD I  
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIVI 164

Query: 58  LDGK--NGWRVE----LSHNSKGGGGRGGRGR 83
                 NG   E    LS           RGR
Sbjct: 165 QKYHTVNGHNCEVRKALSKQEMASASSSQRGR 196

>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 Length = 196

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 9/70 (12%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
          + ++++G L    ++  L   F  +G L    V R     R  G+ FV +    +   A+
Sbjct: 13 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 72

Query: 56 RA----LDGK 61
           A    +DG+
Sbjct: 73 NARPHKVDGR 82

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 44.8 bits (107), Expect = 6e-07
 Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 11/70 (15%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
          +++VG L    +  D++  F  FG +    +       R  G+ FV F+   D V+ +  
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES-EDIVEKVCE 59

Query: 58 -----LDGKN 62
               ++ K 
Sbjct: 60 IHFHEINNKM 69

>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 Length = 75

 Score = 44.4 bits (106), Expect = 9e-07
 Identities = 14/70 (20%), Positives = 28/70 (40%), Gaps = 11/70 (15%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
          +++VG L P   E  + + F  FG + S+ +       +  G+ F+ F +  + V  I  
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKE-EEPVKKIME 59

Query: 58 -----LDGKN 62
               +    
Sbjct: 60 KKYHNVGLSK 69

>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 Length = 103

 Score = 44.1 bits (105), Expect = 2e-06
 Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 8/69 (11%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
          S + V  L  + +E+DL++ F  FG +  V V +        G+ FV F +    V  + 
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75

Query: 57 A---LDGKN 62
              +DG+ 
Sbjct: 76 QRHMIDGRW 84

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124

 Score = 44.0 bits (103), Expect = 3e-06
 Identities = 8/39 (20%), Positives = 15/39 (38%)

Query: 69  SHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLR 107
           ++       +          + CY CG  GHF  +C+ +
Sbjct: 86  AYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK 124

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 43.1 bits (102), Expect = 3e-06
 Identities = 13/77 (16%), Positives = 32/77 (41%), Gaps = 8/77 (10%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALD 59
          V +      V+E+++ +       + ++ + R       GY FV+F +  +   A++  +
Sbjct: 13 VKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CN 70

Query: 60 GKN--GWRVELSHNSKG 74
           +   G  +E+     G
Sbjct: 71 REYMGGRYIEVFREKSG 87

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 45.2 bits (106), Expect = 3e-06
 Identities = 13/66 (19%), Positives = 23/66 (34%), Gaps = 6/66 (9%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP-----GYAFVEFDDRRDAVDAI 55
              VY+       +  D+++     G + ++ + RR       G  FV FD    A   +
Sbjct: 109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQM-RRTLHKAFKGSIFVVFDSIESAKKFV 167

Query: 56  RALDGK 61
                K
Sbjct: 168 ETPGQK 173

>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 Length = 87

 Score = 42.2 bits (100), Expect = 7e-06
 Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 9/70 (12%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
           +++VG L    S++DL+D F  FG +    +       R  G+ F+ F D       + 
Sbjct: 12 GKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD 71

Query: 57 A----LDGKN 62
               LDG+ 
Sbjct: 72 QKEHRLDGRV 81

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

 Score = 42.8 bits (101), Expect = 8e-06
 Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 15 ERDLEDEFRMFGVLRSVWVARRPP-GYAFVEFDDRRDAVDAIRALDG 60
            DL  E   FG +R + +  R P G A V F D  +A   I+ LDG
Sbjct: 40 REDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDG 86

>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 Length = 114

 Score = 42.7 bits (101), Expect = 8e-06
 Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 1/47 (2%)

Query: 15 ERDLEDEFRMFGVLRSVWVARRPP-GYAFVEFDDRRDAVDAIRALDG 60
          + D+ +E    G +  ++V +    G  +V+      A+ A+ AL G
Sbjct: 31 KDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHG 77

>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 Length = 124

 Score = 42.9 bits (101), Expect = 9e-06
 Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 8/77 (10%)

Query: 4   VYVGNLDPRVSERDLEDEFRMFGVLR-SVWVAR----RPPGYAFVEFDDRRDAVDAIRAL 58
           VY+  L      + + D F+   ++  S+++A     +  G  FVEF +  D   A+   
Sbjct: 28  VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CR 86

Query: 59  DGK--NGWRVELSHNSK 73
             +      +++   +K
Sbjct: 87  HKQYMGNRFIQVHPITK 103

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61

 Score = 40.6 bits (95), Expect = 1e-05
 Identities = 12/36 (33%), Positives = 19/36 (52%)

Query: 82  GRGGGEDLKCYECGEPGHFARECRLRIGSRGLGSGR 117
            + G    +C  C   GH A++CR R G++G   G+
Sbjct: 24  RKSGNSRERCQLCNGMGHNAKQCRKRDGNQGQRPGK 59

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61

 Score = 36.0 bits (83), Expect = 8e-04
 Identities = 11/24 (45%), Positives = 13/24 (54%), Gaps = 3/24 (12%)

Query: 82  GRGGGEDLKCYECGEPGHFARECR 105
           GR  G    CY CG PGH+  +C 
Sbjct: 1   GRARG---LCYTCGSPGHYQAQCP 21

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 42.0 bits (99), Expect = 1e-05
 Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 8/91 (8%)

Query: 4   VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALD 59
           V V  +     E D+ D F    V  +V + +    R  G   V+F   +D  +A++  +
Sbjct: 19  VSVHGMPFSAMENDVRDFFHGLRV-DAVHLLKDHVGRNNGNGLVKFLSPQDTFEALK-RN 76

Query: 60  GKN--GWRVELSHNSKGGGGRGGRGRGGGED 88
                   VE+S  ++      G     G  
Sbjct: 77  RMLMIQRYVEVSPATERQWVAAGGHITSGPS 107

>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 Length = 126

 Score = 42.2 bits (99), Expect = 1e-05
 Identities = 13/77 (16%), Positives = 29/77 (37%), Gaps = 8/77 (10%)

Query: 4   VYVGNLDPRVSERDLEDEFRMFG-VLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRAL 58
           V +  L    ++ ++   F     V   + +      +  G AFV+F  +  A  A+   
Sbjct: 45  VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-K 103

Query: 59  DGKN--GWRVELSHNSK 73
             +      +E+  +S+
Sbjct: 104 HKERIGHRYIEVFKSSQ 120

>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 Length = 96

 Score = 41.1 bits (96), Expect = 2e-05
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 8/85 (9%)

Query: 4  VYVGNLDPRVSERDLE----DEFRMFG-VLR-SVWVARRPPGYAFVEFDDRRDAVDAIRA 57
          V V N+D R+S ++L+    + F   G V    +         A V+ ++ +DA+ A+ +
Sbjct: 12 VQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNS 71

Query: 58 LDGKN--GWRVELSHNSKGGGGRGG 80
          L        ++ +S  +   G   G
Sbjct: 72 LHRYKIGSKKILVSLATGASGPSSG 96

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 39.8 bits (94), Expect = 4e-05
 Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 9/69 (13%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
          ++++G L  + ++  L + F  FG ++   V R     R  G+ FV F D+      +  
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 58 ----LDGKN 62
              LD K 
Sbjct: 62 SRHELDSKT 70

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A* Length = 148

 Score = 41.2 bits (96), Expect = 5e-05
 Identities = 9/48 (18%), Positives = 15/48 (31%)

Query: 70  HNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRIGSRGLGSGR 117
           +N  G        +   +  KC+ C    H    C L+        G+
Sbjct: 101 YNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQQGPSSQGK 148

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 40.1 bits (94), Expect = 5e-05
 Identities = 14/77 (18%), Positives = 30/77 (38%), Gaps = 8/77 (10%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWV-----ARRPPGYAFVEFDDRRDAVDAIRAL 58
          V +  L    S+ ++   F    ++ +          R  G AFV+F  +  A  A++  
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-K 76

Query: 59 DGKN--GWRVELSHNSK 73
            +      +E+  +S+
Sbjct: 77 HKERIGHRYIEIFKSSR 93

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 40.3 bits (94), Expect = 5e-05
 Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 7/68 (10%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-------RPPGYAFVEFDDRRDAVDAI 55
          +V+VG L P + E ++   FR FG L   W  +        P GYAF+ F +       I
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69

Query: 56 RALDGKNG 63
           A   ++G
Sbjct: 70 DACLEEDG 77

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 63

 Score = 39.2 bits (91), Expect = 6e-05
 Identities = 11/25 (44%), Positives = 14/25 (56%)

Query: 82  GRGGGEDLKCYECGEPGHFARECRL 106
           G  G    +CY CG   H A+EC+L
Sbjct: 1   GSSGSSGDRCYNCGGLDHHAKECKL 25

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Length = 60

 Score = 38.8 bits (90), Expect = 6e-05
 Identities = 7/35 (20%), Positives = 12/35 (34%)

Query: 78  RGGRGRGGGEDLKCYECGEPGHFARECRLRIGSRG 112
                        C  C    H+A EC+ +  ++G
Sbjct: 20  HAHNNAEPKVPGLCPRCKRGKHWANECKSKTDNQG 54

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Length = 60

 Score = 38.4 bits (89), Expect = 1e-04
 Identities = 8/30 (26%), Positives = 13/30 (43%)

Query: 90  KCYECGEPGHFARECRLRIGSRGLGSGRRR 119
            C++CG+ GHFA+ C     +         
Sbjct: 3   SCFKCGKKGHFAKNCHEHAHNNAEPKVPGL 32

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 39.5 bits (93), Expect = 8e-05
 Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 9/71 (12%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
          + +++VG LD   ++  L   F  +G +    + +     +  G+ FV+F D       +
Sbjct: 16 IGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL 75

Query: 56 RA----LDGKN 62
           +    LDG+N
Sbjct: 76 ASRPHTLDGRN 86

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Length = 74

 Score = 38.4 bits (89), Expect = 1e-04
 Identities = 9/35 (25%), Positives = 14/35 (40%)

Query: 72  SKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRL 106
                      +   +  +CY CG   H A+EC+L
Sbjct: 8   GSHMPKGKSMQKRRSKGDRCYNCGGLDHHAKECKL 42

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 9/69 (13%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
          ++++G L    +E  L + +  +G L    V R     R  G+ FV F    +   A+ A
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88

Query: 58 ----LDGKN 62
              +DG+ 
Sbjct: 89 RPHSIDGRV 97

>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} Length = 107

 Score = 39.1 bits (91), Expect = 2e-04
 Identities = 10/74 (13%), Positives = 21/74 (28%), Gaps = 10/74 (13%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-------RPPGYAFVEFDDRRDAVDAIR 56
          +    L    +  D+ + F    +               +  G A +E +  +D   A+ 
Sbjct: 14 IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL- 72

Query: 57 ALDGKN--GWRVEL 68
                     VE+
Sbjct: 73 EKHRMYMGQRYVEV 86

>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 Length = 112

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 9/80 (11%)

Query: 2   SRV-YVGNL-DPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALD 59
            RV ++ NL     S+  +      +G +++  + R     AF+E + R DA+  +    
Sbjct: 25  GRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-KSQAFIEMETREDAMAMVDHCL 83

Query: 60  GKNGW------RVELSHNSK 73
            K  W      +V+LS   K
Sbjct: 84  KKALWFQGRCVKVDLSEKYK 103

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 17/70 (24%), Positives = 30/70 (42%), Gaps = 9/70 (12%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
           ++++G L  + ++  L + F  FG ++   V R     R  G+ FV F D+      + 
Sbjct: 26 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 85

Query: 57 A----LDGKN 62
               LD K 
Sbjct: 86 QSRHELDSKT 95

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} Length = 83

 Score = 38.1 bits (88), Expect = 2e-04
 Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 3/48 (6%)

Query: 64  WRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRIGSR 111
           WR   ++       +          + CY CG  GHF  +C+ +  SR
Sbjct: 25  WR---AYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEKRSSR 69

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

 Score = 37.5 bits (87), Expect = 6e-04
 Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 7/53 (13%)

Query: 15 ERDLEDEFRMFGVLRSVWVARRPP-------GYAFVEFDDRRDAVDAIRALDG 60
            D+ DE   +G+++S+ + R          G  FVEF    D   A++ L G
Sbjct: 29 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 81

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 37.2 bits (86), Expect = 7e-04
 Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 10/79 (12%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-------RPPGYAFVEFDDRRDAVDAIR 56
          V +  L    S  D+++      +   V           R  G AFVE +   D   A+ 
Sbjct: 20 VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLAL- 78

Query: 57 ALDGKN--GWRVELSHNSK 73
            D ++     +E+  + +
Sbjct: 79 KKDRESMGHRYIEVFKSHR 97

>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 Length = 104

 Score = 36.8 bits (85), Expect = 9e-04
 Identities = 11/54 (20%), Positives = 20/54 (37%), Gaps = 8/54 (14%)

Query: 15 ERDLEDEFRM----FGVLRSVWVARR----PPGYAFVEFDDRRDAVDAIRALDG 60
          +   E+ F      +G +  + V         G  +V+F    DA  A+  L+ 
Sbjct: 37 DEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNN 90

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	223
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.74
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.74
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.73
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.72
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.7
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.7
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.7
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.7
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.7
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.7
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.7
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.69
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.69
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.69
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.69
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.69
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.69
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.68
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.68
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.68
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.68
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.68
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.68
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.68
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.67
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.67
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.67
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.67
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.67
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.67
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.67
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.67
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.67
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.67
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.67
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.66
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.66
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.66
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.66
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.66
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.66
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.66
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.66
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.66
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.66
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.66
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.66
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.66
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.65
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.65
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.65
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.65
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.65
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.65
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.65
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.64
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.64
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.64
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.64
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.64
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.64
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.64
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.64
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.64
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.64
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.64
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.64
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.64
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.64
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.64
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.63
2div_A	99	TRNA selenocysteine associated protein; structural	99.63
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.63
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.63
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.63
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.63
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.63
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.63
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.63
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.63
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.62
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.62
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.62
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.62
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.62
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.62
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.62
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.62
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.61
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.61
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.61
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.61
1x5p_A	97	Negative elongation factor E; structure genomics,	99.61
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.61
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.61
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.6
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.6
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.6
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.6
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.6
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.6
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.6
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.6
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.59
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.59
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.59
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.59
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.59
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.59
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.59
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.59
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.59
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.59
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.59
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.59
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.58
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.58
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.58
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.58
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.58
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.58
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.58
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.58
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.58
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.58
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.58
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.58
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.58
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.57
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.57
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.57
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.57
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.56
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.56
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.56
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.56
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.55
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.55
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.54
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.54
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.31
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.53
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.53
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.53
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.53
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.53
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.52
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.52
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.51
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.51
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.51
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.5
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.5
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.5
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.49
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.49
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.49
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.49
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.48
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.48
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.47
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.47
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.47
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.46
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.46
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.46
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.46
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.46
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.45
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.45
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.45
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.44
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.44
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.43
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.43
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.42
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.42
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.42
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.41
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.41
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.41
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.4
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.4
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.38
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.38
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.37
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.37
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.35
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.35
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.35
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.34
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.33
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.32
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.32
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.32
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.31
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.29
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.28
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.27
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.24
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.21
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.13
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.05
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.01
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.97
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.75
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.45
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.35
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.53
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.25
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.24
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.81
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.81
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.53
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.52
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.2
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	95.06
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	94.71
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	93.47
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	92.95
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	91.8
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	91.3
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	90.67
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	86.9
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	85.67

>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}

Probab=99.74  E-value=7e-18  Score=124.65  Aligned_cols=72  Identities=25%  Similarity=0.417  Sum_probs=64.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.++.     .++|||||+|.+.++|++|++.|||..  +..|.|.+++|
T Consensus        20 t~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           20 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            6899999999999999999999999999999974     357899999999999999999999998  77777777654

>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*

Probab=99.74  E-value=5.4e-17  Score=149.15  Aligned_cols=72  Identities=29%  Similarity=0.624  Sum_probs=64.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||+.||+++|+++|++||+|+.|.|+.     .++|||||+|.+.++|++||+.||+..  +..|.|.++..
T Consensus       103 ~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~  181 (437)
T 3pgw_S          103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG  181 (437)
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            6899999999999999999999999999999864     358999999999999999999999997  66666665544

>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

Probab=99.73  E-value=6.3e-18  Score=127.89  Aligned_cols=59  Identities=37%  Similarity=0.442  Sum_probs=56.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ++|||+|||+++|+++|+++|++||+|+.|.|+.+  |||||+|++.++|++||+.||+.+
T Consensus        17 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~   75 (115)
T 3beg_B           17 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTK   75 (115)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCB
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC--CEEEEEECCHHHHHHHHHHhCCCE
Confidence            58999999999999999999999999999999754  999999999999999999999987

>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

Probab=99.72  E-value=5.8e-17  Score=120.93  Aligned_cols=71  Identities=31%  Similarity=0.365  Sum_probs=65.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--c-----EEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--G-----WRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g-----~~V~v~~~~~~   74 (223)
                      ++|||+|||+++|+++|+++|++||+|+.|.|+.+  |||||+|.+.++|++||+.||+..  +     ..|.|..+.++
T Consensus        16 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~~   93 (108)
T 1x4c_A           16 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPR   93 (108)
T ss_dssp             CEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT--TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC--CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCCCC
Confidence            58999999999999999999999999999999855  999999999999999999999987  6     78888887654

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

Probab=99.70  E-value=7.7e-17  Score=118.39  Aligned_cols=73  Identities=52%  Similarity=0.927  Sum_probs=64.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.++.+++|||||+|.+.++|++|++.||+..  +..|.+..+.+.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            6899999999999999999999999999999987779999999999999999999999887  555555555443

>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

Probab=99.70  E-value=1.1e-16  Score=119.16  Aligned_cols=74  Identities=41%  Similarity=0.780  Sum_probs=65.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee--CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR--RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKGG   75 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~--~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~~   75 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|..  .++|||||+|.+.++|++|++.||+..  +..|.|.++.+..
T Consensus        23 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~  100 (109)
T 1x4a_A           23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGR  100 (109)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcccCC
Confidence            6899999999999999999999999999999864  458999999999999999999999987  7777777765543

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

Probab=99.70  E-value=4.9e-17  Score=122.88  Aligned_cols=72  Identities=28%  Similarity=0.484  Sum_probs=64.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC---CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR---PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~---~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||+++|+++|+++|++||+|..|.|+.+   ++|||||+|.+.++|++||+.||+..  +..|.|.++..
T Consensus         6 ~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            68999999999999999999999999999999753   47899999999999999999999997  77777766644

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

Probab=99.70  E-value=1.4e-16  Score=115.41  Aligned_cols=74  Identities=30%  Similarity=0.531  Sum_probs=64.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||..+|+++|+++|++||+|..|.++.     .++|||||+|.+.++|++|++.||+..  +..|.|.++.++
T Consensus         6 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   85 (95)
T 2dnz_A            6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTER   85 (95)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSCC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcccc
Confidence            6899999999999999999999999999999974     357999999999999999999999987  555555555444


Q ss_pred             C
Q 041602           75 G   75 (223)
Q Consensus        75 ~   75 (223)
                      .
T Consensus        86 ~   86 (95)
T 2dnz_A           86 L   86 (95)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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

Probab=99.70  E-value=6.6e-17  Score=127.93  Aligned_cols=72  Identities=25%  Similarity=0.458  Sum_probs=63.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.+     ++|||||+|.+.++|++||+.||+..  +..|.|.++.+
T Consensus        40 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  118 (156)
T 1h2v_Z           40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAG  118 (156)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            68999999999999999999999999999999753     46899999999999999999999987  66666666544

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.70  E-value=2.7e-17  Score=121.03  Aligned_cols=72  Identities=15%  Similarity=0.372  Sum_probs=63.1

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCC--eEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC------cEEEE
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGV--LRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN------GWRVE   67 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~--I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~------g~~V~   67 (223)
                      |.||||+|||+++|+++|+++|++||.  |.+|.++.     .++|||||+|.+.++|++|++.||+..      |..|.
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~   88 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIG   88 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEE
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEE
Confidence            789999999999999999999999995  66888764     468999999999999999999999863      67777


Q ss_pred             Eeecc
Q 041602           68 LSHNS   72 (223)
Q Consensus        68 v~~~~   72 (223)
                      |.+++
T Consensus        89 V~~Ak   93 (95)
T 2lkz_A           89 VDFAK   93 (95)
T ss_dssp             EEECC
T ss_pred             EEEcc
Confidence            77664

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

Probab=99.70  E-value=1.7e-16  Score=114.33  Aligned_cols=71  Identities=25%  Similarity=0.518  Sum_probs=63.2

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      .++|||+|||.++|+++|+++|++||+|..|.++   +|||||+|.+.++|++|++.||+..  +..|.+.++.++
T Consensus         8 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   80 (90)
T 2dnq_A            8 MVKLFIGNLPREATEQEIRSLFEQYGKVLECDII---KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNK   80 (90)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE---TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCC
Confidence            3689999999999999999999999999999998   8999999999999999999999976  555666665444

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

Probab=99.69  E-value=2.1e-16  Score=114.22  Aligned_cols=71  Identities=30%  Similarity=0.561  Sum_probs=64.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKGG   75 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~~   75 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.++   ++||||+|.+.++|++|++.||+..  +..|.+..+.++.
T Consensus        11 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   83 (92)
T 2dgt_A           11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIV---KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL   83 (92)
T ss_dssp             EEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC---SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCC
Confidence            689999999999999999999999999999997   6799999999999999999999987  7777777765543

>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

Probab=99.69  E-value=2.2e-16  Score=115.33  Aligned_cols=73  Identities=33%  Similarity=0.499  Sum_probs=64.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.     .++|||||+|.+.++|++|++.||+..  +..|.|..+.++
T Consensus         9 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   88 (99)
T 1whw_A            9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIK   88 (99)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            6899999999999999999999999999999964     357999999999999999999999987  666666666554

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

Probab=99.69  E-value=8.6e-17  Score=121.10  Aligned_cols=72  Identities=25%  Similarity=0.304  Sum_probs=64.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      .+|||+|||+++|+++|+++|++||+|.+|.|+.     +++|||||+|++.++|++|++.||+..  +..|.|..+..
T Consensus         7 ~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~~   85 (110)
T 3s8s_A            7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIK   85 (110)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECST
T ss_pred             cEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            5899999999999999999999999999999974     457999999999999999999999997  77777766643

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

Probab=99.69  E-value=8.6e-17  Score=120.65  Aligned_cols=72  Identities=14%  Similarity=0.188  Sum_probs=64.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCC--C--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK--N--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~--~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||+++||++|+++|++||+|++|.|+.+ +|||||+|++.++|++|++.|++.  .  +..|.|.++..+
T Consensus        17 ~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~   92 (105)
T 1sjq_A           17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK   92 (105)
T ss_dssp             CEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCC
Confidence            68999999999999999999999999999999865 899999999999999999988753  3  777777777554

>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}

Probab=99.69  E-value=2.3e-16  Score=119.48  Aligned_cols=72  Identities=25%  Similarity=0.595  Sum_probs=63.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.    .++|||||+|.+.++|++|++.||+..  +..|.|..+.+
T Consensus         8 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   85 (116)
T 2fy1_A            8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKK   85 (116)
T ss_dssp             CEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            6899999999999999999999999999999975    357999999999999999999999987  55555555543

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

Probab=99.69  E-value=1.1e-16  Score=116.16  Aligned_cols=74  Identities=34%  Similarity=0.590  Sum_probs=65.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEE-EEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSV-WVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v-~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++|+++|+++|++||+|..+ .|+.     .++|||||+|.+.++|++|++.||+..  +..|.+..+.+
T Consensus         6 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   85 (96)
T 1x5t_A            6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFK   85 (96)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEecc
Confidence            689999999999999999999999999999 8864     358999999999999999999999987  67777776655


Q ss_pred             CC
Q 041602           74 GG   75 (223)
Q Consensus        74 ~~   75 (223)
                      +.
T Consensus        86 ~~   87 (96)
T 1x5t_A           86 KD   87 (96)
T ss_dssp             CC
T ss_pred             cC
Confidence            43

>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*

Probab=99.68  E-value=1.8e-16  Score=120.93  Aligned_cols=71  Identities=23%  Similarity=0.519  Sum_probs=62.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--c--EEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--G--WRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g--~~V~v~~~~   72 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.+     ++|||||+|.+.++|++|++.||+..  +  +.|+++...
T Consensus        23 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  102 (126)
T 3ex7_B           23 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVR  102 (126)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESEES
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Confidence            58999999999999999999999999999999643     48999999999999999999999987  4  555555543

>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

Probab=99.68  E-value=3.6e-16  Score=115.43  Aligned_cols=70  Identities=36%  Similarity=0.583  Sum_probs=63.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.++   ++||||+|.+.++|++|++.||+..  +..|.|.++.+.
T Consensus        12 ~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   83 (103)
T 2dgu_A           12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPP   83 (103)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCC
Confidence            689999999999999999999999999999987   7899999999999999999999987  666777666544

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

Probab=99.68  E-value=2e-16  Score=115.38  Aligned_cols=74  Identities=24%  Similarity=0.519  Sum_probs=65.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee--------CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR--------RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~--------~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.        .++|||||+|.+.++|++|++.||+..  +..|.|..+
T Consensus         6 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (98)
T 2cpf_A            6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRIS   85 (98)
T ss_dssp             CCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            5899999999999999999999999999999874        346899999999999999999999987  777777776


Q ss_pred             cCCC
Q 041602           72 SKGG   75 (223)
Q Consensus        72 ~~~~   75 (223)
                      .+..
T Consensus        86 ~~~~   89 (98)
T 2cpf_A           86 ERAT   89 (98)
T ss_dssp             SCSS
T ss_pred             cCCC
Confidence            5543

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

Probab=99.68  E-value=2.9e-16  Score=115.34  Aligned_cols=72  Identities=33%  Similarity=0.664  Sum_probs=62.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.     .++|||||+|.+.++|++|++.||+..  +..|.|.++.+
T Consensus        13 ~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   91 (102)
T 1x5s_A           13 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGK   91 (102)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            6899999999999999999999999999999975     358999999999999999999999987  44444444433

>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

Probab=99.68  E-value=2.7e-16  Score=114.89  Aligned_cols=73  Identities=25%  Similarity=0.370  Sum_probs=65.4

Q ss_pred             cEEEEecCCCCCCHHHHH----HHHHcCCCeEEEEEeeC--CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLE----DEFRMFGVLRSVWVARR--PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~----~~F~~~G~I~~v~i~~~--~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++++++|+    ++|++||+|..|.|+.+  .+|||||+|.+.++|++|++.||+..  +..|.|..+.+
T Consensus        10 ~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   89 (96)
T 2dgx_A           10 ADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   89 (96)
T ss_dssp             EEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCC
Confidence            689999999999999999    99999999999999743  38999999999999999999999987  77777777654


Q ss_pred             C
Q 041602           74 G   74 (223)
Q Consensus        74 ~   74 (223)
                      .
T Consensus        90 ~   90 (96)
T 2dgx_A           90 A   90 (96)
T ss_dssp             S
T ss_pred             C
Confidence            4

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

Probab=99.68  E-value=3e-16  Score=121.63  Aligned_cols=74  Identities=28%  Similarity=0.467  Sum_probs=65.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|+.|.|+.+     ++|||||+|.+.++|++|++.||+..  +..|.|..+...
T Consensus        43 ~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  122 (139)
T 1u6f_A           43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASG  122 (139)
T ss_dssp             SEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            68999999999999999999999999999999743     47899999999999999999999987  666676666554


Q ss_pred             C
Q 041602           75 G   75 (223)
Q Consensus        75 ~   75 (223)
                      .
T Consensus       123 ~  123 (139)
T 1u6f_A          123 H  123 (139)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.68  E-value=1.6e-16  Score=116.79  Aligned_cols=74  Identities=27%  Similarity=0.476  Sum_probs=65.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.     .++|||||+|.+.++|++|++.||+..  +..|.|.++.+.
T Consensus        13 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~   92 (102)
T 2cqb_A           13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPM   92 (102)
T ss_dssp             SCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCCCC
Confidence            5899999999999999999999999999999864     368999999999999999999999987  777777776554


Q ss_pred             C
Q 041602           75 G   75 (223)
Q Consensus        75 ~   75 (223)
                      .
T Consensus        93 ~   93 (102)
T 2cqb_A           93 R   93 (102)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.67  E-value=2e-16  Score=116.58  Aligned_cols=73  Identities=38%  Similarity=0.630  Sum_probs=63.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++++++|+++|++||+|..|.|+.     .++|||||+|.+.++|++|++.||+..  +..|.|..+...
T Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~   93 (103)
T 2dnm_A           14 ITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYG   93 (103)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECSSC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECCcC
Confidence            6899999999999999999999999999999874     357999999999999999999999987  555555555443

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

Probab=99.67  E-value=5.1e-16  Score=114.33  Aligned_cols=73  Identities=32%  Similarity=0.500  Sum_probs=64.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC---CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR---PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~---~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++++++|+++|++||+|..|.|+.+   ++|||||+|.+.++|++|++.||+..  +..|.|.++.+.
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   93 (103)
T 2cqi_A           16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTP   93 (103)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCT
T ss_pred             CEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCCC
Confidence            68999999999999999999999999999999753   57999999999999999999999987  666777666543

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

Probab=99.67  E-value=1.6e-16  Score=115.41  Aligned_cols=69  Identities=20%  Similarity=0.173  Sum_probs=62.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ..|||+||++.+||++|+++|.+||+|..+.+.. ++|||||+|.++++|++|++.||+..  +..|.+..+
T Consensus         8 ~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            8 SWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             ceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            4699999999999999999999999999999864 69999999999999999999999987  666666554

>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

Probab=99.67  E-value=6.5e-16  Score=113.77  Aligned_cols=74  Identities=28%  Similarity=0.461  Sum_probs=65.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC---CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR---PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKGG   75 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~---~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~~   75 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.+   ++|||||+|.+.++|++|++.||+..  +..|.|.++.++.
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   94 (103)
T 2cq3_A           16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV   94 (103)
T ss_dssp             CEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcccCC
Confidence            68999999999999999999999999999999753   48999999999999999999999987  6666666665543

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

Probab=99.67  E-value=4.3e-16  Score=113.95  Aligned_cols=72  Identities=26%  Similarity=0.602  Sum_probs=62.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++++++|+++|++||+|..|.|+.     .++|||||+|.+.++|++|++ ||+..  +..|.|..+.++
T Consensus        11 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a~~~   89 (99)
T 2dgs_A           11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAEPR   89 (99)
T ss_dssp             CEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEECCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEECCCC
Confidence            6899999999999999999999999999999974     368999999999999999998 99887  555555555443

>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

Probab=99.67  E-value=3.4e-16  Score=115.54  Aligned_cols=73  Identities=34%  Similarity=0.471  Sum_probs=63.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.++.     .++|||||+|.+.++|++|++.||+..  +..|.|.++.+.
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   95 (105)
T 1x5u_A           16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAH   95 (105)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCC
Confidence            6899999999999999999999999999999864     357999999999999999999999987  555666655443

>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

Probab=99.67  E-value=3.7e-16  Score=110.31  Aligned_cols=73  Identities=27%  Similarity=0.515  Sum_probs=64.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++++++|+++|++||+|..+.++.+     ++|||||+|.+.++|++|++.||+..  +..|.+..+.++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            58999999999999999999999999999998743     37899999999999999999999997  677777666543

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

Probab=99.67  E-value=7e-16  Score=112.92  Aligned_cols=71  Identities=38%  Similarity=0.547  Sum_probs=64.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcC--CCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMF--GVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKGG   75 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~--G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~~   75 (223)
                      ++|||+|||.++|+++|+++|++|  |.|..|.+.   +|||||+|.+.++|++|++.||+..  +..|.|..+.++.
T Consensus        16 ~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   90 (99)
T 2cpd_A           16 KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI---RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   90 (99)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC---SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe---CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCC
Confidence            689999999999999999999999  999999876   8899999999999999999999987  7777777776544

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

Probab=99.67  E-value=3.8e-16  Score=112.45  Aligned_cols=70  Identities=31%  Similarity=0.540  Sum_probs=63.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.++   ++||||+|.+.++|++|++.||+..  +..|.+..+.+.
T Consensus        10 ~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   81 (90)
T 2dnp_A           10 WKIFVGNVSAACTSQELRSLFERRGRVIECDVV---KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKG   81 (90)
T ss_dssp             CCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCC
Confidence            689999999999999999999999999999997   6799999999999999999999987  677777766554

>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}

Probab=99.67  E-value=3.9e-16  Score=111.23  Aligned_cols=72  Identities=24%  Similarity=0.512  Sum_probs=64.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC------CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR------PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~------~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++|+++|+++|++||+|..+.++.+      ++|||||+|.+.++|++|++.||+..  +..|.+..+.+
T Consensus         5 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   84 (88)
T 4a8x_A            5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLA   84 (88)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECCC
Confidence            68999999999999999999999999999998642      68999999999999999999999998  66666666643

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.67  E-value=8.4e-17  Score=116.87  Aligned_cols=74  Identities=27%  Similarity=0.405  Sum_probs=64.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCC-CeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCC-C--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFG-VLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGK-N--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G-~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~-~--g~~V~v~~~~   72 (223)
                      ++|||+|||+++||++|+++|++|| +|.+|.|+.     .++|||||+|.+.++|++|++.|++. .  |..|.|..+.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            5899999999999999999999999 899998863     46899999999999999999988654 3  7788887776


Q ss_pred             CCC
Q 041602           73 KGG   75 (223)
Q Consensus        73 ~~~   75 (223)
                      ++.
T Consensus        82 ~~~   84 (91)
T 2lxi_A           82 PKP   84 (91)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            543

>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

Probab=99.66  E-value=1.6e-16  Score=118.46  Aligned_cols=71  Identities=20%  Similarity=0.236  Sum_probs=62.1

Q ss_pred             cEEEEecCCC-CCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeeccC
Q 041602            2 SRVYVGNLDP-RVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~-~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~~~   73 (223)
                      ++|||+|||+ ++|+++|+++|++||+|..|.|+.+ +|||||+|++.++|++|++.||+..    +..|.|.++..
T Consensus        16 ~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~   91 (102)
T 1x4d_A           16 RVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   91 (102)
T ss_dssp             CEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCC
Confidence            5899999999 9999999999999999999999754 7999999999999999999988642    66666666653

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

Probab=99.66  E-value=5e-16  Score=114.90  Aligned_cols=72  Identities=29%  Similarity=0.578  Sum_probs=62.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC------CCCEEEEEEcCHHHHHHHHHHh-CCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR------PPGYAFVEFDDRRDAVDAIRAL-DGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~------~rGfaFV~F~~~e~A~~Al~~l-ng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||..+|+++|+++|++||+|..|.|+.+      ++|||||+|.+.++|++|++.| |+..  +..|.|.++.
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~a~   95 (107)
T 2cph_A           16 SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWAD   95 (107)
T ss_dssp             CCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEEeCC
Confidence            58999999999999999999999999999999654      4899999999999999999999 8876  5555555554


Q ss_pred             C
Q 041602           73 K   73 (223)
Q Consensus        73 ~   73 (223)
                      +
T Consensus        96 ~   96 (107)
T 2cph_A           96 S   96 (107)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.66  E-value=3.5e-16  Score=114.17  Aligned_cols=69  Identities=28%  Similarity=0.481  Sum_probs=61.7

Q ss_pred             cEEEEecCCC-CCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeeccC
Q 041602            2 SRVYVGNLDP-RVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~-~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~~~   73 (223)
                      ++|||+|||+ .+|+++|+++|++||+|..|.+.   +|||||+|.+.++|++|++.||+..    .+.|+++....
T Consensus        11 ~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   84 (96)
T 2kvi_A           11 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNA   84 (96)
T ss_dssp             EEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE---TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCC
T ss_pred             CEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCC
Confidence            6899999998 99999999999999999999996   8999999999999999999999987    45666665543

>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}

Probab=99.66  E-value=3.8e-16  Score=111.21  Aligned_cols=72  Identities=28%  Similarity=0.586  Sum_probs=63.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++++++|+++|++||+|..|.++.+     ++|||||+|.+.++|++|++.||+..  +..|.+.++.+
T Consensus         7 ~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   85 (87)
T 3bs9_A            7 FHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR   85 (87)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCC
Confidence            58999999999999999999999999999999753     47899999999999999999999987  66666666543

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

Probab=99.66  E-value=3.4e-16  Score=115.31  Aligned_cols=74  Identities=28%  Similarity=0.528  Sum_probs=65.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++++++|+++|++||+|..|.|+.+     ++|||||+|.+.++|++|++.||+..  +..|.|.++.++
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   95 (103)
T 2cq0_A           16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS   95 (103)
T ss_dssp             EEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEECCCC
Confidence            68999999999999999999999999999999753     47899999999999999999999987  777777776554


Q ss_pred             C
Q 041602           75 G   75 (223)
Q Consensus        75 ~   75 (223)
                      .
T Consensus        96 ~   96 (103)
T 2cq0_A           96 T   96 (103)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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*

Probab=99.66  E-value=3.5e-16  Score=110.96  Aligned_cols=70  Identities=29%  Similarity=0.513  Sum_probs=62.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+|||.++++++|+++|++||+|..|.++.+     ++|||||+|.+.++|++|++.||+..  +..|.+.++
T Consensus         8 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            68999999999999999999999999999998643     58999999999999999999999997  666666554

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

Probab=99.66  E-value=1.9e-16  Score=119.74  Aligned_cols=71  Identities=24%  Similarity=0.230  Sum_probs=64.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCC-CeEEEEEe-eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFG-VLRSVWVA-RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G-~I~~v~i~-~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||+++|+++|+++|++|| +|..+.+. .+++|||||+|.+.++|++||+.||+.+  +..|.|..+.
T Consensus        29 ~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~  103 (111)
T 2jvr_A           29 YRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDD  103 (111)
T ss_dssp             EEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            5899999999999999999999999 99999985 5679999999999999999999999987  7777777664

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

Probab=99.66  E-value=2.9e-16  Score=115.68  Aligned_cols=72  Identities=26%  Similarity=0.487  Sum_probs=63.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee---CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~---~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||+++|+++|+++|++||+|..|.|+.   .++|||||+|.+.++|++|++.||+..  +..|.|..+.+
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   92 (103)
T 2d9p_A           16 VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQR   92 (103)
T ss_dssp             CCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEecc
Confidence            6899999999999999999999999999999975   357899999999999999999999987  55555555543

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

Probab=99.66  E-value=4.2e-16  Score=115.88  Aligned_cols=71  Identities=25%  Similarity=0.294  Sum_probs=62.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~~~   73 (223)
                      .+|||+|||.++|+++|+++|++||+|++|.++. .+|||||+|++.++|++|++.|++..    |..|.|..+..
T Consensus        22 ~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~-~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~   96 (100)
T 3r27_A           22 PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTS   96 (100)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc-CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccc
Confidence            4799999999999999999999999999999874 58999999999999999999998764    66666666543

>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

Probab=99.66  E-value=6.7e-16  Score=115.06  Aligned_cols=72  Identities=25%  Similarity=0.501  Sum_probs=65.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||..+++++|+++|++||+|..|.|+.+ +|||||+|.+.++|++|++.||+..  +..|.|.++.+.
T Consensus        26 ~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   99 (109)
T 1x4g_A           26 CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   99 (109)
T ss_dssp             CEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCC
Confidence            68999999999999999999999999999999865 8999999999999999999999987  777777776554

>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

Probab=99.66  E-value=6.3e-16  Score=115.43  Aligned_cols=70  Identities=23%  Similarity=0.251  Sum_probs=59.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~~   72 (223)
                      ++|||+|||+++++++|+++|++||+|..|.|+. .+|||||+|++.++|++|++.|++..    +..|.+.++.
T Consensus        16 ~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~   89 (104)
T 1wex_A           16 PVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYST   89 (104)
T ss_dssp             SEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC-CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcc
Confidence            5899999999999999999999999999998875 48999999999999999999886532    4445555443

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

Probab=99.66  E-value=5.4e-16  Score=113.62  Aligned_cols=73  Identities=19%  Similarity=0.484  Sum_probs=64.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.++.+    ++|||||+|.+.++|++|++.||+..  +..|.|..+.++
T Consensus        18 ~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   96 (100)
T 2do4_A           18 HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSG   96 (100)
T ss_dssp             SCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            58999999999999999999999999999999753    46899999999999999999999886  667777766554

>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

Probab=99.66  E-value=7.2e-16  Score=114.73  Aligned_cols=74  Identities=24%  Similarity=0.384  Sum_probs=65.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhC------CCC--cEEEEE
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALD------GKN--GWRVEL   68 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~ln------g~~--g~~V~v   68 (223)
                      ++|||+|||+++|+++|+++|++||+|..|.|+.     .++|||||+|.+.++|++|++.||      +..  +..|.|
T Consensus        16 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~l~v   95 (111)
T 1x4h_A           16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKV   95 (111)
T ss_dssp             CCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEEEEE
Confidence            5899999999999999999999999999999974     468999999999999999999999      665  777777


Q ss_pred             eeccCCC
Q 041602           69 SHNSKGG   75 (223)
Q Consensus        69 ~~~~~~~   75 (223)
                      .++.++.
T Consensus        96 ~~a~~~~  102 (111)
T 1x4h_A           96 DLAVTRD  102 (111)
T ss_dssp             ECCCCCC
T ss_pred             EECCCCc
Confidence            7765543

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

Probab=99.65  E-value=1.6e-15  Score=113.84  Aligned_cols=74  Identities=28%  Similarity=0.591  Sum_probs=65.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||..+|+++|+++|++||+|..|.|+.+     ++|||||+|.+.++|++|++.||+..  +..|.|.++.++
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   95 (115)
T 2dgo_A           16 FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK   95 (115)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccCC
Confidence            58999999999999999999999999999999754     37899999999999999999999987  777777776554


Q ss_pred             C
Q 041602           75 G   75 (223)
Q Consensus        75 ~   75 (223)
                      .
T Consensus        96 ~   96 (115)
T 2dgo_A           96 P   96 (115)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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

Probab=99.65  E-value=5.2e-16  Score=113.21  Aligned_cols=72  Identities=25%  Similarity=0.497  Sum_probs=63.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.+... +|||||+|.+.++|++|++.||+..    +..|.|.++.++
T Consensus        18 ~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~   93 (97)
T 1why_A           18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             SCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCC
Confidence            68999999999999999999999999999998755 8999999999999999999999875    355566555443

>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

Probab=99.65  E-value=4.9e-16  Score=114.77  Aligned_cols=71  Identities=24%  Similarity=0.508  Sum_probs=62.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee------CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR------RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~------~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++|+++|+++|++|| |..|.|+.      .++|||||+|.+.++|++|| .||+..  +..|.|..+.+
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~   93 (104)
T 1wi8_A           16 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQ   93 (104)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEEccC
Confidence            6899999999999999999999999 99999873      34889999999999999999 899987  66666666654


Q ss_pred             C
Q 041602           74 G   74 (223)
Q Consensus        74 ~   74 (223)
                      +
T Consensus        94 ~   94 (104)
T 1wi8_A           94 A   94 (104)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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

Probab=99.65  E-value=7.2e-16  Score=113.77  Aligned_cols=73  Identities=32%  Similarity=0.492  Sum_probs=63.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC----CCCEEEEEEcCHHHHHHHHHHhCCCC--c---EEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR----PPGYAFVEFDDRRDAVDAIRALDGKN--G---WRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~----~rGfaFV~F~~~e~A~~Al~~lng~~--g---~~V~v~~~~   72 (223)
                      ++|||+|||.++++++|+++|++||+|..|.|+.+    ++|||||+|.+.++|++|++.||+..  +   ..|.|.++.
T Consensus        16 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~   95 (105)
T 2dnh_A           16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFAD   95 (105)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEESC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEECc
Confidence            68999999999999999999999999999999753    37899999999999999999999886  4   666666664


Q ss_pred             CC
Q 041602           73 KG   74 (223)
Q Consensus        73 ~~   74 (223)
                      ..
T Consensus        96 ~~   97 (105)
T 2dnh_A           96 TD   97 (105)
T ss_dssp             SS
T ss_pred             cC
Confidence            43

>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

Probab=99.65  E-value=5.3e-16  Score=115.80  Aligned_cols=69  Identities=32%  Similarity=0.610  Sum_probs=62.4

Q ss_pred             cEEEEecCCCC-CCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPR-VSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~-~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.+ +|+++|+++|++||+|..|.+   ++|||||+|.+.++|++|++.||+..  +..|.|..+..
T Consensus        28 ~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   99 (110)
T 1wf1_A           28 SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE   99 (110)
T ss_dssp             SEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCC
T ss_pred             cEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            68999999999 999999999999999999998   48999999999999999999999987  66666666643

>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

Probab=99.65  E-value=3.5e-16  Score=113.16  Aligned_cols=72  Identities=33%  Similarity=0.548  Sum_probs=61.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCC-eEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCC-CC--cEEEEEeeccCC
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGV-LRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG-KN--GWRVELSHNSKG   74 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~-I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng-~~--g~~V~v~~~~~~   74 (223)
                      .++|||+|||.++|+++|+++|++||+ |..+.+.  ++|||||+|.+.++|++|++.||+ ..  +..|.+.++.++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~   83 (93)
T 2cqh_A            8 MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL--KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   83 (93)
T ss_dssp             CCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE--ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc--CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCc
Confidence            368999999999999999999999999 6666653  489999999999999999999999 65  777777766544

>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

Probab=99.65  E-value=9e-16  Score=109.71  Aligned_cols=72  Identities=28%  Similarity=0.547  Sum_probs=64.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..+.++.+     ++|||||+|.+.++|++|+ .||+..  +..|.+..+.+.
T Consensus         7 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A            7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccCC
Confidence            58999999999999999999999999999998753     4899999999999999999 899987  777777776553

>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

Probab=99.64  E-value=7.8e-16  Score=114.41  Aligned_cols=72  Identities=13%  Similarity=0.182  Sum_probs=62.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhC--CCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALD--GKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~ln--g~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||+.+|+++|+++|++||+|..|.|+.+ +|||||+|++.++|++|++.|+  +..  +..|.|.++..+
T Consensus        16 ~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~   91 (101)
T 2cq1_A           16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   91 (101)
T ss_dssp             SEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcc
Confidence            58999999999999999999999999999988755 8999999999999999999875  333  666666666543

>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

Probab=99.64  E-value=6.9e-16  Score=114.06  Aligned_cols=73  Identities=22%  Similarity=0.443  Sum_probs=62.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC-----cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN-----GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~-----g~~V~v~~~   71 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.     .++|||||+|.+.++|++|++.||+..     +..|.|.++
T Consensus        14 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a   93 (106)
T 2dgp_A           14 IKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPA   93 (106)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEEC
Confidence            6899999999999999999999999999999864     368999999999999999999999854     355555555


Q ss_pred             cCC
Q 041602           72 SKG   74 (223)
Q Consensus        72 ~~~   74 (223)
                      ...
T Consensus        94 ~~~   96 (106)
T 2dgp_A           94 DSE   96 (106)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            443

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

Probab=99.64  E-value=1.1e-15  Score=111.32  Aligned_cols=73  Identities=26%  Similarity=0.410  Sum_probs=64.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++++++|+++|++||+|..|.++.     .++|||||+|.+.++|++|++.||+..  +..|.+..+.++
T Consensus         3 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   82 (96)
T 2x1f_A            3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNS   82 (96)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCS
T ss_pred             cEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCCC
Confidence            6899999999999999999999999999999974     348999999999999999999999987  777777666543

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

Probab=99.64  E-value=5.4e-16  Score=111.68  Aligned_cols=73  Identities=21%  Similarity=0.353  Sum_probs=63.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee---CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~---~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++++++|+++|++||+|..|.++.   .++|||||+|.+.++|++|++.||+..  +..|.+..+.+.
T Consensus         9 ~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   86 (92)
T 2dgv_A            9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNA   86 (92)
T ss_dssp             CEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            6899999999999999999999999999999875   347999999999999999999999987  555555555443

>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}

Probab=99.64  E-value=8.3e-16  Score=111.22  Aligned_cols=69  Identities=28%  Similarity=0.512  Sum_probs=59.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~~~~   74 (223)
                      ++|||+|||+++||++|+++|++||+|.+|.|+.+++|||||+|++.++|++    +++..    ++.|.+..+.++
T Consensus        12 ~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k   84 (89)
T 3d2w_A           12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPK   84 (89)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC--
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCC
Confidence            6899999999999999999999999999999998899999999999999984    45443    678888877553

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

Probab=99.64  E-value=6.6e-16  Score=111.74  Aligned_cols=71  Identities=32%  Similarity=0.479  Sum_probs=63.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||.++++++|+++|++||+|..|.++.     .++|||||+|.+.++|++|++.||+..  +..|.+..+.
T Consensus        16 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   93 (95)
T 2cqc_A           16 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPS   93 (95)
T ss_dssp             GCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCS
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecC
Confidence            5799999999999999999999999999999974     347899999999999999999999987  7777777664

>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

Probab=99.64  E-value=1.1e-15  Score=112.08  Aligned_cols=70  Identities=29%  Similarity=0.489  Sum_probs=63.3

Q ss_pred             cEEEEecCCC-CCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDP-RVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~-~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||. ++++++|+++|++||+|..|.+.   +|||||+|.+.++|++|++.||+..  +..|.+..+..+
T Consensus        23 ~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~---~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             CEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC---SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             CEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence            6899999998 99999999999999999999985   8999999999999999999999987  777777666443

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

Probab=99.64  E-value=1.8e-15  Score=113.84  Aligned_cols=73  Identities=25%  Similarity=0.431  Sum_probs=63.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC-cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN-GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~-g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.     .++|||||+|.+.++|++|++.|++.. +..|.|..+...
T Consensus        18 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~~~   96 (116)
T 2cqd_A           18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLG   96 (116)
T ss_dssp             SEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEESTTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCCcCCCEEEEEEEcccC
Confidence            6899999999999999999999999999999974     357999999999999999999999843 666666666543

>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

Probab=99.64  E-value=6.9e-16  Score=112.97  Aligned_cols=72  Identities=26%  Similarity=0.528  Sum_probs=63.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||..+|+++|+++|++||+|..|.++. .+|||||+|.+.++|++|++.||+..  +..|.+..+.++
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~-~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpj_A           16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK-DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   89 (99)
T ss_dssp             TEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET-TTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEec-CCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCC
Confidence            5899999999999999999999999999999874 48999999999999999999999987  555555555443

>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

Probab=99.64  E-value=7.7e-16  Score=115.67  Aligned_cols=74  Identities=22%  Similarity=0.343  Sum_probs=65.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++++++|+++|++||+|..|.|+.+     ++|||||+|.+.++|++|++.||+..  +..|.|.++.++
T Consensus        26 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~  105 (115)
T 2cpz_A           26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSK  105 (115)
T ss_dssp             CCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCS
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCC
Confidence            58999999999999999999999999999998753     36899999999999999999999987  777777776554


Q ss_pred             C
Q 041602           75 G   75 (223)
Q Consensus        75 ~   75 (223)
                      .
T Consensus       106 ~  106 (115)
T 2cpz_A          106 N  106 (115)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.64  E-value=5.1e-16  Score=113.95  Aligned_cols=71  Identities=24%  Similarity=0.380  Sum_probs=64.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++++++|+++|++||+|..|.+. .++|||||+|.+.++|++|++.||+..  +..|.+.++.+
T Consensus        28 ~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           28 TTAYIGNIPHFATEADLIPLFQNFGFILDFKHY-PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             CEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            689999999999999999999999999999987 568999999999999999999999987  77777776643

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

Probab=99.64  E-value=5.3e-16  Score=114.67  Aligned_cols=70  Identities=21%  Similarity=0.511  Sum_probs=60.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+|||.++++++|+++|++||+|..|.++.     .++|||||+|.+.++|++|++.||+..  +..|.|.++
T Consensus        24 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            5799999999999999999999999999999974     347999999999999999999999987  544444444

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

Probab=99.64  E-value=5.7e-16  Score=116.14  Aligned_cols=74  Identities=23%  Similarity=0.392  Sum_probs=65.7

Q ss_pred             cEEEEecCCCCCCHHHHH---HHHHcCCCeEEEEEeeC--------CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEE
Q 041602            2 SRVYVGNLDPRVSERDLE---DEFRMFGVLRSVWVARR--------PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVEL   68 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~---~~F~~~G~I~~v~i~~~--------~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v   68 (223)
                      ++|||+|||+++++++|+   ++|++||+|..|.|+.+        ++|||||+|.+.++|++|++.||+..  +..|.|
T Consensus        16 ~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V   95 (111)
T 2cpi_A           16 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKA   95 (111)
T ss_dssp             SCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEEEE
Confidence            589999999999999999   99999999999999742        34899999999999999999999997  777888


Q ss_pred             eeccCCC
Q 041602           69 SHNSKGG   75 (223)
Q Consensus        69 ~~~~~~~   75 (223)
                      .++.++.
T Consensus        96 ~~a~~k~  102 (111)
T 2cpi_A           96 SLGTTKY  102 (111)
T ss_dssp             ESCCCCS
T ss_pred             Eeccccc
Confidence            7776543

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

Probab=99.64  E-value=1.1e-15  Score=110.64  Aligned_cols=71  Identities=34%  Similarity=0.501  Sum_probs=63.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||..+++++|+++|++||+|..|.|+.+    ++|||||+|.+.++|++|++.||+..  +..|.|..+.
T Consensus        17 ~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             GEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcC
Confidence            58999999999999999999999999999999753    37899999999999999999999987  7777776653

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

Probab=99.64  E-value=2.4e-15  Score=112.51  Aligned_cols=72  Identities=28%  Similarity=0.441  Sum_probs=64.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++++++|+++|++||+|..|.|+.+    ++|||||+|.+.++|++|++.||+..  +..|.|..+..
T Consensus        16 ~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   93 (114)
T 2do0_A           16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDER   93 (114)
T ss_dssp             SCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEccc
Confidence            58999999999999999999999999999999753    46899999999999999999999987  66677766644

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

Probab=99.63  E-value=1.2e-15  Score=118.57  Aligned_cols=74  Identities=23%  Similarity=0.321  Sum_probs=65.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCE-EEEEEcCHHHHHHHHHHhCCCC--c--EEEEEeeccCC
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGY-AFVEFDDRRDAVDAIRALDGKN--G--WRVELSHNSKG   74 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGf-aFV~F~~~e~A~~Al~~lng~~--g--~~V~v~~~~~~   74 (223)
                      |..|||+||++.+|+++|+++|++||+|.+|.+..+.+|| |||+|.+.++|++|++.|||..  +  ..+.+..++..
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~  106 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  106 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCS
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCC
Confidence            3579999999999999999999999999999998777898 9999999999999999999998  4  56666666443

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

Probab=99.63  E-value=3.5e-16  Score=114.30  Aligned_cols=74  Identities=31%  Similarity=0.581  Sum_probs=63.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeE-EEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEE----EEEe
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLR-SVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWR----VELS   69 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~-~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~----V~v~   69 (223)
                      ++|||+|||.++++++|+++|++||+|. .|.|+.+     ++|||||+|.+.++|++|++.||+..  +..    |.+.
T Consensus        10 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~   89 (99)
T 2div_A           10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLN   89 (99)
T ss_dssp             SEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEe
Confidence            6899999999999999999999999999 9998753     46899999999999999999999886  444    6666


Q ss_pred             eccCCC
Q 041602           70 HNSKGG   75 (223)
Q Consensus        70 ~~~~~~   75 (223)
                      ++.+..
T Consensus        90 ~a~~~~   95 (99)
T 2div_A           90 YATYSG   95 (99)
T ss_dssp             ETTCCS
T ss_pred             ecCCCC
Confidence            665443

>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*

Probab=99.63  E-value=1.2e-15  Score=113.55  Aligned_cols=72  Identities=21%  Similarity=0.465  Sum_probs=63.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||..+|+++|+++|++||+|..|.++.     .++|||||+|.+.++|++|++.||+..  +..|.|.++.+
T Consensus        27 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  105 (110)
T 1oo0_B           27 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV  105 (110)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEccc
Confidence            5799999999999999999999999999999964     347999999999999999999999987  66666666544

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

Probab=99.63  E-value=2.1e-16  Score=116.49  Aligned_cols=71  Identities=23%  Similarity=0.274  Sum_probs=63.0

Q ss_pred             cEEEEecCCC------CCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--c-EEEE
Q 041602            2 SRVYVGNLDP------RVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--G-WRVE   67 (223)
Q Consensus         2 ttLfVgnLp~------~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g-~~V~   67 (223)
                      ++|||+|||.      ++++++|+++|++||+|..|.|+.     .++|||||+|.+.++|++|++.||+..  + ..|.
T Consensus         7 ~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l~   86 (100)
T 3ns6_A            7 QYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLF   86 (100)
T ss_dssp             GEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBCE
T ss_pred             cEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEEE
Confidence            5899999999      999999999999999999999974     458999999999999999999999987  6 6666


Q ss_pred             Eeecc
Q 041602           68 LSHNS   72 (223)
Q Consensus        68 v~~~~   72 (223)
                      +..+.
T Consensus        87 V~~a~   91 (100)
T 3ns6_A           87 LYTMK   91 (100)
T ss_dssp             EEESH
T ss_pred             EEECc
Confidence            65553

>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

Probab=99.63  E-value=1.9e-16  Score=114.31  Aligned_cols=73  Identities=18%  Similarity=0.309  Sum_probs=60.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCC--CeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFG--VLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G--~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      .+|||+|||.++|+++|+++|++||  +|..+.++.     .++|||||+|.+.++|++|++.||+..  |..|.|..+.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  999999875     347899999999999999999999987  6666666665


Q ss_pred             CC
Q 041602           73 KG   74 (223)
Q Consensus        73 ~~   74 (223)
                      +.
T Consensus        82 ~~   83 (90)
T 3p5t_L           82 KL   83 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

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

Probab=99.63  E-value=1.2e-15  Score=114.08  Aligned_cols=74  Identities=32%  Similarity=0.516  Sum_probs=65.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeE--------EEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEE
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLR--------SVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRV   66 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~--------~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V   66 (223)
                      ++|||+|||.++|+++|+++|++||+|.        .|.|+.     .++|||||+|.+.++|++|++.||+..  +..|
T Consensus        16 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   95 (113)
T 2cpe_A           16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKL   95 (113)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCCCEE
Confidence            6899999999999999999999999998        588764     348999999999999999999999987  7777


Q ss_pred             EEeeccCCC
Q 041602           67 ELSHNSKGG   75 (223)
Q Consensus        67 ~v~~~~~~~   75 (223)
                      .|..+.++.
T Consensus        96 ~V~~a~~~~  104 (113)
T 2cpe_A           96 KVSLARKKP  104 (113)
T ss_dssp             EEECSSCCC
T ss_pred             EEEECCCCC
Confidence            777765543

>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

Probab=99.63  E-value=7.5e-16  Score=121.04  Aligned_cols=72  Identities=54%  Similarity=0.980  Sum_probs=64.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||+++|+++|+++|++||+|..|.++.+++|||||+|.+.++|++|++.||+..  +..|.|.++.+
T Consensus        74 ~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  147 (150)
T 2i2y_A           74 CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNG  147 (150)
T ss_dssp             CEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCC
Confidence            6899999999999999999999999999999988889999999999999999999999987  55555555543

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

Probab=99.63  E-value=1.2e-15  Score=110.30  Aligned_cols=70  Identities=31%  Similarity=0.484  Sum_probs=62.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+|||.++++++|+++|++||+|..|.++.     .++|||||+|.+.++|++|++.||+..  +..|.+.++
T Consensus        17 ~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             TSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            5899999999999999999999999999999964     357999999999999999999999987  666666654

>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

Probab=99.63  E-value=6.1e-16  Score=118.45  Aligned_cols=71  Identities=14%  Similarity=0.195  Sum_probs=61.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCC--C--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK--N--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~--~--g~~V~v~~~~~   73 (223)
                      ++|||+|||+++||++|+++|++||+|+.|.|+.+ +|||||+|++.++|++|++.|++.  .  +..|.|..+..
T Consensus        32 ~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~  106 (119)
T 2ad9_A           32 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH  106 (119)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccC
Confidence            58999999999999999999999999999999865 899999999999999999988742  2  55555555543

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

Probab=99.63  E-value=1.1e-15  Score=111.58  Aligned_cols=71  Identities=25%  Similarity=0.405  Sum_probs=60.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEE-eeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWV-ARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i-~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++|+++|+++|++||+|. +.+ ...++|||||+|.+.++|++|++.||+..  +..|.|..+.+
T Consensus        20 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   93 (97)
T 2e5j_A           20 ADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ   93 (97)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCC
T ss_pred             CEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCC
Confidence            6899999999999999999999999997 444 35779999999999999999999999987  55555555543

>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

Probab=99.62  E-value=3.4e-16  Score=112.21  Aligned_cols=74  Identities=24%  Similarity=0.337  Sum_probs=61.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCCcEEEEEeeccCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKNGWRVELSHNSKGG   75 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~g~~V~v~~~~~~~   75 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.+++|||||+|.+.++|++|+.......++.|.+.++.++.
T Consensus         6 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~~~~~~~g~~l~v~~a~~~~   79 (88)
T 1wf0_A            6 SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             CEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTTCEEEETTEEEEEECCCCCC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhcCCceeCCEEEEEEecCCCC
Confidence            68999999999999999999999999999999888899999999999999765321000017788888876543

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

Probab=99.62  E-value=1.3e-15  Score=113.97  Aligned_cols=70  Identities=30%  Similarity=0.532  Sum_probs=64.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.++   +|||||+|.+.++|++|++.||+..  +..|.|..+.+.
T Consensus        32 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~---kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  103 (108)
T 2jvo_A           32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP  103 (108)
T ss_dssp             SEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE---TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            689999999999999999999999999999998   8999999999999999999999987  777777776554

>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

Probab=99.62  E-value=1.1e-15  Score=114.95  Aligned_cols=70  Identities=23%  Similarity=0.256  Sum_probs=61.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+. .+|||||+|.+.++|++|++.||+..  +..|.|.++.
T Consensus        11 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A           11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            5899999999999999999999999999998874 58999999999999999999999987  4444444443

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

Probab=99.62  E-value=1.2e-15  Score=108.31  Aligned_cols=69  Identities=29%  Similarity=0.509  Sum_probs=61.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHh-CCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRAL-DGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~l-ng~~--g~~V~v~~~   71 (223)
                      ++|||+|||.++++++|+++|++||+|..|.++. ++|||||+|.+.++|++|++.| ++..  +..|.+.++
T Consensus        13 ~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~-~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~a   84 (85)
T 2ytc_A           13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ-RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWG   84 (85)
T ss_dssp             CCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG-GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEEC
T ss_pred             cEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC-CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEec
Confidence            6899999999999999999999999999999985 4899999999999999999998 7765  666666554

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

Probab=99.62  E-value=2.4e-15  Score=110.80  Aligned_cols=71  Identities=27%  Similarity=0.459  Sum_probs=62.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++|| |..|.|+.+     ++|||||+|.+.++|++|+ .||+..  +..|.|..+.+.
T Consensus        16 ~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~   93 (103)
T 2dng_A           16 YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGR   93 (103)
T ss_dssp             EEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEecCC
Confidence            5899999999999999999999996 999999753     4789999999999999999 899987  666666666544

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

Probab=99.62  E-value=2.1e-15  Score=113.43  Aligned_cols=73  Identities=25%  Similarity=0.439  Sum_probs=64.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.     .++|||||+|.+.++|++||+. ++..  +..|.|.++.++
T Consensus        28 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~~  106 (116)
T 1x4b_A           28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAR  106 (116)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCCC
Confidence            6899999999999999999999999999999974     3579999999999999999986 7665  777888777655


Q ss_pred             C
Q 041602           75 G   75 (223)
Q Consensus        75 ~   75 (223)
                      .
T Consensus       107 ~  107 (116)
T 1x4b_A          107 E  107 (116)
T ss_dssp             C
T ss_pred             c
Confidence            4

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

Probab=99.62  E-value=2.2e-15  Score=114.46  Aligned_cols=72  Identities=31%  Similarity=0.571  Sum_probs=63.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.++.     .++|||||+|.+.++|++|+ .||+..  +..|.|.++...
T Consensus        37 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~  115 (124)
T 2jwn_A           37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTN  115 (124)
T ss_dssp             TEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCCC
Confidence            5899999999999999999999999999999864     35889999999999999999 799987  777777776543

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

Probab=99.62  E-value=1.8e-15  Score=111.47  Aligned_cols=72  Identities=28%  Similarity=0.378  Sum_probs=62.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHc-CCCeEEEEEeeC----CCCEEEEEEcCHHHHHHHHHHhCCCC---cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRM-FGVLRSVWVARR----PPGYAFVEFDDRRDAVDAIRALDGKN---GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~-~G~I~~v~i~~~----~rGfaFV~F~~~e~A~~Al~~lng~~---g~~V~v~~~~~   73 (223)
                      ++|||+|||.++|+++|+++|++ ||+|..|.|+.+    ++|||||+|.+.++|++|++.||+..   +..|.+..+.+
T Consensus        10 ~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a~~   89 (104)
T 2dhg_A           10 YSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIP   89 (104)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBCCC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEccC
Confidence            68999999999999999999999 999999999753    57899999999999999999999854   55555555543

>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

Probab=99.61  E-value=2.2e-15  Score=111.51  Aligned_cols=70  Identities=31%  Similarity=0.498  Sum_probs=62.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+|||..+|+++|+++|++||+|..|.|+.    .++|||||+|.+.++|++|++.||+..  +..|.|..+
T Consensus        30 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  105 (107)
T 3ulh_A           30 GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV  105 (107)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            5899999999999999999999999999999874    347899999999999999999999987  666666554

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

Probab=99.61  E-value=1.4e-15  Score=113.78  Aligned_cols=72  Identities=29%  Similarity=0.488  Sum_probs=64.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee---CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~---~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.++.   .++|||||+|.+.++|++|++.||+..  +..|.|..+.+
T Consensus        30 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  106 (109)
T 2err_A           30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA  106 (109)
T ss_dssp             CEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            6899999999999999999999999999999974   358999999999999999999999987  77777766644

>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

Probab=99.61  E-value=2.1e-15  Score=113.13  Aligned_cols=71  Identities=34%  Similarity=0.522  Sum_probs=63.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe-----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~-----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++++++|+++|++||+|..|.|+     +.++|||||+|.+.++|++|+ .||+..  +..|.|..+.+
T Consensus        26 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           26 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            589999999999999999999999999999997     356899999999999999999 999987  66666666543

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

Probab=99.61  E-value=1.2e-15  Score=113.56  Aligned_cols=68  Identities=18%  Similarity=0.267  Sum_probs=59.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--c--EEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--G--WRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g--~~V~v~~   70 (223)
                      .+|||+|||+++|+++|+++|++||+|..|.|+.    .++|||||+|.+.++|++|++ +++..  +  +.|+++.
T Consensus        12 ~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A           12 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             GCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            5899999999999999999999999999999974    468999999999999999998 88776  4  4555443

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

Probab=99.61  E-value=7.8e-15  Score=107.02  Aligned_cols=71  Identities=21%  Similarity=0.349  Sum_probs=63.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKGG   75 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~~   75 (223)
                      ++|||+||  ++|+++|+++|++||+|..|.|. .++|||||+|.+.++|++|++.||+..  +..|.|.++.++.
T Consensus        16 ~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~   88 (97)
T 1x5p_A           16 NTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   88 (97)
T ss_dssp             SEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCC
T ss_pred             CEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCC
Confidence            68999996  89999999999999999999985 668999999999999999999999987  7777777775543

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

Probab=99.61  E-value=6.9e-16  Score=109.04  Aligned_cols=61  Identities=26%  Similarity=0.456  Sum_probs=56.5

Q ss_pred             cEEEEecCCCCC------CHHHHHHHHHcCCCeEEEEEee---CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRV------SERDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~------te~~L~~~F~~~G~I~~v~i~~---~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ++|||+|||..+      ++++|+++|++||+|..|.++.   .++|||||+|.+.++|++|++.|||..
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~   71 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYK   71 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcc
Confidence            589999999999      7899999999999999999874   468999999999999999999999886

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

Probab=99.61  E-value=2.8e-15  Score=109.92  Aligned_cols=74  Identities=23%  Similarity=0.410  Sum_probs=61.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEE-eeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWV-ARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKGG   75 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i-~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~~   75 (223)
                      ++|||+|||.++|+++|+++|++||+|.-+.. .+.++|||||+|.+.++|++|++.||+..  +..|.|..+.++.
T Consensus        16 ~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   92 (101)
T 2fc9_A           16 KTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRG   92 (101)
T ss_dssp             SEEEEESCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCC
Confidence            68999999999999999999999998832211 12468999999999999999999999987  7777777765543

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

Probab=99.60  E-value=8.6e-16  Score=111.58  Aligned_cols=74  Identities=24%  Similarity=0.367  Sum_probs=63.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKGG   75 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~~   75 (223)
                      ++|||+|||..+|+++|+++|++||+|..+...+.++|||||+|.+.++|++|++.||+..  +..|.+..+.++.
T Consensus        17 ~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   92 (96)
T 1fjc_A           17 RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             GEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            5899999999999999999999999988773334568999999999999999999999887  7777777775543

>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

Probab=99.60  E-value=8.4e-16  Score=116.51  Aligned_cols=71  Identities=21%  Similarity=0.273  Sum_probs=60.3

Q ss_pred             cEEEEecCCCC-CCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCC--C--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPR-VSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK--N--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~-~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~--~--g~~V~v~~~~~   73 (223)
                      ++|||+|||++ +|+++|+++|++||+|..|.|+ ..+|||||+|++.++|++|++.|++.  .  +..|.|..+..
T Consensus        26 ~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~  101 (112)
T 1x4f_A           26 RVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK  101 (112)
T ss_dssp             CEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECcc
Confidence            58999999998 9999999999999999999987 45899999999999999999988642  2  55555555543

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

Probab=99.60  E-value=4.6e-15  Score=114.36  Aligned_cols=72  Identities=19%  Similarity=0.195  Sum_probs=63.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCE-EEEEEcCHHHHHHHHHHhCCCC--c--EEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGY-AFVEFDDRRDAVDAIRALDGKN--G--WRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGf-aFV~F~~~e~A~~Al~~lng~~--g--~~V~v~~~~~~   74 (223)
                      ..|||+||++.+|+++|+++|++||+|++|.|..+ .|| |||+|++.++|++|+++|||.+  +  ..|.|..+++.
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~  102 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPT  102 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCS
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCC
Confidence            46899999999999999999999999999998765 596 9999999999999999999997  3  46666666543

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

Probab=99.60  E-value=5.2e-16  Score=110.32  Aligned_cols=61  Identities=30%  Similarity=0.505  Sum_probs=56.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ++|||+|||.++++++|+++|++||+|..|.++.     .++|||||+|.+.++|++|++.||+..
T Consensus         6 ~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~   71 (85)
T 1x4e_A            6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASG   71 (85)
T ss_dssp             CEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHT
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCe
Confidence            6899999999999999999999999999999864     348999999999999999999999876

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

Probab=99.60  E-value=3.1e-16  Score=112.68  Aligned_cols=72  Identities=28%  Similarity=0.561  Sum_probs=61.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      |++|||+|||.++++++|+++|++||+|..|.++.     .++|||||+|.+.+ |++|++.||+..  +..|.+..+.+
T Consensus         1 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~   79 (90)
T 2ki2_A            1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANP   79 (90)
T ss_dssp             CEEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC--
T ss_pred             CcEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCC
Confidence            68999999999999999999999999999999973     45899999999999 999999999987  55455544433

>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

Probab=99.60  E-value=1.7e-15  Score=111.45  Aligned_cols=72  Identities=31%  Similarity=0.609  Sum_probs=62.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||..+++++|+++|++||+|..|.++.+     ++|||||+|.+.++|++|++.||+..  +..|.+.++.+
T Consensus         9 ~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   87 (104)
T 1p1t_A            9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             cEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCC
Confidence            58999999999999999999999999999998753     37999999999999999999999987  55555555543

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

Probab=99.60  E-value=2.5e-15  Score=109.96  Aligned_cols=69  Identities=29%  Similarity=0.474  Sum_probs=60.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEE--------EEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEE
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRS--------VWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRV   66 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~--------v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V   66 (223)
                      ++|||+|||.++++++|+++|++||.|..        |.++.+     ++|||||+|.+.++|++|++.||+..  +..|
T Consensus        14 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   93 (99)
T 2la6_A           14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPI   93 (99)
T ss_dssp             SEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence            68999999999999999999999999999        888643     47899999999999999999999987  5444


Q ss_pred             EEee
Q 041602           67 ELSH   70 (223)
Q Consensus        67 ~v~~   70 (223)
                      .+..
T Consensus        94 ~V~~   97 (99)
T 2la6_A           94 KVSF   97 (99)
T ss_dssp             EEEE
T ss_pred             EEEe
Confidence            4444

>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

Probab=99.60  E-value=9e-16  Score=111.88  Aligned_cols=71  Identities=27%  Similarity=0.364  Sum_probs=61.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||.++++++|+++|++||+|..+.++.     .++|||||+|.+.++|++|++.||+..  +..|.|..+.
T Consensus        16 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   93 (98)
T 2cqp_A           16 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGS   93 (98)
T ss_dssp             EEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcC
Confidence            5899999999999999999999999998765543     357999999999999999999999987  6666666654

>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

Probab=99.59  E-value=2.4e-15  Score=116.17  Aligned_cols=72  Identities=29%  Similarity=0.461  Sum_probs=64.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.     .++|||||+|.+.++|++|++.||+..  +..|.|.++.+
T Consensus        47 ~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~~  125 (129)
T 2kxn_B           47 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSIT  125 (129)
T ss_dssp             SCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            5799999999999999999999999999999974     468999999999999999999999987  66666666544

>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

Probab=99.59  E-value=1.5e-15  Score=112.60  Aligned_cols=72  Identities=35%  Similarity=0.361  Sum_probs=60.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKGG   75 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~~   75 (223)
                      ++|||+|||+++|+++|+++|++||.+ .|.|+.    +++|||||+|.+.++|++||+ +|+..  +..|+|..+....
T Consensus        16 ~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~~~~   93 (102)
T 1wez_A           16 HCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAG   93 (102)
T ss_dssp             CEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCCCC
Confidence            589999999999999999999999955 888864    357899999999999999995 78776  6666666665443

>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* ...

Probab=99.59  E-value=3.3e-15  Score=108.51  Aligned_cols=73  Identities=25%  Similarity=0.495  Sum_probs=64.7

Q ss_pred             cEEEEecCCCCCCHHHHH----HHHHcCCCeEEEEEee--CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLE----DEFRMFGVLRSVWVAR--RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~----~~F~~~G~I~~v~i~~--~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++++++|+    ++|++||+|..|.++.  .++|||||+|.+.++|++|++.||+..  +..|.+.++.+
T Consensus         9 ~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   88 (97)
T 1nu4_A            9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT   88 (97)
T ss_dssp             SEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEccC
Confidence            689999999999999999    9999999999999863  458999999999999999999999987  77777766654


Q ss_pred             C
Q 041602           74 G   74 (223)
Q Consensus        74 ~   74 (223)
                      .
T Consensus        89 ~   89 (97)
T 1nu4_A           89 D   89 (97)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.59  E-value=2.6e-15  Score=111.40  Aligned_cols=72  Identities=22%  Similarity=0.369  Sum_probs=64.4

Q ss_pred             cEEEEecCCCCC------CHHHHHHHHHcCCCeEEEEEee---CCCCEEEEEEcCHHHHHHHHHHhCCCC--cE-EEEEe
Q 041602            2 SRVYVGNLDPRV------SERDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDAVDAIRALDGKN--GW-RVELS   69 (223)
Q Consensus         2 ttLfVgnLp~~~------te~~L~~~F~~~G~I~~v~i~~---~~rGfaFV~F~~~e~A~~Al~~lng~~--g~-~V~v~   69 (223)
                      ++|||+|||..+      |+++|+++|++||+|..|.|+.   .++|||||+|.+.++|++|++.|||..  +. .|.+.
T Consensus        16 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~V~   95 (105)
T 2nlw_A           16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVN   95 (105)
T ss_dssp             SEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEEEE
T ss_pred             CEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEEEE
Confidence            589999999999      7899999999999999999873   468999999999999999999999987  66 77777


Q ss_pred             eccC
Q 041602           70 HNSK   73 (223)
Q Consensus        70 ~~~~   73 (223)
                      .+..
T Consensus        96 ~a~~   99 (105)
T 2nlw_A           96 LFTD   99 (105)
T ss_dssp             CSCC
T ss_pred             Ecch
Confidence            7654

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

Probab=99.59  E-value=2.9e-15  Score=112.00  Aligned_cols=72  Identities=31%  Similarity=0.553  Sum_probs=63.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||..+++++|+++|++||+|..|.++.+     ++|||||+|.+.++|++|++.||+..  +..|.|..+.+
T Consensus        27 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~  105 (108)
T 2jrs_A           27 MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTE  105 (108)
T ss_dssp             EEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSCS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEccc
Confidence            58999999999999999999999999999999743     47899999999999999999999987  66666665543

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

Probab=99.59  E-value=2.5e-15  Score=113.18  Aligned_cols=70  Identities=26%  Similarity=0.394  Sum_probs=62.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+|||.++++++|+++|++||+|..|.|+.     .++|||||+|.+.++|++|++.||+..  +..|.|.++
T Consensus        41 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a  117 (118)
T 2khc_A           41 CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK  117 (118)
T ss_dssp             EEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            6899999999999999999999999999999964     458999999999999999999999987  666655543

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

Probab=99.59  E-value=3.6e-15  Score=115.21  Aligned_cols=71  Identities=20%  Similarity=0.321  Sum_probs=61.3

Q ss_pred             cEEEEecCCCCCCHHHHH----HHHHcCCCeEEEEEee--CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLE----DEFRMFGVLRSVWVAR--RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~----~~F~~~G~I~~v~i~~--~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||+.+++++|+    ++|++||+|.+|.+..  .++|||||+|.+.++|++|++.|||..  +..|.|.++.
T Consensus        30 ~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a~  108 (127)
T 2a3j_A           30 QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSE  108 (127)
T ss_dssp             SEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEECC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEcc
Confidence            589999999999999876    6999999999998863  578999999999999999999999987  5555555543

>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

Probab=99.59  E-value=1e-15  Score=110.86  Aligned_cols=71  Identities=28%  Similarity=0.377  Sum_probs=62.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||.++|+++|+++|++||+|..+.++.     .++|||||+|.+.++|++|++.||+..  +..|.|..+.
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           16 TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             EEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            5899999999999999999999999998776653     357999999999999999999999987  7777766553

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

Probab=99.59  E-value=4.6e-15  Score=109.54  Aligned_cols=73  Identities=19%  Similarity=0.419  Sum_probs=64.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++++++|+++|++||+|..|.|+.+     ++|||||+|.+.++|++|++. ++..  +..|.|..+.++
T Consensus        17 ~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~a~~~   95 (105)
T 2dh8_A           17 GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPR   95 (105)
T ss_dssp             SEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCCSCCS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEccCC
Confidence            68999999999999999999999999999999753     368999999999999999998 8776  777887777654


Q ss_pred             C
Q 041602           75 G   75 (223)
Q Consensus        75 ~   75 (223)
                      .
T Consensus        96 ~   96 (105)
T 2dh8_A           96 G   96 (105)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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

Probab=99.59  E-value=3.1e-15  Score=112.06  Aligned_cols=72  Identities=29%  Similarity=0.443  Sum_probs=60.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCe----EEEEEe-eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVL----RSVWVA-RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I----~~v~i~-~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++|+++|+++|++||.|    ..+.+. +.++|||||+|.+.++|++|++.||+..  +..|.|.++.+
T Consensus        26 ~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~  104 (115)
T 2cpx_A           26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN  104 (115)
T ss_dssp             SEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEccC
Confidence            689999999999999999999999998    455544 4678999999999999999999999987  55555555544

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

Probab=99.59  E-value=3.5e-15  Score=118.95  Aligned_cols=71  Identities=24%  Similarity=0.358  Sum_probs=63.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCC--CeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFG--VLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G--~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||+++|+++|+++|++||  +|..|.|+.     .++|||||+|.+.++|++||+.||+..  +..|.|..+.
T Consensus        56 ~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~  135 (156)
T 3n9u_C           56 AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPAT  135 (156)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEECC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEcC
Confidence            5899999999999999999999999  999999974     357899999999999999999999987  7777776664

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

Probab=99.59  E-value=6.2e-15  Score=112.21  Aligned_cols=73  Identities=32%  Similarity=0.494  Sum_probs=64.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||..+++++|+++|++||+|..|.|+.    .++|||||+|.+.++|++|++.||+..  +..|.|..+...
T Consensus        36 ~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  114 (124)
T 2kt5_A           36 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ  114 (124)
T ss_dssp             EEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECCT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCC
Confidence            5899999999999999999999999999999975    368999999999999999999999987  666666665443

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

Probab=99.58  E-value=1.6e-15  Score=105.32  Aligned_cols=67  Identities=21%  Similarity=0.388  Sum_probs=58.6

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEee
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSH   70 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~   70 (223)
                      +|||+|||+++++++|+++|++||+|..|.++.     .++|||||+|.+.++|++|++ ||+..  +..|.+.+
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   74 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKK   74 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEEC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEe
Confidence            589999999999999999999999999998864     347999999999999999998 88876  55555543

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

Probab=99.58  E-value=3.9e-15  Score=119.88  Aligned_cols=74  Identities=23%  Similarity=0.264  Sum_probs=64.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-CCCCEEEEEEcCHHHHHHHHHHhCCCC--c--EEEEEeeccCC
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-RPPGYAFVEFDDRRDAVDAIRALDGKN--G--WRVELSHNSKG   74 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-~~rGfaFV~F~~~e~A~~Al~~lng~~--g--~~V~v~~~~~~   74 (223)
                      +.+|||+||++.+|+++|+++|++||+|++|.|.. .++|||||+|++.++|++|++.|||..  +  ..|.|.+++++
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~  124 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  124 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCC
Confidence            35799999999999999999999999999999864 457899999999999999999999987  3  56666665443

>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

Probab=99.58  E-value=2.3e-15  Score=108.06  Aligned_cols=70  Identities=21%  Similarity=0.294  Sum_probs=63.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||+++++++|+++|++| +|..+.+. .++|||||+|.+.++|++|++.||+..  +..|.+.++..
T Consensus         6 ~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   77 (88)
T 1wg1_A            6 SGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCC
Confidence            589999999999999999999999 99999886 679999999999999999999999987  77777777644

>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

Probab=99.58  E-value=4e-15  Score=110.43  Aligned_cols=72  Identities=24%  Similarity=0.426  Sum_probs=61.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCC-eEEEEEee------CCCCEEEEEEcCHHHHHHHHHHhC-C-CC--cEEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGV-LRSVWVAR------RPPGYAFVEFDDRRDAVDAIRALD-G-KN--GWRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~-I~~v~i~~------~~rGfaFV~F~~~e~A~~Al~~ln-g-~~--g~~V~v~~   70 (223)
                      ++|||+|||.++|+++|+++|++||+ |..|.++.      .++|||||+|.+.++|++|++.|+ + ..  +..|.+.+
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V~~   88 (109)
T 2dis_A            9 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   88 (109)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEEEE
Confidence            58999999999999999999999998 99999872      568999999999999999999995 3 44  55555555


Q ss_pred             ccC
Q 041602           71 NSK   73 (223)
Q Consensus        71 ~~~   73 (223)
                      +.+
T Consensus        89 a~~   91 (109)
T 2dis_A           89 AEP   91 (109)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            544

>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

Probab=99.58  E-value=4.7e-15  Score=105.74  Aligned_cols=68  Identities=22%  Similarity=0.449  Sum_probs=59.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~   70 (223)
                      ++|||+|||+++++++|+++|++||+|..|.++.+     ++|||||+|.+.++|++|++. ++..  +..|.+.+
T Consensus        12 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~~g~~i~v~~   86 (87)
T 3s7r_A           12 GKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-KEHRLDGRVIDPKK   86 (87)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-SCEEETTEEEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-CCCEECCEEEEEEe
Confidence            68999999999999999999999999999999743     478999999999999999964 5554  66666654

>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

Probab=99.58  E-value=7.1e-15  Score=108.13  Aligned_cols=73  Identities=23%  Similarity=0.347  Sum_probs=60.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCCcEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKNGWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++++++|+++|++||+|..|.|+.+     ++|||||+|.+.++|++|++.++...+..|.+..+.++
T Consensus        16 ~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~l~v~~a~~~   93 (103)
T 2cqg_A           16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSK   93 (103)
T ss_dssp             CCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCCTT
T ss_pred             CEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHcCCeeCCeEEEEEecCCC
Confidence            58999999999999999999999999999999753     46899999999999999998422112667777776554

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

Probab=99.58  E-value=1.2e-15  Score=106.12  Aligned_cols=68  Identities=21%  Similarity=0.444  Sum_probs=58.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~   70 (223)
                      ++|||+|||.++++++|+++|++||+|..+.++.     .++|||||+|.+.++|++|++.++ ..  +..|.+.+
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~   75 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKV   75 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEe
Confidence            5899999999999999999999999999999864     347999999999999999999888 44  55444443

>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

Probab=99.58  E-value=4.5e-15  Score=118.66  Aligned_cols=73  Identities=21%  Similarity=0.467  Sum_probs=64.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||..+|+++|+++|++||+|..|.|+.+     ++|||||+|.+.++|++||+.||+..  +..|.|.++.++
T Consensus        73 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  152 (165)
T 1rk8_A           73 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK  152 (165)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            57999999999999999999999999999999753     47999999999999999999999987  666666665443

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

Probab=99.58  E-value=7.5e-15  Score=115.88  Aligned_cols=73  Identities=36%  Similarity=0.617  Sum_probs=65.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||+++|+++|+++|++||+|..|.|+.     .++|||||+|.+.++|++|++.||+..  +..|.+..+.++
T Consensus        71 ~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  150 (158)
T 2kn4_A           71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG  150 (158)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            5899999999999999999999999999999864     468999999999999999999999987  666777766544

>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

Probab=99.58  E-value=6.2e-15  Score=110.55  Aligned_cols=70  Identities=26%  Similarity=0.431  Sum_probs=61.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee--CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR--RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~--~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+|||..+|+++|+++|++||+|..|.++.  .++|||||+|.+.++|++|++.|||..  +..|.+..+
T Consensus         9 ~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            5899999999999999999999999999999974  458999999999999999999999987  544444444

>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

Probab=99.58  E-value=6.3e-15  Score=122.23  Aligned_cols=72  Identities=22%  Similarity=0.341  Sum_probs=65.8

Q ss_pred             cEEEEecCC-CCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLD-PRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp-~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+||| ..+|+++|+++|++||+|.+|+++.+.+|||||+|.+.++|++||+.|||..  +..|.|..+..
T Consensus         5 ~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~   79 (205)
T 3tyt_A            5 PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQ   79 (205)
T ss_dssp             SEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccC
Confidence            689999999 7999999999999999999999988789999999999999999999999998  77777766643

>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

Probab=99.58  E-value=1.7e-15  Score=127.82  Aligned_cols=70  Identities=17%  Similarity=0.309  Sum_probs=61.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCC--CeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFG--VLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G--~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+||++++|+++|+++|++||  +|+.|.|+.     +++|||||+|.+.++|++||+.||+..  +..|.|..+
T Consensus        69 ~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a  147 (229)
T 3q2s_C           69 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPV  147 (229)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEEC
Confidence            6899999999999999999999999  999999975     357899999999999999999999887  555555543

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

Probab=99.58  E-value=7e-15  Score=105.83  Aligned_cols=71  Identities=18%  Similarity=0.367  Sum_probs=63.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++| +|..|.|+.+    ++|||||+|.+.++|++|++ ||+..  +..|.+..+.++
T Consensus        11 ~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~~~   87 (91)
T 2dgw_A           11 HTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKSG   87 (91)
T ss_dssp             CEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEESSC
T ss_pred             cEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECCcC
Confidence            589999999999999999999999 9999998753    47899999999999999999 99987  777777777554

>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

Probab=99.57  E-value=5.8e-15  Score=112.18  Aligned_cols=60  Identities=22%  Similarity=0.388  Sum_probs=55.5

Q ss_pred             cEEEE--ecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYV--GNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfV--gnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      .+|||  |||+.++|+++|+++|++||+|..|.|+. .+|||||+|++.++|++|++.|||.+
T Consensus        26 ~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~-~rgfaFV~f~~~~~A~~Ai~~lnG~~   87 (114)
T 2cq2_A           26 QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-NKPYSFARYRTTEESKRAYVTLNGKE   87 (114)
T ss_dssp             SEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-TCSCEEEEESSHHHHHHHHHHTTTCE
T ss_pred             CEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCE
Confidence            47999  77999999999999999999999998864 48999999999999999999999973

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

Probab=99.57  E-value=4.5e-15  Score=108.89  Aligned_cols=74  Identities=26%  Similarity=0.386  Sum_probs=59.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe--eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA--RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKGG   75 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~--~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~~   75 (223)
                      ++|||+|||.++|+++|+++|++|+.|.-+...  +.++|||||+|.+.++|++|++.||+..  +..|.|.++.++.
T Consensus        16 ~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   93 (102)
T 2fc8_A           16 KTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKG   93 (102)
T ss_dssp             SSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCCC
Confidence            589999999999999999999988644333221  2347899999999999999999999987  6677777765543

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

Probab=99.57  E-value=1.5e-14  Score=104.89  Aligned_cols=72  Identities=21%  Similarity=0.346  Sum_probs=60.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      +.+|||+|||.++|+++|+++|++||+|..|.+......||||+|.+.++|++|++ ||+..  +..|.|..+.+
T Consensus         8 ~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~   81 (94)
T 2e5g_A            8 LRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQ   81 (94)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCc
Confidence            36899999999999999999999999999983322211299999999999999999 99987  77777776543

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

Probab=99.57  E-value=8.5e-15  Score=112.95  Aligned_cols=69  Identities=29%  Similarity=0.536  Sum_probs=62.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~   70 (223)
                      ++|||+|||..+|+++|+++|++||+|..|.++.     .++|||||+|.+.++|++|++.||+..  +..|.|..
T Consensus        64 ~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             cEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            5899999999999999999999999999999864     368999999999999999999999886  66666654

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

Probab=99.56  E-value=2.7e-15  Score=110.30  Aligned_cols=69  Identities=23%  Similarity=0.501  Sum_probs=60.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC------CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR------PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~------~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||.++++++|+++|++|| |..|.|+.+      ++|||||+|.+.++|++|+ .||+..  +..|.+..+.
T Consensus        20 ~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~a~   96 (100)
T 2j76_E           20 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVAD   96 (100)
T ss_dssp             CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEECC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEecc
Confidence            6899999999999999999999999 999998643      4899999999999999999 899987  5555555543

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

Probab=99.56  E-value=9.6e-15  Score=108.15  Aligned_cols=71  Identities=20%  Similarity=0.269  Sum_probs=60.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEE-EEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRS-VWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~-v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||+++|+++|+++|++||.|.. |.|+.    .++|||||+|.+.++|++||+. ++..  +..|+|..+.+
T Consensus        16 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~~~   93 (104)
T 1wg5_A           16 GFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKSSR   93 (104)
T ss_dssp             CEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEECT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEECCH
Confidence            58999999999999999999999999987 77753    4689999999999999999986 7766  66666666543

>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

Probab=99.56  E-value=1e-14  Score=103.67  Aligned_cols=67  Identities=28%  Similarity=0.517  Sum_probs=60.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcC----C-------CeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEE
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMF----G-------VLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVEL   68 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~----G-------~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v   68 (223)
                      ++|||+|||.++++++|+++|++|    |       +|..+.+..+ +|||||+|.+.++|++|+ .||+..  +..|.+
T Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   84 (87)
T 2hzc_A            7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-KNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKI   84 (87)
T ss_dssp             GEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-SSEEEEEESSHHHHHHHG-GGTTCEETTEECEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-CcEEEEEcCCHHHHHHHH-hcCCCEECCeEEEE
Confidence            689999999999999999999999    8       9999998754 899999999999999999 999987  777766


Q ss_pred             ee
Q 041602           69 SH   70 (223)
Q Consensus        69 ~~   70 (223)
                      .+
T Consensus        85 ~r   86 (87)
T 2hzc_A           85 RR   86 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            54

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

Probab=99.56  E-value=1.3e-14  Score=108.55  Aligned_cols=72  Identities=19%  Similarity=0.398  Sum_probs=62.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.     .++|||||+|.+.++|++|++.++ ..  +..|.+..+.++
T Consensus        26 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~g~~l~V~~a~~~  104 (109)
T 2rs2_A           26 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVAFPR  104 (109)
T ss_dssp             CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSC-EEETTEEEEEEECCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCC-CcCCCEEEEEEEccCC
Confidence            5899999999999999999999999999999974     458999999999999999999765 43  677777666543

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

Probab=99.55  E-value=4.1e-15  Score=114.61  Aligned_cols=72  Identities=19%  Similarity=0.389  Sum_probs=61.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEE--EEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCC----C--cEEEEE
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRS--VWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGK----N--GWRVEL   68 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~--v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~----~--g~~V~v   68 (223)
                      ++|||+|||+++|+++|+++|++||+|..  |.|+.     .++|||||+|.+. +|++|++.||+.    .  +..|.|
T Consensus        24 ~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~l~V  102 (131)
T 2m2b_A           24 DTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKTINV  102 (131)
T ss_dssp             CEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCCCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEEEEE
Confidence            58999999999999999999999999966  88864     4589999999999 999999999998    5  555555


Q ss_pred             eeccCC
Q 041602           69 SHNSKG   74 (223)
Q Consensus        69 ~~~~~~   74 (223)
                      ..+.+.
T Consensus       103 ~~a~~~  108 (131)
T 2m2b_A          103 EFAKGS  108 (131)
T ss_dssp             EECCCS
T ss_pred             EECCCC
Confidence            555443

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

Probab=99.55  E-value=4.6e-15  Score=115.32  Aligned_cols=73  Identities=36%  Similarity=0.617  Sum_probs=63.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.     .++|||||+|.+.++|++|++.||+..  +..|.|.++.++
T Consensus        48 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~  127 (135)
T 2lea_A           48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG  127 (135)
T ss_dssp             CCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            5899999999999999999999999999999863     468999999999999999999999987  555555555443

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

Probab=99.54  E-value=2.8e-15  Score=109.93  Aligned_cols=72  Identities=21%  Similarity=0.376  Sum_probs=59.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEE----eeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWV----ARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i----~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..+.+    .+.++|||||+|.+.++|++|++ ||+..  +..|.|..+.++
T Consensus        18 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~~~   95 (101)
T 1fj7_A           18 FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGR   95 (101)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcCCC
Confidence            58999999999999999999999998766222    24679999999999999999998 99887  666666665443

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

Probab=99.54  E-value=1.6e-14  Score=108.63  Aligned_cols=70  Identities=23%  Similarity=0.267  Sum_probs=62.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      .+|||+|||+++|+++|+++|++| .|..|.|+.    .++|||||+|.+.++|++|| .||+..  +..|+|..+.+
T Consensus        17 ~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           17 LYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            489999999999999999999999 899999874    46899999999999999999 688887  77888877643

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

Probab=99.31  E-value=4.5e-16  Score=117.27  Aligned_cols=73  Identities=27%  Similarity=0.475  Sum_probs=62.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEE--------EEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEE
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRS--------VWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRV   66 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~--------v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V   66 (223)
                      ++|||+|||.++++++|+++|++||+|..        |.|+.     .++|||||+|.+.++|++|++.||+..  +..|
T Consensus         8 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   87 (116)
T 2lcw_A            8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPI   87 (116)
Confidence            58999999999999999999999999988        77753     458999999999999999999999987  6666


Q ss_pred             EEeeccCC
Q 041602           67 ELSHNSKG   74 (223)
Q Consensus        67 ~v~~~~~~   74 (223)
                      .|..+.++
T Consensus        88 ~V~~a~~~   95 (116)
T 2lcw_A           88 KVSFATRR   95 (116)
Confidence            66665443

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

Probab=99.53  E-value=2.7e-14  Score=118.23  Aligned_cols=71  Identities=35%  Similarity=0.568  Sum_probs=63.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++||||+|||+++||++|+++|++||+|.+|.|+.     .++|||||+|.+.++|++|++.+|+..  +..+.+..+
T Consensus        15 ~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            47999999999999999999999999999999975     347899999999999999999999887  666665554

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

Probab=99.53  E-value=7.4e-15  Score=111.45  Aligned_cols=70  Identities=21%  Similarity=0.231  Sum_probs=61.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCC---eEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGV---LRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~---I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||+++|+++|+++|++||.   |..|.|+.    +++|||||+|.+.++|++||+ ||+..  +..|+|..+.
T Consensus        18 ~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~   96 (118)
T 2db1_A           18 YVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVFKSH   96 (118)
T ss_dssp             CEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEECC
Confidence            58999999999999999999999998   88998874    357899999999999999999 99876  7777776653

>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

Probab=99.53  E-value=2.9e-14  Score=106.71  Aligned_cols=61  Identities=25%  Similarity=0.481  Sum_probs=56.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC----CCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR----PPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~----~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.+    ++|||||+|.+.++|++|++.||+..
T Consensus        26 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~   90 (114)
T 1x5o_A           26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKF   90 (114)
T ss_dssp             TEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCE
Confidence            68999999999999999999999999999999753    47899999999999999999999875

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

Probab=99.53  E-value=1.1e-14  Score=109.61  Aligned_cols=67  Identities=31%  Similarity=0.496  Sum_probs=56.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee--------CCCCEEEEEEcCHHHHHHHHHHhCCCCcEEEEEe
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR--------RPPGYAFVEFDDRRDAVDAIRALDGKNGWRVELS   69 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~--------~~rGfaFV~F~~~e~A~~Al~~lng~~g~~V~v~   69 (223)
                      ++|||+|||+++|+++|+++|++||+|. +.++.        .++|||||+|.+.++|++||+.|++..+..+.+.
T Consensus         9 ~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~~~~~~   83 (114)
T 2dnl_A            9 RKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLYLCV   83 (114)
T ss_dssp             CCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEETTEEEEEE
T ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhcCCcEEEec
Confidence            6899999999999999999999999999 66642        4589999999999999999999944334444433

>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

Probab=99.53  E-value=9.7e-15  Score=109.87  Aligned_cols=71  Identities=20%  Similarity=0.173  Sum_probs=61.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCe-EEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVL-RSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I-~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      .+|||+|||+++|+++|+++|++||.| ..|.|+.    .++|||||+|.+.++|++||+. |+..  +..|.|..+.+
T Consensus        16 ~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a~~   93 (114)
T 2cpy_A           16 VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVVTL   93 (114)
T ss_dssp             CEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEECH
T ss_pred             cEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEECCH
Confidence            589999999999999999999999999 7888863    4689999999999999999986 7766  67777766643

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

Probab=99.52  E-value=2.6e-14  Score=103.64  Aligned_cols=72  Identities=17%  Similarity=0.305  Sum_probs=61.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEE-EeeC-CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVW-VARR-PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~-i~~~-~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||+++|+++|+++|++||+|..|+ ++.+ ..+.|||+|.+.++|++|++.||+..  +..|.+..+.+
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   91 (96)
T 2e44_A           16 RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPD   91 (96)
T ss_dssp             CCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCC
T ss_pred             CEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCc
Confidence            5799999999999999999999999999994 6543 34569999999999999999999987  55555555544

>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

Probab=99.52  E-value=4.4e-15  Score=102.91  Aligned_cols=66  Identities=21%  Similarity=0.483  Sum_probs=56.3

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEe
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELS   69 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~   69 (223)
                      +|||+|||.++++++|+++|++||+|..|.++.     .++|||||+|.+.++|++|++. ++..  +..|.+.
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~   73 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIK   73 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEE
Confidence            699999999999999999999999999998863     4589999999999999999984 5554  5444443

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

Probab=99.51  E-value=3.5e-15  Score=117.07  Aligned_cols=71  Identities=30%  Similarity=0.292  Sum_probs=60.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      .+|||+|||+++||++|+++|++|| |..|.|+.    +++|||||+|++.++|++|| .+|+..  +..|+|..+.+.
T Consensus        47 ~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~  123 (139)
T 2hgn_A           47 HCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTT  123 (139)
T ss_dssp             CCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCC
Confidence            4799999999999999999999999 66888864    46899999999999999999 688876  666666655443

>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

Probab=99.51  E-value=9.3e-15  Score=114.22  Aligned_cols=70  Identities=21%  Similarity=0.209  Sum_probs=61.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCC---eEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGV---LRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~---I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||+++|+++|+++|++||.   |..|.|+.    +++|||||+|.+.++|++||+ ||+..  +..|+|..+.
T Consensus        45 ~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~a~  123 (136)
T 2hgl_A           45 FVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSH  123 (136)
T ss_dssp             CEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEECC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEECC
Confidence            58999999999999999999999999   88888874    457899999999999999999 99886  6777776653

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

Probab=99.51  E-value=3.5e-14  Score=115.35  Aligned_cols=69  Identities=35%  Similarity=0.546  Sum_probs=61.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--c--EEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--G--WRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g--~~V~v~~   70 (223)
                      ++|||+|||..+++++|+++|++||+|+.|.|+.    .++|||||+|.+.++|++|++.||+..  +  +.|+++.
T Consensus        89 ~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~  165 (177)
T 2f3j_A           89 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             EEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            5899999999999999999999999999999974    468999999999999999999999987  4  4555544

>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

Probab=99.50  E-value=3.8e-15  Score=113.62  Aligned_cols=69  Identities=19%  Similarity=0.263  Sum_probs=58.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEE-e----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWV-A----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i-~----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+|||+++|+++|+++|++||+|..+.+ .    +.++|||||+|.+.++|++||+ ||+..  +..|.|..+
T Consensus        26 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           26 FCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            58999999999999999999999999877433 3    2458999999999999999999 99887  555555554

>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}

Probab=99.50  E-value=3.6e-14  Score=110.48  Aligned_cols=72  Identities=26%  Similarity=0.421  Sum_probs=61.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEE--------EEEe--eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEe
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRS--------VWVA--RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELS   69 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~--------v~i~--~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~   69 (223)
                      ++|||+|||+.+|+++|+++|++||.|..        +.+.  +.++|||||+|.+.++|++|++.||+..  +..|.|.
T Consensus        46 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~  125 (143)
T 3egn_A           46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQ  125 (143)
T ss_dssp             SEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEECEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            58999999999999999999999998876        3332  3678999999999999999999999998  7666666


Q ss_pred             eccC
Q 041602           70 HNSK   73 (223)
Q Consensus        70 ~~~~   73 (223)
                      .+..
T Consensus       126 ~a~~  129 (143)
T 3egn_A          126 FARS  129 (143)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            6644

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

Probab=99.49  E-value=2.9e-14  Score=104.62  Aligned_cols=69  Identities=26%  Similarity=0.517  Sum_probs=59.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||.++++++|+++|++||+|..|.++.+    ++|||||+|.+.++|++|++  ++..  +..+.+.++.
T Consensus        10 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A           10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECC
Confidence            58999999999999999999999999999999753    57899999999999999998  5544  5556555554

>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

Probab=99.49  E-value=1.6e-13  Score=107.37  Aligned_cols=71  Identities=25%  Similarity=0.434  Sum_probs=63.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||+++|+++|+++|++||+|..+.++.+     ++|||||+|.+.++|++|++.|++..  +..+.+..+.
T Consensus         3 ~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            68999999999999999999999999999999753     35899999999999999999999987  6777776654

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

Probab=99.49  E-value=7.1e-14  Score=115.64  Aligned_cols=72  Identities=28%  Similarity=0.484  Sum_probs=64.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC---CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR---PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~---~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||..+|+++|+++|++||+|..|.|+.+   ++|||||+|.+.++|++|++.|||..  +..|.|.++.+
T Consensus       104 ~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            58999999999999999999999999999999753   47899999999999999999999998  77777776644

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-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

Probab=99.49  E-value=1.4e-13  Score=108.09  Aligned_cols=72  Identities=29%  Similarity=0.506  Sum_probs=64.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++++++|+++|++||+|..|.++.+     ++|||||+|.+.++|++|++.|++..  +..|.+.++.+
T Consensus         4 ~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   82 (168)
T 1b7f_A            4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   82 (168)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCC
Confidence            68999999999999999999999999999998753     46899999999999999999999987  77777776643

>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}

Probab=99.48  E-value=1e-14  Score=108.51  Aligned_cols=69  Identities=14%  Similarity=0.120  Sum_probs=59.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCC---eEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGV---LRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~---I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+|||+++|+++|+++|++||.   |..|.|+.    .++|||||+|.+.++|++||+ +|+..  +..|++..+
T Consensus        12 ~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~a   89 (107)
T 2lmi_A           12 FLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVYEI   89 (107)
T ss_dssp             CEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEEEC
Confidence            58999999999999999999999988   88998864    468999999999999999999 88876  555555554

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

Probab=99.48  E-value=1.2e-13  Score=107.95  Aligned_cols=72  Identities=31%  Similarity=0.489  Sum_probs=63.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      .+|||+|||.++|+++|+++|++||+|..|.++.    .++|||||+|.+.++|++|++.|++..  +..+.+..+..
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~   78 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQ   78 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCC
Confidence            3899999999999999999999999999999974    357899999999999999999999997  66667666533

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=1.2e-13  Score=101.32  Aligned_cols=66  Identities=23%  Similarity=0.288  Sum_probs=56.6

Q ss_pred             EEEEecCCCCCCHHH----HHHHHHcCC-CeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            3 RVYVGNLDPRVSERD----LEDEFRMFG-VLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         3 tLfVgnLp~~~te~~----L~~~F~~~G-~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      .|||+|||+.+++++    |+++|++|| +|.+|  .   .|+|||.|.+.++|++|++.|||.+  +..|.+..+..
T Consensus        11 ~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V--t---gG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~   83 (96)
T 2diu_A           11 LLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI--T---GCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPK   83 (96)
T ss_dssp             EEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC--C---TTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE--e---cCEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCC
Confidence            499999999999987    568999994 99888  2   4999999999999999999999998  66666666544

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

Probab=99.47  E-value=1.8e-13  Score=110.41  Aligned_cols=74  Identities=23%  Similarity=0.470  Sum_probs=66.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||..+++++|+++|++||+|..|.++.+     ++|||||+|.+.++|++|++.||+..  +..|.+.++.++
T Consensus       115 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  194 (198)
T 2yh0_A          115 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG  194 (198)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            68999999999999999999999999999999754     37899999999999999999999987  777777777654


Q ss_pred             C
Q 041602           75 G   75 (223)
Q Consensus        75 ~   75 (223)
                      .
T Consensus       195 ~  195 (198)
T 2yh0_A          195 A  195 (198)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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

Probab=99.47  E-value=1.2e-13  Score=109.04  Aligned_cols=61  Identities=31%  Similarity=0.557  Sum_probs=56.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-------CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-------RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-------~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ++|||+|||+++|+++|+++|++||+|..|.++.       .++|||||+|.+.++|++|++.|++..
T Consensus         4 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~   71 (175)
T 3nmr_A            4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMK   71 (175)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcE
Confidence            5899999999999999999999999999999874       357899999999999999999999865

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

Probab=99.46  E-value=1.9e-13  Score=106.77  Aligned_cols=71  Identities=27%  Similarity=0.536  Sum_probs=63.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||..+|+++|+++|++||+|..+.++.     .++|||||+|.+.++|++|++.||+..  +..|.+.++.
T Consensus        88 ~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A           88 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             ceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecC
Confidence            5799999999999999999999999999999974     347899999999999999999999998  7777777664

>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

Probab=99.46  E-value=1.7e-13  Score=108.28  Aligned_cols=70  Identities=21%  Similarity=0.461  Sum_probs=63.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+|||..+|+++|+++|++||+|..+.++.+     ++|||||+|.+.++|++|++.||+..  +..|.+.++
T Consensus        95 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           95 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            57999999999999999999999999999999754     37899999999999999999999987  777776654

>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

Probab=99.46  E-value=1.3e-13  Score=115.23  Aligned_cols=72  Identities=26%  Similarity=0.387  Sum_probs=64.8

Q ss_pred             cEEEEecCCC-CCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDP-RVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~-~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||. ++++++|+++|++||+|..|.++.+.+|||||+|.+.++|++|++.||+..  +..|.+..+..
T Consensus        35 ~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  109 (229)
T 2adc_A           35 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH  109 (229)
T ss_dssp             SEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecC
Confidence            5899999999 999999999999999999999998878999999999999999999999987  66666665543

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

Probab=99.46  E-value=2.6e-14  Score=109.83  Aligned_cols=70  Identities=21%  Similarity=0.237  Sum_probs=59.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCe----EEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVL----RSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I----~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+|||+++|+++|+++|++||+|    ..|.|+.    +++|||||+|.+.++|++||+. |+..  +..|+|..+
T Consensus        24 ~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~~a  102 (123)
T 2dha_A           24 VIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELFRS  102 (123)
T ss_dssp             CEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEEEC
Confidence            589999999999999999999999986    5788764    3579999999999999999985 6665  667777665


Q ss_pred             c
Q 041602           72 S   72 (223)
Q Consensus        72 ~   72 (223)
                      .
T Consensus       103 ~  103 (123)
T 2dha_A          103 T  103 (123)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.46  E-value=2.3e-13  Score=111.31  Aligned_cols=70  Identities=27%  Similarity=0.510  Sum_probs=62.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.++.     .++|||||+|.+.++|++|++.|++..  +..|.+..+
T Consensus        29 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            6899999999999999999999999999999964     368999999999999999999999887  666666544

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

Probab=99.45  E-value=3.1e-13  Score=110.49  Aligned_cols=73  Identities=25%  Similarity=0.545  Sum_probs=63.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.++.+     ++|||||+|.+.++|++|++.||+..  +..|.|.++...
T Consensus       126 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~  205 (216)
T 2qfj_A          126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP  205 (216)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSC
T ss_pred             cEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCC
Confidence            58999999999999999999999999999999754     37899999999999999999999987  555666555443

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

Probab=99.45  E-value=1.1e-13  Score=112.37  Aligned_cols=71  Identities=27%  Similarity=0.390  Sum_probs=63.8

Q ss_pred             cEEEEecCCC-CCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDP-RVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~-~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||+ ++++++|+++|++||+|..|.++.+.+|||||+|.+.++|++|++.||+..  +..|.+..+.
T Consensus         4 ~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             cEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            6899999999 999999999999999999999988778999999999999999999999987  5555555543

>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

Probab=99.45  E-value=2.3e-13  Score=109.59  Aligned_cols=72  Identities=22%  Similarity=0.455  Sum_probs=61.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.++.+     ++|||||+|.+.++|++|++. ++..  +..|.+.++.++
T Consensus       105 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k  183 (196)
T 1l3k_A          105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSK  183 (196)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC--
T ss_pred             ceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCCh
Confidence            58999999999999999999999999999999753     478999999999999999985 5655  777777776554

>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

Probab=99.44  E-value=2.7e-13  Score=106.99  Aligned_cols=70  Identities=26%  Similarity=0.480  Sum_probs=61.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC----CCCEEEEEEcCHHHHHHHHHHhCCCC---c--EEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR----PPGYAFVEFDDRRDAVDAIRALDGKN---G--WRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~----~rGfaFV~F~~~e~A~~Al~~lng~~---g--~~V~v~~~   71 (223)
                      ++|||+|||..+|+++|+++|++||+|..+.++.+    ++|||||+|.+.++|++|++.|||..   +  ..|.|.++
T Consensus        96 ~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~a  174 (175)
T 3nmr_A           96 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA  174 (175)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEEC
T ss_pred             CeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEec
Confidence            57999999999999999999999999999999753    47899999999999999999999875   1  45555543

>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

Probab=99.44  E-value=9.3e-14  Score=107.24  Aligned_cols=68  Identities=16%  Similarity=0.189  Sum_probs=56.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeE--EEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLR--SVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~--~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+|||+++|+++|+++|++| .|.  .|.|+.    .++|||||+|.+.++|++||+. ++..  +..|+|..+
T Consensus        43 ~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~~a  118 (126)
T 2hgm_A           43 GFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVFKS  118 (126)
T ss_dssp             CEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEEEC
Confidence            589999999999999999999999 677  888863    4689999999999999999985 5554  555555544

>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

Probab=99.43  E-value=4.3e-13  Score=114.65  Aligned_cols=71  Identities=27%  Similarity=0.309  Sum_probs=63.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC---cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN---GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~---g~~V~v~~~~   72 (223)
                      ++|||+|||..+|+++|+++|++||+|..|.++.+.+|||||+|.+.++|++|++.|||..   +..|.|.+++
T Consensus       208 ~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          208 HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            5799999999999999999999999999999987767999999999999999999999986   5566666553

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

Probab=99.43  E-value=2.7e-13  Score=115.42  Aligned_cols=60  Identities=22%  Similarity=0.354  Sum_probs=56.0

Q ss_pred             cEEEEecCCCCC---------CHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRV---------SERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~---------te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ++|||+||+..+         +|++|+++|++||+|..|.|+. ++|||||+|.+.++|++|+++|++..
T Consensus       135 rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~-~kG~AFV~F~~~~~Ae~A~~am~g~~  203 (240)
T 3u1l_A          135 KTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-SKNCGFVKFKYQANAEFAKEAMSNQT  203 (240)
T ss_dssp             CEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG-GGTEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             ceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC-CCCEEEEEeCCHHHHHHHHHHhCCCE
Confidence            689999999998         7999999999999999999974 48999999999999999999999864

>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

Probab=99.42  E-value=4.5e-13  Score=107.92  Aligned_cols=70  Identities=23%  Similarity=0.455  Sum_probs=60.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||+++|+++|+++|++||+|..|.++.+     ++|||||+|.+.++|++|++. ++..  +..|.+..+.
T Consensus        14 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~~   90 (196)
T 1l3k_A           14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAV   90 (196)
T ss_dssp             GEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeeccc
Confidence            68999999999999999999999999999999753     478999999999999999975 6554  6667666653

>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

Probab=99.42  E-value=3.2e-13  Score=107.26  Aligned_cols=72  Identities=24%  Similarity=0.351  Sum_probs=63.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||..+|+++|+++|++||+|..+...+.++|||||+|.+.++|++|++.|||..  +..|.+.++.+
T Consensus       100 ~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  173 (175)
T 1fje_B          100 RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE  173 (175)
T ss_dssp             GEEEEESCCSSCCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCC
Confidence            5899999999999999999999999998872234678999999999999999999999987  77777777654

>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

Probab=99.42  E-value=2.7e-13  Score=106.58  Aligned_cols=71  Identities=17%  Similarity=0.427  Sum_probs=61.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||..+|+++|+++|++||+|..+.++.     .++|||||+|.+.++|++|++ +++..  +..|.+.++.+
T Consensus        88 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~p  165 (167)
T 2cjk_A           88 GKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEP  165 (167)
T ss_dssp             EEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCC
T ss_pred             CeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCC
Confidence            4899999999999999999999999999999864     357999999999999999998 77766  66666666644

>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

Probab=99.41  E-value=3.8e-13  Score=110.57  Aligned_cols=71  Identities=17%  Similarity=0.207  Sum_probs=61.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC-cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN-GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~-g~~V~v~~~~   72 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.    .++|||||+|++.++|++|++.++... |..|.|.++.
T Consensus       110 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~  185 (193)
T 2voo_A          110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD  185 (193)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETT
T ss_pred             CEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhH
Confidence            5899999999999999999999999999999974    457999999999999999998665533 7777776653

>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

Probab=99.41  E-value=6.2e-13  Score=103.97  Aligned_cols=61  Identities=28%  Similarity=0.597  Sum_probs=56.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ++|||+|||..+++++|+++|++||+|..+.++.+     ++|||||+|.+.++|++|++.|||..
T Consensus        89 ~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~  154 (167)
T 1fxl_A           89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQK  154 (167)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             CcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCc
Confidence            57999999999999999999999999999998754     37899999999999999999999987

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

Probab=99.41  E-value=9.1e-13  Score=97.70  Aligned_cols=62  Identities=21%  Similarity=0.215  Sum_probs=52.6

Q ss_pred             CCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCCcEEEEEeecc
Q 041602           11 PRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKNGWRVELSHNS   72 (223)
Q Consensus        11 ~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~g~~V~v~~~~   72 (223)
                      ..+++++|+++|++||+|..|.|++.++|||||+|++.++|++|++.+++..+..|.|.++.
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~~~g~~l~V~~a~   88 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVGLVDNPLKISWLE   88 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCBCSSSBCEEECSS
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCCCCCCeEEEEEcc
Confidence            45899999999999999999999988899999999999999999998777664444444443

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-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

Probab=99.40  E-value=7.2e-13  Score=104.03  Aligned_cols=68  Identities=29%  Similarity=0.544  Sum_probs=59.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC-----CCCEEEEEEcCHHHHHHHHHHhCCCC--c--EEEEEe
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRALDGKN--G--WRVELS   69 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~-----~rGfaFV~F~~~e~A~~Al~~lng~~--g--~~V~v~   69 (223)
                      ++|||+|||..+++++|+++|++||+|..+.++.+     ++|||||+|.+.++|++|++.||+..  +  ..|.|.
T Consensus        90 ~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~  166 (168)
T 1b7f_A           90 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR  166 (168)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEE
Confidence            58999999999999999999999999999998753     36899999999999999999999986  3  444444

>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

Probab=99.40  E-value=8.8e-13  Score=112.72  Aligned_cols=72  Identities=25%  Similarity=0.505  Sum_probs=62.8

Q ss_pred             cEEEEecCCCCCCHHHHH----HHHHcCCCeEEEEEee--CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLE----DEFRMFGVLRSVWVAR--RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~----~~F~~~G~I~~v~i~~--~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++|+++|+    ++|++||+|..|.++.  +++|||||+|.+.++|++|++.||+..  +..|.|.++..
T Consensus        10 ~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   89 (282)
T 3pgw_A           10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT   89 (282)
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEEecc
Confidence            689999999999999976    8999999999999864  568999999999999999999999987  65666655533

>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

Probab=99.38  E-value=5.3e-13  Score=104.84  Aligned_cols=70  Identities=16%  Similarity=0.451  Sum_probs=57.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCCcEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKNGWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~g~~V~v~~~   71 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.++.     .++|||||+|.+.++|++|++.++...+..|.+..+
T Consensus         4 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~   78 (167)
T 2cjk_A            4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRA   78 (167)
T ss_dssp             GEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHSCCEETTEECCCEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhcccccCCeEcccccc
Confidence            6899999999999999999999999999999864     457999999999999999998522112555544443

>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

Probab=99.38  E-value=1.5e-12  Score=108.84  Aligned_cols=72  Identities=22%  Similarity=0.369  Sum_probs=63.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCC-CeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC---cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFG-VLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN---GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G-~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~---g~~V~v~~~~~   73 (223)
                      ++|||+|||..+++++|+++|++|| +|..|.++.+.+|||||+|.+.++|++|++.||+..   +..|.+.++.+
T Consensus       152 ~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  227 (229)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecC
Confidence            5799999999999999999999999 999999976678999999999999999999999886   45666665543

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

Probab=99.37  E-value=8.2e-13  Score=107.13  Aligned_cols=71  Identities=23%  Similarity=0.374  Sum_probs=62.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCC-CeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC---cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFG-VLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN---GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G-~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~---g~~V~v~~~~   72 (223)
                      ++|||+|||..+++++|+++|++|| +|..|.++.+.+|+|||+|.+.++|++|++.|||..   +..|.+.++.
T Consensus       121 ~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~  195 (198)
T 1qm9_A          121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK  195 (198)
T ss_dssp             CEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeec
Confidence            4799999999999999999999999 999999977679999999999999999999999886   4445555443

>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

Probab=99.37  E-value=1.2e-12  Score=111.57  Aligned_cols=70  Identities=27%  Similarity=0.521  Sum_probs=62.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.+.. .+|||||+|.+.++|++|++.||+..  +..|.+..+.
T Consensus        23 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~-~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~   94 (261)
T 3sde_A           23 CRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR-DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT   94 (261)
T ss_dssp             GEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET-TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC-CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeecc
Confidence            5899999999999999999999999999999864 58999999999999999999999987  6666666554

>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

Probab=99.35  E-value=1.2e-12  Score=108.34  Aligned_cols=61  Identities=21%  Similarity=0.247  Sum_probs=55.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCe--EEEEEee---CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVL--RSVWVAR---RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I--~~v~i~~---~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ++|||+|||+++|+++|+++|++||.|  ..+.+..   +.+|||||+|.+.++|.+||..||+.+
T Consensus       124 ~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~  189 (205)
T 3tyt_A          124 NVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQ  189 (205)
T ss_dssp             SEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCE
T ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCC
Confidence            379999999999999999999999998  8888864   346899999999999999999999886

>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

Probab=99.35  E-value=3.2e-12  Score=100.84  Aligned_cols=70  Identities=27%  Similarity=0.490  Sum_probs=61.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcC----C-------CeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEE
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMF----G-------VLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVEL   68 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~----G-------~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v   68 (223)
                      ++|||+|||.++|+++|+++|++|    |       .|..+.+. .++|||||+|.+.++|++|+ .||+..  +..+.+
T Consensus         5 ~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~-~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~v   82 (172)
T 2g4b_A            5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-QDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKI   82 (172)
T ss_dssp             GEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE-TTTTEEEEEESSHHHHHHHG-GGTTCEETTEECEE
T ss_pred             cEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec-CCCCEEEEEeCCHHHHHHHH-HhCCcEecCceeee
Confidence            689999999999999999999999    7       77777765 45899999999999999999 799987  777777


Q ss_pred             eeccC
Q 041602           69 SHNSK   73 (223)
Q Consensus        69 ~~~~~   73 (223)
                      ..+..
T Consensus        83 ~~~~~   87 (172)
T 2g4b_A           83 RRPHD   87 (172)
T ss_dssp             ECCSS
T ss_pred             cCCcc
Confidence            76543

>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*

Probab=99.35  E-value=1.2e-12  Score=116.82  Aligned_cols=60  Identities=22%  Similarity=0.373  Sum_probs=55.5

Q ss_pred             cEEEEec--CCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGN--LDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgn--Lp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      .+|||+|  |+..+||++|+++|++||+|+.|.+.. .||||||+|++.++|++|+++|||++
T Consensus        19 ~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-~kgfaFV~f~~~~~A~~Ai~~lnG~~   80 (345)
T 3tht_A           19 QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-NKPYSFARYRTTEESKRAYVTLNGKE   80 (345)
T ss_dssp             SEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-TCSEEEEEESSHHHHHHHHHHTTTCE
T ss_pred             CEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCc
Confidence            5899999  578999999999999999999988764 68999999999999999999999986

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

Probab=99.34  E-value=1.5e-12  Score=100.74  Aligned_cols=70  Identities=17%  Similarity=0.314  Sum_probs=57.7

Q ss_pred             cEEEEecC----CCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcC----HHH----HHHHHH--HhCCCC
Q 041602            2 SRVYVGNL----DPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDD----RRD----AVDAIR--ALDGKN   62 (223)
Q Consensus         2 ttLfVgnL----p~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~----~e~----A~~Al~--~lng~~   62 (223)
                      ++|||+||    |+.|++++|+++|++||+|..+.++.     .++|||||+|.+    +++    |.+|++  .+|+..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            58999999    99999999999999999999999975     458999999996    433    788887  678776


Q ss_pred             --cEEEEEeec
Q 041602           63 --GWRVELSHN   71 (223)
Q Consensus        63 --g~~V~v~~~   71 (223)
                        |..|.|...
T Consensus        83 I~Gr~irV~ln   93 (136)
T 2j8a_A           83 IMGFKFEVILN   93 (136)
T ss_dssp             ETTEEEEEEEC
T ss_pred             ecCcEEEEEEC
Confidence              666666654

>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

Probab=99.33  E-value=4.7e-12  Score=108.26  Aligned_cols=69  Identities=19%  Similarity=0.327  Sum_probs=61.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||.++|+++|+++|++|| |..+.+ ..++|||||+|.+.++|++|++.||+..  +..|.+..+.
T Consensus        23 ~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~-~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~   93 (284)
T 3smz_A           23 RKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP   93 (284)
T ss_dssp             CEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE-ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC
Confidence            6899999999999999999999999 999888 5679999999999999999999999987  6666665543

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

Probab=99.32  E-value=8.2e-12  Score=93.11  Aligned_cols=71  Identities=20%  Similarity=0.290  Sum_probs=59.9

Q ss_pred             cEEEEecCCC-----CCCHHHHHHHHHcCCCeEEEEEee------CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEE
Q 041602            2 SRVYVGNLDP-----RVSERDLEDEFRMFGVLRSVWVAR------RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVEL   68 (223)
Q Consensus         2 ttLfVgnLp~-----~~te~~L~~~F~~~G~I~~v~i~~------~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v   68 (223)
                      .+|+|.||..     +.++++|+++|++||+|..|.|+.      +++|||||+|.+.++|++|++.|||..  |..|.+
T Consensus         9 ~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~v   88 (105)
T 2pe8_A            9 KVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKA   88 (105)
T ss_dssp             SEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEEEE
Confidence            4789999963     237899999999999999999974      348999999999999999999999998  777776


Q ss_pred             eecc
Q 041602           69 SHNS   72 (223)
Q Consensus        69 ~~~~   72 (223)
                      ..+.
T Consensus        89 ~~a~   92 (105)
T 2pe8_A           89 CFYN   92 (105)
T ss_dssp             EECC
T ss_pred             EEcC
Confidence            6653

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

Probab=99.32  E-value=5.5e-12  Score=101.62  Aligned_cols=71  Identities=27%  Similarity=0.464  Sum_probs=61.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcC----C-------CeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEE
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMF----G-------VLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVEL   68 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~----G-------~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v   68 (223)
                      ++|||+|||.++|+++|+++|++|    |       .|..+.+. .++|||||+|.+.++|++|+ .||+..  +..|.+
T Consensus         5 ~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~-~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~v   82 (198)
T 2yh0_A            5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-QDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKI   82 (198)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE-TTTTEEEEEESCSHHHHHHG-GGTTEEETTEEEEE
T ss_pred             eEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec-CCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEEE
Confidence            689999999999999999999999    5       67777664 56999999999999999999 799887  788888


Q ss_pred             eeccCC
Q 041602           69 SHNSKG   74 (223)
Q Consensus        69 ~~~~~~   74 (223)
                      .++...
T Consensus        83 ~~~~~~   88 (198)
T 2yh0_A           83 RRPHDY   88 (198)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            776443

>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

Probab=99.32  E-value=9.9e-12  Score=93.04  Aligned_cols=73  Identities=27%  Similarity=0.379  Sum_probs=60.5

Q ss_pred             cEEEEecCCCCCC-----------HHHHHHHHHcCCCeEEEEEee-CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEE
Q 041602            2 SRVYVGNLDPRVS-----------ERDLEDEFRMFGVLRSVWVAR-RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVE   67 (223)
Q Consensus         2 ttLfVgnLp~~~t-----------e~~L~~~F~~~G~I~~v~i~~-~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~   67 (223)
                      .+|+|.||....+           +++|+++|++||+|..|.|.. .++|||||+|.+.++|++|++.|||..  +..|.
T Consensus        16 ~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~   95 (112)
T 2dit_A           16 RVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT   95 (112)
T ss_dssp             CEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTEECE
T ss_pred             eEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            4799999954332           689999999999999997742 468999999999999999999999987  77777


Q ss_pred             EeeccCC
Q 041602           68 LSHNSKG   74 (223)
Q Consensus        68 v~~~~~~   74 (223)
                      +..+.+.
T Consensus        96 v~~a~~~  102 (112)
T 2dit_A           96 AQAWDGT  102 (112)
T ss_dssp             EEECCSC
T ss_pred             EEEeCCC
Confidence            7776543

>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

Probab=99.31  E-value=4.1e-12  Score=109.08  Aligned_cols=71  Identities=20%  Similarity=0.360  Sum_probs=64.1

Q ss_pred             cEEEEecCCCC-CCHHHHHHHHHcCCCeEEEEEee------CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPR-VSERDLEDEFRMFGVLRSVWVAR------RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~-~te~~L~~~F~~~G~I~~v~i~~------~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||.. +|+++|+++|++||+|..|.++.      .++|||||+|.+.++|++|+ .|||..  +..|.+.++.
T Consensus       211 ~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~  289 (292)
T 2ghp_A          211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLAD  289 (292)
T ss_dssp             TEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECC
T ss_pred             ceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEec
Confidence            58999999999 99999999999999999999863      45799999999999999999 999987  7778877775


Q ss_pred             C
Q 041602           73 K   73 (223)
Q Consensus        73 ~   73 (223)
                      +
T Consensus       290 ~  290 (292)
T 2ghp_A          290 K  290 (292)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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

Probab=99.29  E-value=7.7e-12  Score=107.35  Aligned_cols=69  Identities=26%  Similarity=0.239  Sum_probs=61.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC---CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR---PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~---~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.+   ++|||||+|.+.++|++|++ +++..  +..|.+..+
T Consensus        42 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~~~  115 (292)
T 2ghp_A           42 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL  115 (292)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEEEC
Confidence            68999999999999999999999999999999763   47999999999999999995 88876  666666554

>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

Probab=99.28  E-value=1.6e-12  Score=103.08  Aligned_cols=71  Identities=21%  Similarity=0.384  Sum_probs=59.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEE----eeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWV----ARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i----~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++|+++|+++|++||.|..+.+    .+.++|||||+|.+.++|++|+ +||+..  +..|.+.++..
T Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~~~~   90 (175)
T 1fje_B           14 FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKG   90 (175)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEECCCC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEecCCC
Confidence            58999999999999999999999986554222    2467999999999999999999 499887  77788877644

>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

Probab=99.27  E-value=6.9e-12  Score=107.24  Aligned_cols=73  Identities=21%  Similarity=0.247  Sum_probs=64.7

Q ss_pred             cEEEEecCCCCC-CHHHHHHHHHcCCCeEEEEEeeC----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRV-SERDLEDEFRMFGVLRSVWVARR----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~-te~~L~~~F~~~G~I~~v~i~~~----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||..+ |+++|+++|++||.|..+.|+.+    ++|+|||+|.+.++|++|++.|||..  +..|.+.++.++
T Consensus       185 ~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  264 (284)
T 3smz_A          185 RCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPG  264 (284)
T ss_dssp             SEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSS
T ss_pred             cEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCC
Confidence            589999999995 99999999999999999998753    57899999999999999999999998  777777776554

>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

Probab=99.24  E-value=1.1e-11  Score=105.47  Aligned_cols=71  Identities=28%  Similarity=0.340  Sum_probs=59.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeC----CCCEEEEEEcCHHHHHHHHHHhCCCC------cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR----PPGYAFVEFDDRRDAVDAIRALDGKN------GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~----~rGfaFV~F~~~e~A~~Al~~lng~~------g~~V~v~~~   71 (223)
                      ++|||+|||..+|+++|+++|++||+|..|.++.+    ++|||||+|.+.++|.+|++.||+..      +..|.+..+
T Consensus        97 ~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~  176 (261)
T 3sde_A           97 AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPM  176 (261)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEEC
T ss_pred             CcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeec
Confidence            58999999999999999999999999999998753    57899999999999999999996432      444555544


Q ss_pred             c
Q 041602           72 S   72 (223)
Q Consensus        72 ~   72 (223)
                      .
T Consensus       177 ~  177 (261)
T 3sde_A          177 E  177 (261)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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

Probab=99.21  E-value=5.6e-12  Score=93.77  Aligned_cols=66  Identities=20%  Similarity=0.384  Sum_probs=53.0

Q ss_pred             EecCCCCCCHHHHHHHH------------HcCCCeEEEEEeeC----CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEE
Q 041602            6 VGNLDPRVSERDLEDEF------------RMFGVLRSVWVARR----PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVE   67 (223)
Q Consensus         6 VgnLp~~~te~~L~~~F------------~~~G~I~~v~i~~~----~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~   67 (223)
                      +.||+..+++++|+++|            ++||+|..|.|+.+    ++|||||+|.+.++|++|++.|||..  |..|.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            34566666777766666            99999999999753    58999999999999999999999997  76666


Q ss_pred             Eeec
Q 041602           68 LSHN   71 (223)
Q Consensus        68 v~~~   71 (223)
                      +..+
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            6543

>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

Probab=99.13  E-value=1.5e-10  Score=86.12  Aligned_cols=69  Identities=25%  Similarity=0.360  Sum_probs=56.3

Q ss_pred             EEEEecC--CCCCC--------HHHHHHHHHcCCCeEEEEEee-------CCCCEEEEEEcCHHHHHHHHHHhCCCC--c
Q 041602            3 RVYVGNL--DPRVS--------ERDLEDEFRMFGVLRSVWVAR-------RPPGYAFVEFDDRRDAVDAIRALDGKN--G   63 (223)
Q Consensus         3 tLfVgnL--p~~~t--------e~~L~~~F~~~G~I~~v~i~~-------~~rGfaFV~F~~~e~A~~Al~~lng~~--g   63 (223)
                      .|.+.|+  |.++.        +++|+++|++||+|.+|.|+.       .++|||||+|.+.++|++|+++|||..  +
T Consensus         7 vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f~G   86 (105)
T 3v4m_A            7 VLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFAN   86 (105)
T ss_dssp             EEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             EEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            4667787  22332        368999999999999999974       257999999999999999999999998  7


Q ss_pred             EEEEEeec
Q 041602           64 WRVELSHN   71 (223)
Q Consensus        64 ~~V~v~~~   71 (223)
                      ..|.+...
T Consensus        87 R~i~v~~~   94 (105)
T 3v4m_A           87 RVVVTKYC   94 (105)
T ss_dssp             EECEEEEE
T ss_pred             CEEEEEEe
Confidence            77666654

>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

Probab=99.05  E-value=5.7e-10  Score=84.85  Aligned_cols=70  Identities=24%  Similarity=0.330  Sum_probs=57.2

Q ss_pred             cEEEEecCCC--CC---CHHHHHHHHHcCCCeEEEEEeeC---------CCCEEEEEEcCHHHHHHHHHHhCCCC--cEE
Q 041602            2 SRVYVGNLDP--RV---SERDLEDEFRMFGVLRSVWVARR---------PPGYAFVEFDDRRDAVDAIRALDGKN--GWR   65 (223)
Q Consensus         2 ttLfVgnLp~--~~---te~~L~~~F~~~G~I~~v~i~~~---------~rGfaFV~F~~~e~A~~Al~~lng~~--g~~   65 (223)
                      ..|++.|+-.  ++   -++||++.|++||+|.+|.|+.+         .+||+||+|.+.++|++|++.|||..  ++.
T Consensus        21 ~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR~  100 (118)
T 3ue2_A           21 TVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRK  100 (118)
T ss_dssp             CEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            3678888842  22   36899999999999999998753         24899999999999999999999998  766


Q ss_pred             EEEeec
Q 041602           66 VELSHN   71 (223)
Q Consensus        66 V~v~~~   71 (223)
                      |.+...
T Consensus       101 i~v~~~  106 (118)
T 3ue2_A          101 VVAEVY  106 (118)
T ss_dssp             CEEEEE
T ss_pred             EEEEEc
Confidence            666654

>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

Probab=99.01  E-value=5.2e-10  Score=84.61  Aligned_cols=57  Identities=21%  Similarity=0.346  Sum_probs=49.8

Q ss_pred             HHHHHHHHHcCCCeEEEEEeeC-CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602           15 ERDLEDEFRMFGVLRSVWVARR-PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus        15 e~~L~~~F~~~G~I~~v~i~~~-~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++||+++|++||+|.+|.|..+ ++|||||+|.+.++|++|++.|||..  |..|.+...
T Consensus        31 ~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i~v~~~   90 (114)
T 3s6e_A           31 KDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYV   90 (114)
T ss_dssp             HHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             HHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEE
Confidence            3588999999999999999764 48999999999999999999999998  766666655

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

Probab=98.97  E-value=3e-09  Score=81.36  Aligned_cols=59  Identities=12%  Similarity=0.144  Sum_probs=52.7

Q ss_pred             cEEEEecCCCC-CCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcC-HHHHHHHHHHhCCC
Q 041602            2 SRVYVGNLDPR-VSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDD-RRDAVDAIRALDGK   61 (223)
Q Consensus         2 ttLfVgnLp~~-~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~-~e~A~~Al~~lng~   61 (223)
                      +-|||+||+.+ +++++|+++|++||+|..|.++.. .-.|||.|.+ .++|++|++++|..
T Consensus        19 ~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g-~~tgfVrf~~~~~~A~~av~~ln~~   79 (121)
T 1owx_A           19 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-AKEGIILFKEKAKEALGKAKDANNG   79 (121)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-CSEEEEEESSCHHHHHHHHHHTTTS
T ss_pred             eEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecC-CCEEEEEECCChHHHHHHHHHhhcC
Confidence            46899999999 999999999999999999999755 3389999999 89999999999633

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

Probab=98.75  E-value=3.2e-08  Score=71.75  Aligned_cols=69  Identities=19%  Similarity=0.328  Sum_probs=55.5

Q ss_pred             cEEEEecCCC----CCCH----HHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDP----RVSE----RDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~----~~te----~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      .||+|.-++.    +.-.    .+|.+.|++||+|..++++.   +.+||+|.+.++|.+|++ |||.+  ++.++|..+
T Consensus         8 ~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~---d~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~lk   83 (91)
T 2dnr_A            8 GTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVE---DKMWVTFLEGSSALNVLS-LNGKELLNRTITIALK   83 (91)
T ss_dssp             CEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECS---SSEEEEESSHHHHHHGGG-GTTCEETTEEEEEEEC
T ss_pred             CeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEec---CCEEEEECChHHHHHHHh-cCCeEeCCeEEEEEeC
Confidence            3778876652    2323    57999999999999999984   459999999999999998 99998  777777776


Q ss_pred             cCC
Q 041602           72 SKG   74 (223)
Q Consensus        72 ~~~   74 (223)
                      .+.
T Consensus        84 t~d   86 (91)
T 2dnr_A           84 SPS   86 (91)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            543

>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

Probab=98.45  E-value=5e-07  Score=65.85  Aligned_cols=67  Identities=25%  Similarity=0.408  Sum_probs=54.4

Q ss_pred             cEEEEecCCCC-----C-CH---HHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEee
Q 041602            2 SRVYVGNLDPR-----V-SE---RDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~-----~-te---~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~   70 (223)
                      .||+|.-++..     + .+   .+|.+.|++||+|..++++.+   -+||+|.+.++|.+||+ |||.+  ++.+++..
T Consensus        16 ~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d---~~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~~   91 (95)
T 1ufw_A           16 ATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG---QMLVTFADSHSALSVLD-VDGMKVKGRAVKISG   91 (95)
T ss_dssp             CEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT---EEEEECSCSHHHHHHHH-GGGSEETTEEEEEEC
T ss_pred             CeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC---cEEEEEcChHHHHHHHh-cCCeeeCCeEEEEec
Confidence            47888877643     2 21   468999999999999999854   49999999999999998 99998  78887776


Q ss_pred             cc
Q 041602           71 NS   72 (223)
Q Consensus        71 ~~   72 (223)
                      ..
T Consensus        92 k~   93 (95)
T 1ufw_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            53

>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}

Probab=98.35  E-value=6e-07  Score=74.15  Aligned_cols=58  Identities=28%  Similarity=0.359  Sum_probs=49.0

Q ss_pred             CHHHHHHHHHcCCCeEEEEEee---------CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602           14 SERDLEDEFRMFGVLRSVWVAR---------RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus        14 te~~L~~~F~~~G~I~~v~i~~---------~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      .+++|.+.|++||+|..+.|+.         .++|++||+|.+.++|++|++.|||..  |+.|.+...
T Consensus       142 ~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~  210 (222)
T 3dxb_A          142 LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVY  210 (222)
T ss_dssp             HHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             HHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEc
Confidence            4678999999999999999862         347899999999999999999999998  655555543

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

Probab=97.53  E-value=0.00035  Score=52.14  Aligned_cols=67  Identities=16%  Similarity=0.151  Sum_probs=58.2

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcC-----CCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEee
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMF-----GVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSH   70 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~-----G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~   70 (223)
                      +|-+-|||..++...|+.+.+.+     |.|+.+.+.-+ .+-|+|+|.+...|.+|.-+|+|.+  +.++.+..
T Consensus        23 tiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD-H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           23 LICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD-FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT-TTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             EEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC-CCceEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            56678999999999999999999     99999988766 4579999999999999988899998  66666553

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

Probab=97.25  E-value=0.0017  Score=46.75  Aligned_cols=62  Identities=16%  Similarity=0.263  Sum_probs=52.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-C------CCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-R------PPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-~------~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      |++|-|.+||+.+||+++.+.+....++.....+. +      .-.-|+|.|.+.+++.+-.+.++|..
T Consensus         1 ~~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~   69 (91)
T 1uw4_A            1 LSKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYV   69 (91)
T ss_dssp             CCEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcE
Confidence            68999999999999999999999888776665542 1      13579999999999999999999875

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

Probab=97.24  E-value=0.0026  Score=46.77  Aligned_cols=53  Identities=23%  Similarity=0.147  Sum_probs=46.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHc---C--CCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHH
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRM---F--GVLRSVWVARRPPGYAFVEFDDRRDAVDAIRA   57 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~---~--G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~   57 (223)
                      ++|.|.|||+.+.++.|+-+|++   -  |+|..+....   +-|+|+|.+.+.|+..++.
T Consensus         9 ~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~---~~AvItF~d~~va~rVL~k   66 (104)
T 2dhx_A            9 VAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG---CGGVLTFREPADAERVLAQ   66 (104)
T ss_dssp             CEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHTC
T ss_pred             cEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhcC
Confidence            57999999999999999999987   2  5899988763   7899999999999999875

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=96.81  E-value=0.0037  Score=45.56  Aligned_cols=53  Identities=19%  Similarity=0.192  Sum_probs=43.4

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhC
Q 041602            4 VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALD   59 (223)
Q Consensus         4 LfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~ln   59 (223)
                      ||+-++|.++...||+++|+.||.| .|..+.  .--|||.|.+++.|..|+..+.
T Consensus        18 Vf~l~FP~ewKt~DI~~lFs~fggv-~I~Wid--DTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           18 VLHVTFPKEWKTSDLYQLFSAFGNI-QISWID--DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             EEEEECCTTCCHHHHHHHHTTTCSC-CCEEEE--TTEEEEECSCHHHHHHHHHHHH
T ss_pred             EEEEeCChhhhhHHHHHHhhccCCE-EEEEEc--CCeEEEEecCHHHHHHHHHhcc
Confidence            4444999999999999999999943 344443  3489999999999999999774

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.81  E-value=0.0032  Score=46.04  Aligned_cols=53  Identities=19%  Similarity=0.161  Sum_probs=43.8

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhC
Q 041602            4 VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALD   59 (223)
Q Consensus         4 LfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~ln   59 (223)
                      ||+-++|.++...||.++|+.||. ..|..+.+  .-|||.|.+++.|..|+..+.
T Consensus         8 V~~l~FP~ewKt~Di~~lFs~fgg-v~I~WidD--TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHVTFPKEWKTSDLYQLFSAFGN-IQISWIDD--TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEECCTTCCHHHHHHHTTTSEE-EEEEEEET--TEEEEEEEEECHHHHHHHHHT
T ss_pred             EEEEeCChhhhhHHHHHHHhccCC-EEEEEEcC--CeEEEEecCHHHHHHHHHhcc
Confidence            444499999999999999999993 34555543  489999999999999999774

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.53  E-value=0.014  Score=44.02  Aligned_cols=65  Identities=12%  Similarity=0.183  Sum_probs=50.4

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC---cEEEEEee
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN---GWRVELSH   70 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~---g~~V~v~~   70 (223)
                      -|-|-+.|+.. .+.|..+|++||+|.+.... ....+-.|.|+++.+|++||. .||..   .+.|-+..
T Consensus        26 wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~-~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p   93 (119)
T 1wwh_A           26 WVTVFGFPQAS-ASYILLQFAQYGNILKHVMS-NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKP   93 (119)
T ss_dssp             EEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC-SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEE
T ss_pred             EEEEECCCHHH-HHHHHHHHHhhCcEEEeccC-CCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEE
Confidence            46778888774 67788899999999988763 335799999999999999997 57765   35555554

>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

Probab=96.52  E-value=0.0045  Score=45.62  Aligned_cols=70  Identities=20%  Similarity=0.182  Sum_probs=55.6

Q ss_pred             cEEEEecCCCCC-CH----HHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRV-SE----RDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~-te----~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|+|.||+.++ +.    +.++++|.+|+++......+ +-.-..|.|.++++|.+|-..|++..  |..+++..++
T Consensus         6 ntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lk-SFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq   82 (104)
T 1wey_A            6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET-TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             ceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecC-cceEEEEEeCChHHHHHHHHHhccceecCceeEEEecC
Confidence            789999998865 22    57799999999887766553 33467999999999999999999987  6666666664

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.20  E-value=0.0025  Score=58.61  Aligned_cols=54  Identities=19%  Similarity=0.231  Sum_probs=41.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHH
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIR   56 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~   56 (223)
                      .+|+|. .|..+++++|.+.|++||+|.++.+-.+..-||.|+|.+.+++++++.
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            368996 799999999999999999999998865545699999999999997764

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*

Probab=95.06  E-value=0.0021  Score=50.29  Aligned_cols=89  Identities=25%  Similarity=0.369  Sum_probs=45.6

Q ss_pred             HHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcC--------HHHHHHHHHHh--CCC----CcEEEEEeeccCCC------
Q 041602           16 RDLEDEFRMFGVLRSVWVARRPPGYAFVEFDD--------RRDAVDAIRAL--DGK----NGWRVELSHNSKGG------   75 (223)
Q Consensus        16 ~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~--------~e~A~~Al~~l--ng~----~g~~V~v~~~~~~~------   75 (223)
                      +|+.++|...|.|+....   .+||+||+-++        .+|+---+.++  .+.    ++..|++.......      
T Consensus         2 ~~~~~l~~~~G~Vkwfn~---~kGfGFI~~~~~~g~p~~~g~DvFvH~s~i~~~g~~~l~eG~~V~f~~~~g~kG~~A~~   78 (148)
T 3ts2_A            2 ADEPQLLHGAGICKWFNV---RMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIR   78 (148)
T ss_dssp             ----CCEEEEEEEEEEET---TTTEEEEEEEEETTEEEEEEEEEEEEGGGBCSSSSCCCCTTCEEEEEEEEETTEEEEEE
T ss_pred             CcccccccceeEEEEEEC---CCCeeEEeeCccccccCCCCccEEEEhHHhcccCCccCCCCCEEEEEEEEccccchhhc
Confidence            456667777777766543   48999999763        12211111122  221    14455544432210      


Q ss_pred             ------CCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCC
Q 041602           76 ------GGRGGRGRGGGEDLKCYECGEPGHFARECRLR  107 (223)
Q Consensus        76 ------r~~~~~~~~~~~~~~~~~~g~~G~~~r~~~~~  107 (223)
                            ..-.+..+.......|+.|+..||.+++|+..
T Consensus        79 V~~pgg~pv~GS~rrp~~~~~C~~Cg~~GH~a~~C~~~  116 (148)
T 3ts2_A           79 VTGPGGVFCIGSERRPKGGDRCYNCGGLDHHAKECKLP  116 (148)
T ss_dssp             EESGGGCCCCCCTTSCCCSCCCTTTCCSSCCGGGCCSC
T ss_pred             ccccCCccccccccccCCCCcccEeCCccchhhhCCCC
Confidence                  00001112233356799999999999999864

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

Probab=94.71  E-value=0.046  Score=39.67  Aligned_cols=60  Identities=18%  Similarity=0.234  Sum_probs=44.4

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe-e------CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-R------RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~-~------~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      +|-|..||+.+||+++.+.++..=++.....+ +      ..-.-|||.|.+.+++..-.+..+|..
T Consensus        11 KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~   77 (97)
T 2l08_A           11 MVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYI   77 (97)
T ss_dssp             CEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEE
T ss_pred             eEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcE
Confidence            68899999999999987766654343322222 1      113478999999999999999998774

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

Probab=93.47  E-value=0.041  Score=42.09  Aligned_cols=26  Identities=15%  Similarity=0.083  Sum_probs=23.1

Q ss_pred             CCCCEEEEEEcCHHHHHHHHHHhCCC
Q 041602           36 RPPGYAFVEFDDRRDAVDAIRALDGK   61 (223)
Q Consensus        36 ~~rGfaFV~F~~~e~A~~Al~~lng~   61 (223)
                      ..+|||||+|.+.++|++|++.+++.
T Consensus        11 ~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A           11 TLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             SCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cccchhHHHHHHHHhHHHHHHhhccc
Confidence            46899999999999999999988754

>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A

Probab=92.95  E-value=0.17  Score=32.89  Aligned_cols=28  Identities=32%  Similarity=0.666  Sum_probs=22.9

Q ss_pred             CCCCCCCCCCCcCCCCCCCCCCCCCCCC
Q 041602           81 RGRGGGEDLKCYECGEPGHFARECRLRI  108 (223)
Q Consensus        81 ~~~~~~~~~~~~~~g~~G~~~r~~~~~~  108 (223)
                      .++.......|+.||..|||.++|+...
T Consensus        16 ~~~~~~~~~~C~~Cge~GH~ardCp~~~   43 (56)
T 1u6p_A           16 RRRSQLDRDQCAYCKEKGHWAKDCPKKP   43 (56)
T ss_dssp             CCSTTCCTTBCSSSCCBSSCGGGCTTCC
T ss_pred             cCCCCCCCCcceeCCCCCcccccCcCCc
Confidence            3445566788999999999999998863

>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1

Probab=91.80  E-value=0.4  Score=28.91  Aligned_cols=25  Identities=28%  Similarity=0.634  Sum_probs=21.2

Q ss_pred             CCCCCCCCcCCCCCCCCCCCCCCCC
Q 041602           84 GGGEDLKCYECGEPGHFARECRLRI  108 (223)
Q Consensus        84 ~~~~~~~~~~~g~~G~~~r~~~~~~  108 (223)
                      .......|+.|+..|||+++|+...
T Consensus         6 ~~~~~~~C~~Cgk~GH~ardCP~~~   30 (40)
T 1a6b_B            6 SQLDRDQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             CSCCSSSCSSSCCTTCCTTSCSSSC
T ss_pred             CCCCCCeeeECCCCCcchhhCcCCc
Confidence            3456788999999999999999864

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=91.30  E-value=0.65  Score=42.92  Aligned_cols=58  Identities=19%  Similarity=0.228  Sum_probs=45.6

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCCcEE
Q 041602            4 VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKNGWR   65 (223)
Q Consensus         4 LfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~g~~   65 (223)
                      ++|+ +|..+...+|.++|+.||.| .|..+.  ...|||.|.+.+.|..++++++.....+
T Consensus       443 l~v~-f~~~~~~~~i~~~fs~fg~v-~V~wid--dt~a~V~~~~~~~a~~~l~~~~~~~~~~  500 (507)
T 3d45_A          443 LHVT-FPKEWKTSDLYQLFSAFGNI-QISWID--DTSAFVSLSQPEQVQIAVNTSKYAESYR  500 (507)
T ss_dssp             EEEE-CCTTCCHHHHHHHGGGGCCC-EEEECS--SSEEEEECSCHHHHHHHHHHHTTCSSCE
T ss_pred             EEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEc--CCeEEEEECCHHHHHHHHHHHHhCCceE
Confidence            4554 88899999999999999964 444443  4579999999999999999996544333

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=90.67  E-value=0.21  Score=38.08  Aligned_cols=65  Identities=20%  Similarity=0.284  Sum_probs=44.7

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEE-EEEee------------------CCCCEEEEEEcCHHHHHHHHHHhCCCC-
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRS-VWVAR------------------RPPGYAFVEFDDRRDAVDAIRALDGKN-   62 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~-v~i~~------------------~~rGfaFV~F~~~e~A~~Al~~lng~~-   62 (223)
                      -|.|-+.|+.. ...+-+.|++||.|.+ +.+..                  .......|+|+++.+|++||. .||.. 
T Consensus         9 ~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~ii   86 (132)
T 3p3d_A            9 AILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAVF   86 (132)
T ss_dssp             EEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCEE
T ss_pred             EEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeEe
Confidence            46677887554 4566689999999866 21110                  124578999999999999996 66665 


Q ss_pred             -cEEEEEe
Q 041602           63 -GWRVELS   69 (223)
Q Consensus        63 -g~~V~v~   69 (223)
                       +.-|-+.
T Consensus        87 ~G~mIGV~   94 (132)
T 3p3d_A           87 NGVLLGVI   94 (132)
T ss_dssp             TTEECEEE
T ss_pred             CcEEEEEE
Confidence             5444443

>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

Probab=86.90  E-value=0.21  Score=37.88  Aligned_cols=35  Identities=14%  Similarity=0.136  Sum_probs=29.5

Q ss_pred             CCCCEEEEEEcCHHHHHHHHHHh-CCCC--cEEEEEeec
Q 041602           36 RPPGYAFVEFDDRRDAVDAIRAL-DGKN--GWRVELSHN   71 (223)
Q Consensus        36 ~~rGfaFV~F~~~e~A~~Al~~l-ng~~--g~~V~v~~~   71 (223)
                      +.+|+++|+|.+.++|++|++.| |+..  + .+.+..+
T Consensus        11 ~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a   48 (150)
T 2i2y_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDA   48 (150)
T ss_dssp             SSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETT
T ss_pred             cccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccc
Confidence            45899999999999999999999 8776  6 6666655

>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1

Probab=85.67  E-value=0.54  Score=25.38  Aligned_cols=19  Identities=37%  Similarity=1.132  Sum_probs=16.9

Q ss_pred             CCCcCCCCCCCCCCCCCCC
Q 041602           89 LKCYECGEPGHFARECRLR  107 (223)
Q Consensus        89 ~~~~~~g~~G~~~r~~~~~  107 (223)
                      ..|+.||..||++++|+..
T Consensus         3 ~~Cf~CG~~GH~ardC~~~   21 (26)
T 1dsq_A            3 PVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTCC
T ss_pred             CeeEeCCCCCcccccCCCc
Confidence            5699999999999999875

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	223
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-15
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-14
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	5e-14
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	6e-14
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-13
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-13
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-13
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-13
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-12
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	5e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	5e-12
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	9e-12
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-11
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-11
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-11
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	6e-11
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-11
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-11
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	8e-11
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-10
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-10
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-10
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-10
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-10
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-10
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	4e-10
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	5e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	6e-10
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	7e-10
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	7e-10
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-09
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-09
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-09
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-09
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	4e-09
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	5e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-08
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-08
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-08
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-08
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	2e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-08
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-08
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-05
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	4e-08
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	5e-08
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	7e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	1e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	1e-07
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-07
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-07
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-07
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	5e-07
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 9e-07
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	3e-06
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	4e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	4e-06
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	5e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	7e-06
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	1e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-05
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-05
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	3e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	3e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-05
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	5e-05
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-04
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	2e-04
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	4e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.001
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	0.001

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 66.5 bits (162), Expect = 3e-15
 Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 6/66 (9%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR------RPPGYAFVEFDDRRDAVDAI 55
          S++ V N+  + ++R++ + F  FG L++V + +         G+ FV+F  ++DA  A 
Sbjct: 9  SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 68

Query: 56 RALDGK 61
           AL   
Sbjct: 69 NALCHS 74

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.1 bits (156), Expect = 3e-14
 Identities = 25/86 (29%), Positives = 45/86 (52%), Gaps = 6/86 (6%)

Query: 2  SRVYVGNLDP-RVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          SRV++GNL+   V + D+E  F  +G +    V     G+AFV++ + R+A  A+   DG
Sbjct: 16 SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---HKGFAFVQYVNERNARAAVAGEDG 72

Query: 61 K--NGWRVELSHNSKGGGGRGGRGRG 84
          +   G  ++++  ++    R G   G
Sbjct: 73 RMIAGQVLDINLAAEPKVNRSGPSSG 98

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 63.0 bits (153), Expect = 5e-14
 Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIR 56
          + +YV NL   +++  L+  F  +G +    + R      P G AFV ++ R +A +AI 
Sbjct: 7  TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 66

Query: 57 ALDGK 61
          AL+  
Sbjct: 67 ALNNV 71

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 63.1 bits (153), Expect = 6e-14
 Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 2/79 (2%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK- 61
           +   NL   ++E +L++ F     +R V    +  G A++EF    DA   +    G  
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAE 77

Query: 62 -NGWRVELSHNSKGGGGRG 79
           +G  V L +  + GG RG
Sbjct: 78 IDGRSVSLYYTGEKGGTRG 96

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

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

 Score = 62.2 bits (151), Expect = 1e-13
 Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 5/63 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRAL 58
          +YVG+L P V+E  L ++F   G + S+ V R        GYA+V F    DA  A+  +
Sbjct: 3  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 59 DGK 61
          +  
Sbjct: 63 NFD 65

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.7 bits (152), Expect = 1e-13
 Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP--GYAFVEFDDRRDAVDAIRALDGK 61
          +Y+ NL  +++  ++ D F  +G +R + V   P   G A+V ++D  DA +A   L G 
Sbjct: 10 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 69

Query: 62 N 62
          N
Sbjct: 70 N 70

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

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

 Score = 62.3 bits (151), Expect = 2e-13
 Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFG-VLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          R+ V NL   V+   L   F  FG VL+ +   +     A +++ D   A  A  +LDG+
Sbjct: 9  RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 68

Query: 62 N 62
          N
Sbjct: 69 N 69

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

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

 Score = 61.5 bits (149), Expect = 2e-13
 Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 4/63 (6%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRAL 58
          ++ V NLD  VS+ D+++ F  FG L+   V      R  G A V F+ + DA+ A++  
Sbjct: 2  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 59 DGK 61
          +G 
Sbjct: 62 NGV 64

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

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

 Score = 60.4 bits (146), Expect = 6e-13
 Identities = 17/70 (24%), Positives = 30/70 (42%), Gaps = 3/70 (4%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
            VY G +   ++++ +   F  FG +  + V      Y+FV F     A  AI +++G 
Sbjct: 19 CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG-YSFVRFSTHESAAHAIVSVNGT 77

Query: 62 --NGWRVELS 69
             G  V+  
Sbjct: 78 TIEGHVVKCY 87

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 2e-12
 Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 4/73 (5%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          M+++Y+GNL P V+  DL   F    +  +  V     GYAFV++ D+  A+ AI  L G
Sbjct: 1  MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-LLKSGYAFVDYPDQNWAIRAIETLSG 59

Query: 61 K---NGWRVELSH 70
          K   +G  +E+ +
Sbjct: 60 KVELHGKIMEVDY 72

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

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

 Score = 58.4 bits (141), Expect = 3e-12
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 3/77 (3%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          SR++VGNL P ++E ++   F  +G    V++  +  G+ F+  + R  A  A   LD  
Sbjct: 9  SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-HKDKGFGFIRLETRTLAEIAKVELDNM 67

Query: 62 --NGWRVELSHNSKGGG 76
             G ++ +        
Sbjct: 68 PLRGKQLRVRFACHSAS 84

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.4 bits (141), Expect = 3e-12
 Identities = 20/84 (23%), Positives = 39/84 (46%), Gaps = 7/84 (8%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVW-----VARRPPGYAFVEFDDRRDAVDAIR 56
            +YVGNL    +E  + + F   G ++ +      + +   G+ FVE+  R DA +A+R
Sbjct: 8  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 57 ALDGK--NGWRVELSHNSKGGGGR 78
           ++G   +   +    ++    GR
Sbjct: 68 YINGTRLDDRIIRTDWDAGFKEGR 91

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.1 bits (140), Expect = 5e-12
 Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 5/73 (6%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
          S + V  L  + +E+DL++ F  FG +  V V +        G+ FV F +    V  + 
Sbjct: 9  SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 57 ALDGKNGWRVELS 69
               +G   +  
Sbjct: 69 QRHMIDGRWCDCK 81

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

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]

 Score = 57.8 bits (139), Expect = 5e-12
 Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVW-----VARRPPGYAFVEFDDRRDAVDAIR 56
          + +YV  L   +++++LE  F  +G + +       V     G  F+ FD R +A +AI+
Sbjct: 7  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 57 ALDGK 61
           L+G+
Sbjct: 67 GLNGQ 71

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.4 bits (138), Expect = 9e-12
 Identities = 15/68 (22%), Positives = 26/68 (38%), Gaps = 7/68 (10%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFG-------VLRSVWVARRPPGYAFVEFDDRRDAVDA 54
           R+++G +       ++ +E            V  S     +  G+AFVE++  R A  A
Sbjct: 2  CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 55 IRALDGKN 62
           R L    
Sbjct: 62 RRKLMPGR 69

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 3e-11
 Identities = 12/69 (17%), Positives = 25/69 (36%), Gaps = 9/69 (13%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRP-----PGYAFVEFDDRRDAVDAIRA 57
          +++VG L P   E  + + F  FG + S+ +          G+ F+ F +       +  
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 58 ----LDGKN 62
              +    
Sbjct: 61 KYHNVGLSK 69

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 55.0 bits (132), Expect = 5e-11
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 7/76 (9%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIR 56
          + + V  L   +++R+L   FR  G + +  + R        GYAFV+F    D+  AI+
Sbjct: 3  TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

Query: 57 ALDGK--NGWRVELSH 70
           L+G      R+++S+
Sbjct: 63 VLNGITVRNKRLKVSY 78

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.6 bits (131), Expect = 5e-11
 Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 6/71 (8%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRP-----PGYAFVEFDDRRDAVDAIRA 57
          ++++G L    +++DL+D F  FG +    +   P      G+ FV F +       +  
Sbjct: 1  KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 58 LDGK-NGWRVE 67
           + K NG  ++
Sbjct: 61 KEHKLNGKVID 71

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.5 bits (133), Expect = 6e-11
 Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 1/58 (1%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          V  G L   VS   L       G++ ++ +      Y+F  +    ++  A   L+GK
Sbjct: 23 VANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAYVTLNGK 79

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.7 bits (131), Expect = 6e-11
 Identities = 17/81 (20%), Positives = 32/81 (39%), Gaps = 12/81 (14%)

Query: 5  YVGNLDPRVSERDLEDEFRMFGVL--------RSVWVARRPPGYAFVEFDDRRDAVDAIR 56
          ++ NL+   +E  L+  F   G +        ++        G+ FVE+     A  A++
Sbjct: 2  FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 57 ALDGK--NGW--RVELSHNSK 73
           L G   +G    V +S  + 
Sbjct: 62 QLQGHTVDGHKLEVRISERAT 82

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.6 bits (131), Expect = 7e-11
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 7/80 (8%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSV-----WVARRPPGYAFVEFDDRRDAVDAIRA 57
          ++++G L   +++  +++    FG L++             GYAF E+ D      AI  
Sbjct: 3  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 58 LDGK--NGWRVELSHNSKGG 75
          L+G      ++ +   S G 
Sbjct: 63 LNGMQLGDKKLLVQRASVGA 82

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.2 bits (130), Expect = 8e-11
 Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 9/69 (13%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRP-----PGYAFVEFDDRRDAVDAIRA 57
          ++++G L  + ++  L + F  FG ++   V R P      G+ FV F D+      +  
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 58 ----LDGKN 62
              LD K 
Sbjct: 62 SRHELDSKT 70

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 1e-10
 Identities = 17/84 (20%), Positives = 33/84 (39%), Gaps = 4/84 (4%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRA---L 58
          S V+VG     ++E +L + F  +G +  V++ +    +AFV F D + A         +
Sbjct: 6  SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLII 65

Query: 59 DGKNGWRVELSHNSKGGGGRGGRG 82
           G +   +  +            G
Sbjct: 66 KGIS-VHISNAEPKHNSNSGPSSG 88

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.9 bits (129), Expect = 1e-10
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 7/73 (9%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWV-----ARRPPGYAFVEFDDRRDAVDAIR 56
            + V  L    +ERDL + F  +G +  V +     +RR  G+AFV F++  DA +A  
Sbjct: 10 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 57 ALDGK--NGWRVE 67
            +G   +G R+ 
Sbjct: 70 RANGMELDGRRIR 82

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (129), Expect = 1e-10
 Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 12/83 (14%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFG------VLRSVWVARRPPGYAFVEFDDRRDAVDAIRA 57
          +++GNLDP + E+ L D F  FG       +          GYAF+ F     +  AI A
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 58 LDGK--NGWRVELSH----NSKG 74
          ++G+      + +S+    +SKG
Sbjct: 61 MNGQYLCNRPITVSYAFKKDSKG 83

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

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]

 Score = 53.6 bits (128), Expect = 2e-10
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 7/76 (9%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFG-----VLRSVWVARRPPGYAFVEFDDRRDAVDAIR 56
          + + V  L   +++ +    F   G      L    +  +  GY FV + D +DA  AI 
Sbjct: 3  TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 57 ALDGK--NGWRVELSH 70
           L+G       +++S+
Sbjct: 63 TLNGLRLQTKTIKVSY 78

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

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

 Score = 53.5 bits (128), Expect = 2e-10
 Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 5/75 (6%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDAVDAIRA 57
          +  +++ NLD  +  + L D F  FG + S  V        GY FV F+ +  A  AI  
Sbjct: 8  VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 67

Query: 58 LDGK--NGWRVELSH 70
          ++G   N  +V +  
Sbjct: 68 MNGMLLNDRKVFVGR 82

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.1 bits (127), Expect = 3e-10
 Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRS-----VWVARRPPGYAFVEFDDRRDAVDAIRA 57
           VYVG LD +VSE  L + F   G + +       V  +  GY FVEF    DA  AI+ 
Sbjct: 11 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 70

Query: 58 LDGK--NGWRVELSH 70
          +D     G  + ++ 
Sbjct: 71 MDMIKLYGKPIRVNK 85

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

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

 Score = 52.7 bits (126), Expect = 4e-10
 Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRP---PGYAFVEFDDRRDAVDAIRALD 59
           +YVGNL   V+E  +   F   G  +S  +         Y FVEF + RDA  A+ A++
Sbjct: 10 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 69

Query: 60 GK--NGWRVELSH 70
          G+   G  V+++ 
Sbjct: 70 GRKILGKEVKVNW 82

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 5e-10
 Identities = 34/81 (41%), Positives = 49/81 (60%), Gaps = 6/81 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR--PPGYAFVEFDDRRDAVDAIRALD 59
           R+YVGNL P +  +D+ED F  +G +R + +  R   P +AFVEF+D RDA DA+   D
Sbjct: 15 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRD 74

Query: 60 GK--NGW--RVELSHNSKGGG 76
          G   +G+  RVE   + +G G
Sbjct: 75 GYDYDGYRLRVEFPRSGRGTG 95

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.8 bits (126), Expect = 6e-10
 Identities = 27/91 (29%), Positives = 37/91 (40%), Gaps = 8/91 (8%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIR 56
           R++V NL    SE DLE  F  +G L  +          P G+AFV F     AV A  
Sbjct: 9  GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 57 ALDGK--NGWRVELSH-NSKGGGGRGGRGRG 84
           +DG+   G  + +     K    + G   G
Sbjct: 69 EVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (124), Expect = 7e-10
 Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 7/74 (9%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
           +YVG L   V ++ L   F  FG +  + +       +  G+AFVEF+   DA  AI  
Sbjct: 7  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 58 LDGK--NGWRVELS 69
          ++     G  + ++
Sbjct: 67 MNESELFGRTIRVN 80

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (124), Expect = 7e-10
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAI 55
           + + V NL     E DL++ FR FG +  +++A+        G+AF+ F  R DA  AI
Sbjct: 8  NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 67

Query: 56 RALDGK--NGWRVELS 69
            + G   +   + + 
Sbjct: 68 AGVSGFGYDHLILNVE 83

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 1e-09
 Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 6/71 (8%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPG-----YAFVEFDDRRDAVDAIRA 57
          ++++G L    ++  L   F  +G L    V R P       + FV +    +   A+ A
Sbjct: 8  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 58 LDGK-NGWRVE 67
             K +G  VE
Sbjct: 68 RPHKVDGRVVE 78

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.2 bits (122), Expect = 1e-09
 Identities = 29/74 (39%), Positives = 41/74 (55%), Gaps = 6/74 (8%)

Query: 1  MSRV---YVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRA 57
          MS V   YV NL    SE  +E EF          V ++   YAFV F +R DAV+A++A
Sbjct: 5  MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-KKIRDYAFVHFSNREDAVEAMKA 63

Query: 58 LDGK--NGWRVELS 69
          L+GK  +G  +E++
Sbjct: 64 LNGKVLDGSPIEVT 77

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 1e-09
 Identities = 18/73 (24%), Positives = 30/73 (41%), Gaps = 6/73 (8%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP-----GYAFVEFDDRRDAVDAI 55
            ++++G L    +E  L + +  +G L    V R P      G+ FV F    +   A+
Sbjct: 20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 79

Query: 56 RALDGK-NGWRVE 67
           A     +G  VE
Sbjct: 80 AARPHSIDGRVVE 92

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.2 bits (122), Expect = 2e-09
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA---RRPPGYAFVEFDDRRDAVDAIRALD 59
          R++V N+  R  + DL   F  FG +  V +    R   G+ FV F++  DA  A   L 
Sbjct: 13 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLH 72

Query: 60 GK--NGWRVELSH 70
          G    G ++E+++
Sbjct: 73 GTVVEGRKIEVNN 85

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.7 bits (118), Expect = 4e-09
 Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 8/72 (11%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRA 57
          +++VG L    +  D++  F  FG +    +          G+ FV F+      + +  
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIV-EKVCE 59

Query: 58 LDGK--NGWRVE 67
          +     N   VE
Sbjct: 60 IHFHEINNKMVE 71

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 4e-09
 Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 5/64 (7%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP-----GYAFVEFDDRRDAVDAIRAL 58
          +Y+  L P  +++DL    + +G + S             GY FV+FD    A  A+ AL
Sbjct: 1  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 59 DGKN 62
              
Sbjct: 61 KASG 64

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

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

 Score = 49.8 bits (118), Expect = 5e-09
 Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 15/83 (18%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-------------RPPGYAFVEFDDR 48
          S +YV  L+  V+  DL D F+  GV++                   +P G A V ++D 
Sbjct: 9  SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 68

Query: 49 RDAVDAIRALDGK--NGWRVELS 69
            A  A+   DGK   G ++++S
Sbjct: 69 PTAKAAVEWFDGKDFQGSKLKVS 91

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 1e-08
 Identities = 24/93 (25%), Positives = 42/93 (45%), Gaps = 7/93 (7%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFG-----VLRSVWVARRPPGYAFVEFDDRRDAVDAI 55
           +  V+VGN+    +E  L+D F   G      L       +P GY F E+ D+  A+ A+
Sbjct: 8   LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67

Query: 56  RALDGK--NGWRVELSHNSKGGGGRGGRGRGGG 86
           R L+G+  +G  + + + +        +  G G
Sbjct: 68  RNLNGREFSGRALRVDNAASEKNKEELKSLGTG 100

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 1e-08
 Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 6/65 (9%)

Query: 3  RVYVGNLDPRVSERDLEDE----FRMFGVLRS--VWVARRPPGYAFVEFDDRRDAVDAIR 56
           +Y+ NL+ ++ + +L+      F  FG +    V  + +  G AFV F +   A +A+R
Sbjct: 5  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 57 ALDGK 61
          ++ G 
Sbjct: 65 SMQGF 69

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.0 bits (116), Expect = 1e-08
 Identities = 20/91 (21%), Positives = 34/91 (37%), Gaps = 9/91 (9%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
           +++VG L    ++  L   F  FG +    V       +  GY FV   DR  A  A + 
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 58  LDGK-NGWRVELSHNSKGG---GGRGGRGRG 84
            +   +G +  ++    G      + G   G
Sbjct: 72  PNPIIDGRKANVNLAYLGAKPRSLQTGFAIG 102

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 48.6 bits (115), Expect = 1e-08
 Identities = 17/81 (20%), Positives = 40/81 (49%), Gaps = 8/81 (9%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIR 56
            ++V ++     E +++++F  +G ++++ +          GYA VE++  + A+ A  
Sbjct: 8  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 57 ALDGK--NGWRVELSH-NSKG 74
          AL+G    G  +++     KG
Sbjct: 68 ALNGAEIMGQTIQVDWCFVKG 88

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 1e-08
 Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIR 56
          + +++ +L     ++DL   F  FG + S  V           + FV +D+   A  AI+
Sbjct: 19 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 78

Query: 57 ALDGK 61
          +++G 
Sbjct: 79 SMNGF 83

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

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

 Score = 48.2 bits (114), Expect = 2e-08
 Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 7/75 (9%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFG-----VLRSVWVARRPPGYAFVEFDDRRDAVDAIRA 57
          +++VG L    +E+ LE  F  +G     V+      +R  G+ FV F++  DA DA+ A
Sbjct: 7  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 58 LDGK--NGWRVELSH 70
          ++GK  +G ++ +  
Sbjct: 67 MNGKSVDGRQIRVDQ 81

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

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

 Score = 48.3 bits (114), Expect = 2e-08
 Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 1/58 (1%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          V+V  L   V E DL +    FG +  V +       A VEF++   A + +      
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMM-MPFKRQALVEFENIDSAKECVTFAADV 74

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.1 bits (114), Expect = 2e-08
 Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 7/81 (8%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          +R++VG L P  S   L  EF  FG +R++    +   +A+++++    A  A   + G 
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDH-VKGDSFAYIQYESLDAAQAACAKMRGF 76

Query: 62 --NGW----RVELSHNSKGGG 76
             G     RV+ + +    G
Sbjct: 77 PLGGPDRRLRVDFAKSGPSSG 97

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 3e-08
 Identities = 21/75 (28%), Positives = 31/75 (41%), Gaps = 8/75 (10%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRA 57
           V+   L  R+  RDLED F   G +R V +       R  G A+VEF + +        
Sbjct: 20 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV-PLAIG 78

Query: 58 LDGK--NGWRVELSH 70
          L G+   G  + +  
Sbjct: 79 LTGQRLLGVPIIVQA 93

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.2 bits (116), Expect = 4e-08
 Identities = 25/137 (18%), Positives = 41/137 (29%), Gaps = 7/137 (5%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRA 57
           ++++G L    ++  L   F  +G L    V      +R  G+ FV +    +   A+ A
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 58  LDGKNGWRVELSHNSKGGGGRGGRGRGGGEDLKCYECGEPGHFARECRLRIGSRGLGSGR 117
              K   RV     +        +  G    +K    G       E  LR      G   
Sbjct: 68  RPHKVDGRVVEPKRAV--SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 125

Query: 118 RRSPSPRRRRSPSYGYG 134
                  R      G+ 
Sbjct: 126 VIEIMTDRGSGKKRGFA 142

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.9 bits (97), Expect = 1e-05
 Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 8/76 (10%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAI 55
           + +++VG +     E  L D F  +G +  + +       +  G+AFV FDD       +
Sbjct: 97  VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156

Query: 56  RALDGK--NGWRVELS 69
                   NG   E+ 
Sbjct: 157 -IQKYHTVNGHNCEVR 171

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

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

 Score = 47.8 bits (113), Expect = 4e-08
 Identities = 23/89 (25%), Positives = 38/89 (42%), Gaps = 5/89 (5%)

Query: 2  SRVYVGNLDPR-VSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          S + V NL+P  V+ + L   F ++G ++ V +       A V+  D   A  A+  L+G
Sbjct: 3  SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNG 62

Query: 61 K----NGWRVELSHNSKGGGGRGGRGRGG 85
                  R+ LS +      R G+   G
Sbjct: 63 HKLHGKPIRITLSKHQNVQLPREGQEDQG 91

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 48.4 bits (114), Expect = 5e-08
 Identities = 22/91 (24%), Positives = 34/91 (37%), Gaps = 8/91 (8%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPG-----YAFVEFDDRRDAVDAIRA 57
            + V  +   V E  L   F  +G + SV +           Y FV+F     A  AI  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 58  LDGK--NGWRVELSHNSKGGGGRGGRGRGGG 86
           L+G      R++++  +  G  R G     G
Sbjct: 104 LNGFNILNKRLKVAL-AASGHQRPGIAGAVG 133

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.1 bits (111), Expect = 7e-08
 Identities = 11/72 (15%), Positives = 20/72 (27%), Gaps = 6/72 (8%)

Query: 2  SRVYVGNLDPRV-----SERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIR 56
          S +     +  V     +    E  FR +    +     +      + F +   A DA  
Sbjct: 6  SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQY-FKSFKRVRINFSNPLSAADARL 64

Query: 57 ALDGKNGWRVEL 68
           L        E+
Sbjct: 65 RLHKTEFLGKEM 76

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 1e-07
 Identities = 13/63 (20%), Positives = 23/63 (36%), Gaps = 4/63 (6%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGV----LRSVWVARRPPGYAFVEFDDRRDAVDAIRAL 58
           +Y+ NL   + E++LE+  + FG           +    G  F   +        I   
Sbjct: 20 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 79

Query: 59 DGK 61
          +GK
Sbjct: 80 NGK 82

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 1e-07
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 5/70 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          + +YV   D  ++   L   F  FG +  + +   P   AFV ++    A  A+  L+G 
Sbjct: 6  NTLYVYGED--MTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGT 62

Query: 62 --NGWRVELS 69
               +++++
Sbjct: 63 QVESVQLKVN 72

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

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

 Score = 45.9 bits (108), Expect = 1e-07
 Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 6/77 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEF-RMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG 60
          + +++ N+ P VSE DL+  F    GV++     ++    A ++     +AV A+  L  
Sbjct: 11 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHN 70

Query: 61 KNGW-----RVELSHNS 72
           +       RV  S ++
Sbjct: 71 HDLGENHHLRVSFSKST 87

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 45.6 bits (107), Expect = 1e-07
 Identities = 10/64 (15%), Positives = 26/64 (40%), Gaps = 5/64 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLR-----SVWVARRPPGYAFVEFDDRRDAVDAIRA 57
           +++ N  P  ++R++ D  +   V+                +A+++   + DA   +  
Sbjct: 3  TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 58 LDGK 61
          L+G 
Sbjct: 63 LNGL 66

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.9 bits (108), Expect = 1e-07
 Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 13/80 (16%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----------RPPGYAFVEFDDRRDAV 52
          R+YVGN+   ++E  + D F     L  +  A           +   +AF+EF    +  
Sbjct: 3  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 53 DAIRALDGK--NGWRVELSH 70
           A+   DG    G  +++  
Sbjct: 63 QAMA-FDGIIFQGQSLKIRR 81

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 2e-07
 Identities = 20/74 (27%), Positives = 31/74 (41%), Gaps = 8/74 (10%)

Query: 1  MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPG-----YAFVEFDDRRDAVDAI 55
          + +++VG +     E  L D F  +G +  + +           +AFV FDD  D+VD I
Sbjct: 2  VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKI 60

Query: 56 RALDGK--NGWRVE 67
                  NG   E
Sbjct: 61 VIQKYHTVNGHNCE 74

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.2 bits (106), Expect = 3e-07
 Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 5/64 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRA 57
           V++ NL     E  L +  + FG L+ V V          G AF +F  +  A   + A
Sbjct: 10 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 69

Query: 58 LDGK 61
             +
Sbjct: 70 ASLE 73

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 5e-07
 Identities = 15/74 (20%), Positives = 27/74 (36%), Gaps = 6/74 (8%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          S + V NL    + +++ D  + + +        R    AFV   +   A +AI+     
Sbjct: 6  SGILVKNLPQDSNCQEVHDLLKDYDLKYCYV--DRNKRTAFVTLLNGEQAQNAIQMFHQY 63

Query: 62 --NG--WRVELSHN 71
             G    V+L   
Sbjct: 64 SFRGKDLIVQLQPT 77

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 9e-07
 Identities = 16/77 (20%), Positives = 27/77 (35%), Gaps = 8/77 (10%)

Query: 1   MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPG----YAFVEFDDRRDAVDAIR 56
           +S V +        E    +    +G +  + V            +V+F    DA  A+ 
Sbjct: 27  VSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVI 86

Query: 57  ALDGK--NGW--RVELS 69
            L+ +  NG     ELS
Sbjct: 87  DLNNRWFNGQPIHAELS 103

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

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 = 43.5 bits (102), Expect = 1e-06
 Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 7/75 (9%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIR 56
          + + V N+   VS  ++ D F  + V+      +      P G A V F+ R +A  A+ 
Sbjct: 10 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 57 ALDGK--NGWRVELS 69
           L+ +     +V+L 
Sbjct: 70 DLNDRPIGSRKVKLV 84

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

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

 Score = 41.6 bits (97), Expect = 3e-06
 Identities = 11/67 (16%), Positives = 21/67 (31%), Gaps = 4/67 (5%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPG----YAFVEFDDRRDAVDAIRAL 58
           VY+       +  D+++     G + ++ + R          FV FD    A   +   
Sbjct: 8  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 67

Query: 59 DGKNGWR 65
            K    
Sbjct: 68 GQKYKET 74

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.8 bits (98), Expect = 4e-06
 Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 3/59 (5%)

Query: 15 ERDLEDEFRMFGVLRSVWVARRPP-GYAFVEFDDRRDAVDAIRALDGK--NGWRVELSH 70
            DL  E   FG +R + +  R P G A V F D  +A   I+ LDG+   G ++    
Sbjct: 33 REDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 91

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

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

 Score = 42.1 bits (98), Expect = 4e-06
 Identities = 11/60 (18%), Positives = 24/60 (40%), Gaps = 2/60 (3%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRR-DAVDAIRALDGKN 62
           + G+LD +    DL   F   G ++ +    R      + F ++  +A+   +  +  N
Sbjct: 14 KFSGDLDDQTCREDLHILFSNHGEIKWIDFV-RGAKEGIILFKEKAKEALGKAKDANNGN 72

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.4 bits (96), Expect = 5e-06
 Identities = 23/85 (27%), Positives = 29/85 (34%), Gaps = 6/85 (7%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK- 61
          RV V  L P  S +DL+D  R  G     +      G   VEF  + D   A+R LD   
Sbjct: 2  RVVVSGLPPSGSWQDLKDHMREAG--DVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTK 59

Query: 62 ---NGWRVELSHNSKGGGGRGGRGR 83
             +            G      GR
Sbjct: 60 FRSHEGETAYIRVKVDGPRSPSYGR 84

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.3 bits (96), Expect = 7e-06
 Identities = 23/84 (27%), Positives = 31/84 (36%), Gaps = 4/84 (4%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK- 61
          RV V  L P  S +DL+D  R  G     +   +  G   VE+  + D   A+R LD   
Sbjct: 17 RVLVSGLPPSGSWQDLKDHMREAG--DVCYADVQKDGMGMVEYLRKEDMEYALRKLDDTK 74

Query: 62 -NGWRVELSHNSKGGGGRGGRGRG 84
                E S+         G   G
Sbjct: 75 FRSHEGETSYIRVYPERSSGPSSG 98

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 1e-05
 Identities = 14/88 (15%), Positives = 30/88 (34%), Gaps = 10/88 (11%)

Query: 3   RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFD----DRRDAVDAIRAL 58
             ++GNL   V+E  +++ FR   +                 F     +  D++ +  +L
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 76

Query: 59  DGK--NGWRVELSH----NSKGGGGRGG 80
           + +     R+ +        K  G   G
Sbjct: 77  NEESLGNKRIRVDVADQAQDKDSGPSSG 104

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.3 bits (94), Expect = 1e-05
 Identities = 8/69 (11%), Positives = 19/69 (27%), Gaps = 6/69 (8%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIR----A 57
          + V V       +   L  +F  +G +    +      +  + +  +  A  A+      
Sbjct: 5  TWVTVFGFPQASASYILL-QFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALSKDGRI 62

Query: 58 LDGKNGWRV 66
                  V
Sbjct: 63 FGESIMIGV 71

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

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

 Score = 39.8 bits (92), Expect = 2e-05
 Identities = 17/80 (21%), Positives = 35/80 (43%), Gaps = 13/80 (16%)

Query: 3  RVYVGNLDPRVSERDL---EDEFRMFGVLRSVWVAR--------RPPGYAFVEFDDRRDA 51
           V+V  L  R+++ ++    + F  FG +  V +           P   A+V +    DA
Sbjct: 10 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 52 VDAIRALDGK--NGWRVELS 69
          + AI+ ++    +G  ++ S
Sbjct: 70 LRAIQCVNNVVVDGRTLKAS 89

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.2 bits (93), Expect = 2e-05
 Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 5/65 (7%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIR 56
            +Y+ NL PRV+ERDL   F  F   +   +  R       G AF+ F ++  A  A+ 
Sbjct: 19 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 57 ALDGK 61
           ++G 
Sbjct: 79 LVNGY 83

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.7 bits (89), Expect = 3e-05
 Identities = 17/73 (23%), Positives = 28/73 (38%), Gaps = 4/73 (5%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPP---GYAFVEFDDRRDAVDAIRAL 58
          + V V NL    ++  +   F+  G +  V VA        +A +EF     A+ AI   
Sbjct: 1  TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKT 60

Query: 59 DGK-NGWRVELSH 70
                  + +SH
Sbjct: 61 HKVVGQNEIIVSH 73

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 39.1 bits (90), Expect = 3e-05
 Identities = 16/61 (26%), Positives = 23/61 (37%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
            +++ NL    +E  L   F  F   + V +       AFVEF     +  A  AL G 
Sbjct: 9  QILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGF 68

Query: 62 N 62
           
Sbjct: 69 K 69

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.5 bits (91), Expect = 4e-05
 Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 1/67 (1%)

Query: 2  SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK 61
          + +   NL       ++++ F  FG L  V +       A VEF +  +A  A R L   
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-PEGGITAIVEFLEPLEARKAFRHLAYS 69

Query: 62 NGWRVEL 68
              V L
Sbjct: 70 KFHHVPL 76

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.1 bits (90), Expect = 5e-05
 Identities = 14/87 (16%), Positives = 28/87 (32%), Gaps = 8/87 (9%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARR-----PPGYAFVEFDDRRDAVDAIRAL 58
           ++ N+   +++ D+        V  +             G A V+F +  DA  + R L
Sbjct: 11 AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-L 69

Query: 59 DGK--NGWRVELSHNSKGGGGRGGRGR 83
            K  NG    +   +        +  
Sbjct: 70 HRKKLNGREAFVHVVTLEDMREIEKNP 96

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 36.6 bits (84), Expect = 2e-04
 Identities = 13/76 (17%), Positives = 29/76 (38%), Gaps = 10/76 (13%)

Query: 3  RVYVGNLDPRV-SERDLEDEFRMFGVLRSVWVA------RRPPGYAFVEFDDRRDAVDAI 55
           + + NL   +  E  L + F  FG +  + +             AF+ F+++  A  A+
Sbjct: 6  EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 56 RALDGK--NGWRVELS 69
            ++        + +S
Sbjct: 66 -QMNRSLLGNREISVS 80

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 35.6 bits (82), Expect = 2e-04
 Identities = 10/18 (55%), Positives = 14/18 (77%)

Query: 88  DLKCYECGEPGHFARECR 105
           ++KC+ CG+ GH AR CR
Sbjct: 1   NVKCFNCGKEGHTARNCR 18

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (83), Expect = 4e-04
 Identities = 10/75 (13%), Positives = 26/75 (34%), Gaps = 7/75 (9%)

Query: 3  RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN 62
           +++  L   V+E ++      FG   +  +  +    AF+E      A+  +       
Sbjct: 10 VLHIRKLPGEVTETEVIALGLPFGK-VTNILMLKGKNQAFLELATEEAAITMVNYYSAVT 68

Query: 63 GW------RVELSHN 71
                   ++ S++
Sbjct: 69 PHLRNQPIYIQYSNH 83

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (80), Expect = 0.001
 Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 7/63 (11%)

Query: 6  VGNLDPRVSERDLEDEFRMFGVLRSVWVAR-------RPPGYAFVEFDDRRDAVDAIRAL 58
          + + +      D+ DE   +G+++S+ + R          G  FVEF    D   A++ L
Sbjct: 19 LDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGL 78

Query: 59 DGK 61
           G+
Sbjct: 79 TGR 81

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.5 bits (78), Expect = 0.001
 Identities = 12/72 (16%), Positives = 22/72 (30%), Gaps = 6/72 (8%)

Query: 4  VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKNG 63
          + +  L   V+ +++ D    +          +  G AFV   +   A  AI        
Sbjct: 1  ILIRGLPGDVTNQEVHDLLSDYE--LKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRL 58

Query: 64 W----RVELSHN 71
                V+L   
Sbjct: 59 RERELSVQLQPT 70

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	223
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.75
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.74
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.73
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.72
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.72
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.71
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.71
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.71
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.71
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.71
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.7
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.7
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.7
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.7
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.7
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.7
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.7
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.69
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.69
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.69
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.69
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.69
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.69
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.69
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.69
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.68
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.68
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.68
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.68
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.68
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.68
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.68
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.68
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.68
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.67
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.67
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.67
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.67
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.67
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.66
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.66
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.66
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.66
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.66
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.65
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.65
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.65
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.64
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.64
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.64
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.64
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.63
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.63
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.63
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.63
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.62
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.62
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.61
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.61
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.61
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.6
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.6
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.6
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.6
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.59
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.58
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.58
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.57
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.56
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.53
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.52
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.5
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.5
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.48
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.48
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.47
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.47
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.46
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.46
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.36
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.35
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.32
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.29
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.28
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.1
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.89
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.36
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.17
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	95.58
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	93.49
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	81.9

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.75  E-value=2.2e-18  Score=121.19  Aligned_cols=72  Identities=29%  Similarity=0.499  Sum_probs=65.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||+++|+++|+++|++||+|..+.++.     .++|||||+|.+.++|++|++.||+..  +..|.+.++++
T Consensus         3 t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           3 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            6899999999999999999999999999999864     358899999999999999999999998  77777777754

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

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=99.74  E-value=4.5e-18  Score=119.44  Aligned_cols=72  Identities=25%  Similarity=0.433  Sum_probs=64.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++++++|+++|++||+|..|.++.     .++|||||+|.++++|++|++.||+..  +..|.+.+++|
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            6899999999999999999999999999999874     447899999999999999999999987  77777777654

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=1.2e-17  Score=121.59  Aligned_cols=73  Identities=33%  Similarity=0.499  Sum_probs=64.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||+++|+++|+++|++||+|..|.|+.     .++|||||+|.+.++|++||+.||+..  +..|.|..+..+
T Consensus         9 ~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~~   88 (99)
T d1whwa_           9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIK   88 (99)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCC
T ss_pred             CEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            5899999999999999999999999999999863     468999999999999999999999987  666666666543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.2e-17  Score=120.45  Aligned_cols=71  Identities=25%  Similarity=0.470  Sum_probs=63.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      +||||+|||.++|+++|+++|++||+|.+|.++.     .++|||||+|.+.++|++|++.||+..  +..|.|.++.
T Consensus         8 ~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~   85 (93)
T d1h2vz_           8 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA   85 (93)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            7999999999999999999999999999999975     346899999999999999999999987  6666666653

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

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

Probab=99.72  E-value=8.9e-18  Score=117.79  Aligned_cols=71  Identities=34%  Similarity=0.549  Sum_probs=64.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||+++||++|+++|++||+|..|+|+.     .++|||||+|.++++|++|++.|||..  +..|.+.++.
T Consensus         1 aslfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           1 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            4799999999999999999999999999999975     346899999999999999999999997  7777777764

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=5.5e-18  Score=119.02  Aligned_cols=73  Identities=34%  Similarity=0.505  Sum_probs=63.6

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC---cEEEEEeeccCC
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN---GWRVELSHNSKG   74 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~---g~~V~v~~~~~~   74 (223)
                      |++|||+|||.++|+++|+++|++||.|..+.+.. ++|||||+|.+.++|++|++.|||..   |..|.|.++.++
T Consensus         1 mn~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~-~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k   76 (80)
T d2cqha1           1 MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   76 (80)
T ss_dssp             CCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec-ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCc
Confidence            78999999999999999999999999987776654 48999999999999999999999863   777777766553

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

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

Probab=99.71  E-value=1.3e-17  Score=119.29  Aligned_cols=73  Identities=27%  Similarity=0.470  Sum_probs=65.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee---CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~---~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||+++|+++|+++|++||+|..+.|+.   .++|||||+|++.++|++|++.|||..  +..|.|..+.++
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           9 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            5899999999999999999999999999999974   358999999999999999999999987  777777776543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.8e-17  Score=119.57  Aligned_cols=73  Identities=34%  Similarity=0.471  Sum_probs=64.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.     .++|||||+|.+.++|++|++.||+..  +..|.|.++.++
T Consensus        10 ~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~   89 (93)
T d1x5ua1          10 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAH   89 (93)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTT
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCC
Confidence            6899999999999999999999999999999864     468999999999999999999999997  666666666544

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=1.8e-17  Score=117.28  Aligned_cols=71  Identities=24%  Similarity=0.540  Sum_probs=63.4

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeEEEEEee--------CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            4 VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR--------RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         4 LfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~--------~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      |||+|||.++|+++|+++|++||+|..|.|+.        .++|||||+|.+.++|++|++.||+..  +..|.|.++.+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            79999999999999999999999999999864        237899999999999999999999987  77777777654


Q ss_pred             C
Q 041602           74 G   74 (223)
Q Consensus        74 ~   74 (223)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.71  E-value=1.4e-17  Score=116.74  Aligned_cols=72  Identities=15%  Similarity=0.361  Sum_probs=62.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe-----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~-----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      |||||+|||+++|+++|+++|++||+|..+.++     +.++|||||+|.+.++|++|++.||+..  +..|.+..++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            699999999999999999999999999877664     3568999999999999999999999998  77777766543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=3.3e-17  Score=118.47  Aligned_cols=72  Identities=40%  Similarity=0.776  Sum_probs=64.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee--CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR--RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~--~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||+++|+++|+++|++||+|..+.+..  .+++||||+|++.++|++||+.||+..  +..|+|.+++.
T Consensus        15 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~   90 (95)
T d1x4aa1          15 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   90 (95)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccC
Confidence            5899999999999999999999999999998864  468999999999999999999999998  77777777654

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=3.8e-17  Score=119.95  Aligned_cols=73  Identities=25%  Similarity=0.431  Sum_probs=63.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC-cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN-GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~-g~~V~v~~~~~~   74 (223)
                      ++|||+|||+.+||++|+++|++||+|.+|.|+.     .++|||||+|.+.++|++||+.+|+.. |..|.|..+...
T Consensus        11 ~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~~a~~~   89 (103)
T d2cqda1          11 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLG   89 (103)
T ss_dssp             SEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEESTTT
T ss_pred             cEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEcCCC
Confidence            6899999999999999999999999999999964     468999999999999999999888644 777777666543

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.70  E-value=3.3e-17  Score=118.91  Aligned_cols=71  Identities=25%  Similarity=0.506  Sum_probs=65.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++++++|+++|++||+|.+|+++.+ +|||||+|.+.++|++|++.||+..  +..|.+.++++
T Consensus        19 ~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~-kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~   91 (96)
T d1x4ga1          19 CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             CEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            58999999999999999999999999999999855 8999999999999999999999997  77777777644

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

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=99.70  E-value=2.1e-17  Score=117.25  Aligned_cols=61  Identities=28%  Similarity=0.587  Sum_probs=57.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ++|||+|||+++|+++|+++|++||+|.+++++.     .++|||||+|.+.++|++|++.|||..
T Consensus         7 ~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~   72 (85)
T d1fxla2           7 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQK   72 (85)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCE
Confidence            5899999999999999999999999999999974     357899999999999999999999887

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

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

Probab=99.70  E-value=6.2e-17  Score=119.26  Aligned_cols=71  Identities=27%  Similarity=0.390  Sum_probs=63.1

Q ss_pred             cEEEEecCCC-CCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDP-RVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~-~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+||++ .+|+++|+++|++||+|..|.|+.+.+|||||+|++.++|++|++.||+..  +..|.+.++.
T Consensus         3 ~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           3 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             SEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            5899999965 599999999999999999999998889999999999999999999999997  5555555553

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=6e-17  Score=116.66  Aligned_cols=73  Identities=29%  Similarity=0.477  Sum_probs=65.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee---CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~---~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||+++++++|+++|++||+|..|.++.   .++|||||+|.+.++|++|++.||+..  +..|.|.++.++
T Consensus        12 ~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r   89 (93)
T d2cq3a1          12 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR   89 (93)
T ss_dssp             CEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSS
T ss_pred             CEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcC
Confidence            5899999999999999999999999999999874   358899999999999999999999998  777777776554

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.70  E-value=4.2e-17  Score=125.47  Aligned_cols=74  Identities=28%  Similarity=0.475  Sum_probs=65.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||+++|+++|+++|++||+|+.|.|+.     .++|||||+|.+.++|++||+.||+..  +..|.|..+..+
T Consensus        43 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~~  122 (139)
T d1u6fa1          43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASG  122 (139)
T ss_dssp             SEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            5799999999999999999999999999999874     347899999999999999999999987  777777776544


Q ss_pred             C
Q 041602           75 G   75 (223)
Q Consensus        75 ~   75 (223)
                      .
T Consensus       123 ~  123 (139)
T d1u6fa1         123 H  123 (139)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

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

Probab=99.70  E-value=4e-17  Score=113.89  Aligned_cols=69  Identities=32%  Similarity=0.504  Sum_probs=61.5

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      +|||+|||+++++++|+++|++||+|..+.|+.    +++|||||+|.+.++|++|++.||+..  +..|.+..+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a   76 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV   76 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            699999999999999999999999999999964    468899999999999999999999987  655555543

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.69  E-value=7.5e-17  Score=115.40  Aligned_cols=72  Identities=32%  Similarity=0.512  Sum_probs=64.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee---CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~---~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      .+|||+|||.++|+++|+++|++||+|..|.++.   ..+|||||+|.+.++|++|++.||+..  +..|.+.++.+
T Consensus         9 ~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~   85 (90)
T d2cqia1           9 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   85 (90)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            5899999999999999999999999999999864   347899999999999999999999987  77777777644

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.69  E-value=4e-17  Score=115.16  Aligned_cols=70  Identities=23%  Similarity=0.296  Sum_probs=62.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC---cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN---GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~---g~~V~v~~~   71 (223)
                      ++|||+|||.++|+++|.++|++||+|..|.++.+.+|||||+|.+.++|++|++.|||..   +..|.+.++
T Consensus         9 ~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~a   81 (83)
T d2b0ga1           9 QILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFA   81 (83)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEe
Confidence            5899999999999999999999999999999988778999999999999999999999876   344555554

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=2.4e-17  Score=117.81  Aligned_cols=73  Identities=27%  Similarity=0.487  Sum_probs=65.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      .+|||+|||+++|+++|+++|++||+|..|.++.     .++|||||+|.+.++|++|++.||+..  +..|.+.++.++
T Consensus         6 ~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p~   85 (89)
T d2cqba1           6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPM   85 (89)
T ss_dssp             SCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             cEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCCC
Confidence            4799999999999999999999999999999863     568999999999999999999999987  777777777543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=2.5e-17  Score=117.97  Aligned_cols=73  Identities=29%  Similarity=0.549  Sum_probs=65.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||.++|+++|+++|++||+|..|.|+.     .++|||||+|.+.++|++|++.||+..  +..|.+.++++.
T Consensus         9 ~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp~   88 (90)
T d2cq0a1           9 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS   88 (90)
T ss_dssp             EEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeCC
Confidence            6899999999999999999999999999999874     357899999999999999999999987  777777776543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=2.6e-17  Score=116.75  Aligned_cols=73  Identities=23%  Similarity=0.465  Sum_probs=63.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      .+|||+|||.++|+++|+++|++||+|..|+|+.     .++|||||+|.++++|+.|++.||+..  +..|.|.++...
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            4799999999999999999999999999999964     458999999999999999999999987  656666665443

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=3.9e-17  Score=115.08  Aligned_cols=67  Identities=31%  Similarity=0.497  Sum_probs=60.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEE
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVEL   68 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v   68 (223)
                      ++|||+|||..+|+++|+++|++||+|.+|.|+.     .++|||||+|.+.++|++|+++||+..  +..|+|
T Consensus        10 ~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          10 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            5799999999999999999999999999999864     347899999999999999999999987  666654

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.69  E-value=4.2e-17  Score=116.35  Aligned_cols=72  Identities=21%  Similarity=0.465  Sum_probs=63.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      .+|||+|||.++|+++|.++|++||+|..|.++.     .++|||||+|.+.++|++|++.|||..  +..|.|.++..
T Consensus         8 ~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~   86 (88)
T d1rk8a_           8 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV   86 (88)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecC
Confidence            4799999999999999999999999999999874     347899999999999999999999987  66666666544

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.8e-17  Score=118.03  Aligned_cols=59  Identities=37%  Similarity=0.440  Sum_probs=55.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      .+|||+|||+++|+++|+++|++||+|..+.+..  +|||||+|.+.++|++||+.||+.+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~--~g~afV~f~~~~~a~~Ai~~l~g~~   59 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR--DGTGVVEFVRKEDMTYAVRKLDNTK   59 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT--TSEEEEEESSHHHHHHHHHHHTTCB
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc--cceeeEEeCCHHHHHHHHHHhCCCE
Confidence            4799999999999999999999999999999863  5899999999999999999999997

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=6.5e-17  Score=116.79  Aligned_cols=73  Identities=29%  Similarity=0.551  Sum_probs=63.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee------CCCCEEEEEEcCHHHHHHHHHHh-CCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR------RPPGYAFVEFDDRRDAVDAIRAL-DGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~------~~rGfaFV~F~~~e~A~~Al~~l-ng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||.++++++|+++|++||+|..|.|+.      .++|||||+|.+.++|++|++.| |+..  |..|.+.++.
T Consensus         9 ~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~   88 (94)
T d2cpha1           9 SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWAD   88 (94)
T ss_dssp             CCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEcC
Confidence            5899999999999999999999999999999853      46899999999999999999998 7765  6666666654


Q ss_pred             CC
Q 041602           73 KG   74 (223)
Q Consensus        73 ~~   74 (223)
                      .+
T Consensus        89 ~~   90 (94)
T d2cpha1          89 SE   90 (94)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=1.9e-17  Score=118.18  Aligned_cols=71  Identities=25%  Similarity=0.412  Sum_probs=63.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||+++||++|+++|++||+|..|.++.++++||||+|++.++|++|+.  ++..  +..|.+.++.++
T Consensus         6 ~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k   78 (88)
T d1wf0a_           6 SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPK   78 (88)
T ss_dssp             CEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCC
Confidence            6899999999999999999999999999999988889999999999999999985  4444  778888777554

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=4.8e-17  Score=112.74  Aligned_cols=67  Identities=21%  Similarity=0.443  Sum_probs=59.1

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEee
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSH   70 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~   70 (223)
                      +|||+|||+++||++|+++|++||+|..+.|+.     +++|||||+|.++++|++|++ +++..  |..|++.+
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeE
Confidence            599999999999999999999999999999864     468999999999999999997 66665  77776654

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.68  E-value=4.5e-17  Score=115.31  Aligned_cols=61  Identities=33%  Similarity=0.597  Sum_probs=57.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ++|||+|||.++++++|+++|++||+|..+.++.     .++|||||+|.+.++|++|++.||+..
T Consensus         7 t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   72 (85)
T d1b7fa2           7 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI   72 (85)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCE
Confidence            6899999999999999999999999999999874     357899999999999999999999886

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=4.7e-17  Score=120.20  Aligned_cols=69  Identities=23%  Similarity=0.258  Sum_probs=60.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+|||+.+++++|+++|++||+|..|.|. ..+|||||+|.+.++|++|++.|||..  +..|.+.++
T Consensus        11 ~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~-~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a   81 (111)
T d1whxa_          11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CEEEEECCCCCCCHHHHHhhhhccCCccEEEee-ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEEC
Confidence            589999999999999999999999999999885 458999999999999999999999998  444444444

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=5.7e-17  Score=118.13  Aligned_cols=69  Identities=32%  Similarity=0.582  Sum_probs=60.9

Q ss_pred             cEEEEecCC-CCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLD-PRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp-~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+||| ..+++++|+++|++||+|..|.|.   +|||||+|++.++|++||+.||+..  +..|.|.++.+
T Consensus        16 ~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~---rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   87 (98)
T d1wf2a_          16 SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH---KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAE   87 (98)
T ss_dssp             CCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE---TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTS
T ss_pred             cEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe---CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            579999997 468899999999999999999985   8999999999999999999999988  66666666643

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

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

Probab=99.68  E-value=1e-16  Score=114.42  Aligned_cols=72  Identities=33%  Similarity=0.664  Sum_probs=62.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      .+|||+|||+++|+++|+++|++||+|..+.++.     .++|||||+|.++++|++|++.||+..  +..|.|.++.+
T Consensus         6 ~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~   84 (90)
T d1x5sa1           6 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGK   84 (90)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEEC
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            4799999999999999999999999999998753     568999999999999999999999988  55555555543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=1.6e-17  Score=115.88  Aligned_cols=68  Identities=21%  Similarity=0.447  Sum_probs=59.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~   70 (223)
                      |+|||+|||+++|+++|+++|++||+|.++.|+.     +++|||||+|.+.++|++|++ +++..  |..|++..
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~   75 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKV   75 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEE
Confidence            7899999999999999999999999999999863     568999999999999999997 67776  55555544

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

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

Probab=99.68  E-value=4.2e-17  Score=115.97  Aligned_cols=71  Identities=27%  Similarity=0.535  Sum_probs=63.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++++++|+++|++||+|.+|.+..+ +|||||+|++.++|++|++.||+..  +..|.|.++..
T Consensus         9 ~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~   81 (86)
T d2cpja1           9 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             TEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            58999999999999999999999999999998754 8999999999999999999999998  66666666543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.3e-16  Score=118.54  Aligned_cols=70  Identities=26%  Similarity=0.411  Sum_probs=62.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee--CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR--RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~--~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      .+|||+|||..+|+++|+++|++||+|..|.+..  .++|||||+|.+.++|+.|++.|||..  +..|.|..+
T Consensus         8 r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           8 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            4799999999999999999999999999999874  468999999999999999999999998  665555554

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=5.8e-17  Score=118.76  Aligned_cols=73  Identities=22%  Similarity=0.338  Sum_probs=64.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+|||+++|+++|+++|++||+|..+.++.     .++|||||+|.+.++|+.||+.||+..  +..|.|.++.++
T Consensus        19 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~k   98 (102)
T d2cpza1          19 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSK   98 (102)
T ss_dssp             CCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCCC
Confidence            5799999999999999999999999999998864     347899999999999999999999997  777777776554

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=5.9e-17  Score=114.02  Aligned_cols=71  Identities=34%  Similarity=0.608  Sum_probs=61.5

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeEEE-EEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            4 VYVGNLDPRVSERDLEDEFRMFGVLRSV-WVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         4 LfVgnLp~~~te~~L~~~F~~~G~I~~v-~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      |||+|||+++|+++|+++|++||+|..+ .++.     +++|||||+|.+.++|++|++.|++..  +..|.+.++.++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            7999999999999999999999998664 4542     468999999999999999999999987  777777776554

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=2.2e-16  Score=111.86  Aligned_cols=73  Identities=36%  Similarity=0.462  Sum_probs=64.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKGG   75 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~~   75 (223)
                      .+|||+|||.++|+++|+++|++||.|..+.+. .++|||||+|.+.++|++|++.||+..  +..|.+.++.+..
T Consensus         9 k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~-~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1           9 KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE-ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             CEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc-cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            689999999999999999999999998877764 468999999999999999999999987  7788887776543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=8e-17  Score=115.61  Aligned_cols=73  Identities=23%  Similarity=0.351  Sum_probs=62.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCCcEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKNGWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~g~~V~v~~~~~~   74 (223)
                      ++|||+|||+++|+++|+++|++||+|..|.|+.     .++|||||+|.+.++|++||+.++...|..|.+..+.++
T Consensus         9 ~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~~l~Gr~i~v~~a~~k   86 (90)
T d2cqga1           9 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSK   86 (90)
T ss_dssp             CCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCCTT
T ss_pred             CeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCCccCCEEeEEEeCCCC
Confidence            5899999999999999999999999999999874     457899999999999999998654333777777776543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.3e-16  Score=111.05  Aligned_cols=70  Identities=23%  Similarity=0.498  Sum_probs=61.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      +.+|||+|||+++|+++|+++|++||+|..+.++.     .++|||||+|.++++|++|++ +|+..  |..|+|..|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            57899999999999999999999999999998864     357899999999999999995 88887  777777654

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.66  E-value=4.8e-17  Score=117.78  Aligned_cols=74  Identities=24%  Similarity=0.367  Sum_probs=66.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKGG   75 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~~   75 (223)
                      .+|||+|||.++|+++|+++|++||+|..+...+.++|||||+|.+.++|++|++.||+..  +..|.|.++.++.
T Consensus        17 ~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~   92 (96)
T d1fjca_          17 RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             GEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            5899999999999999999999999998887766778999999999999999999999887  7777877776543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=4.2e-17  Score=113.29  Aligned_cols=67  Identities=19%  Similarity=0.433  Sum_probs=56.5

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC-cEEEEEe
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN-GWRVELS   69 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~-g~~V~v~   69 (223)
                      +|||+|||+++|+++|+++|++||+|..|.|+.     .++|||||+|.+.++|++||+..+... +..|++.
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~i~g~~i~vk   73 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIK   73 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEE
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEE
Confidence            699999999999999999999999999999864     468999999999999999997533332 5455544

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.66  E-value=2.1e-16  Score=114.61  Aligned_cols=70  Identities=24%  Similarity=0.479  Sum_probs=61.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~~   72 (223)
                      ++|||+|||+++++++|+++|++||+|..+++..+ ++||||+|.+.++|++|++.||+..    .++|.+.+++
T Consensus        18 ~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak   91 (97)
T d1whya_          18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK   91 (97)
T ss_dssp             SCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECC
T ss_pred             CEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCC
Confidence            68999999999999999999999999999998754 7899999999999999999999887    2345555543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.9e-16  Score=116.36  Aligned_cols=72  Identities=24%  Similarity=0.432  Sum_probs=64.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      .+|||+|||+++|+++|+++|++||+|..+.|+.     .++|||||+|.+.++|++|++ +++..  |..|.|.++.++
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSSC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECccc
Confidence            5899999999999999999999999999999864     468999999999999999996 67766  788888877654

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.4e-16  Score=112.74  Aligned_cols=69  Identities=23%  Similarity=0.473  Sum_probs=60.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      .+|||+|||.++|+++|+++|++||+|..+.|+.     .++|||||+|.+.++|++|++ +++..  |..|++..|
T Consensus         7 ~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             cEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEee
Confidence            5899999999999999999999999999999864     458999999999999999997 56655  777777665

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

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

Probab=99.65  E-value=7.2e-17  Score=119.25  Aligned_cols=73  Identities=23%  Similarity=0.250  Sum_probs=64.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-CCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-RPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~~~~   74 (223)
                      .+|||+|||+.+|+++|+++|++||+|..|.+.. +.+|||||+|.++++|++|++.||+..    ++.|.+.++...
T Consensus         8 ~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~   85 (108)
T d2adba1           8 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT   85 (108)
T ss_dssp             EEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSC
T ss_pred             EEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCc
Confidence            5799999999999999999999999999998865 467999999999999999999999986    566777666543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=4.4e-16  Score=113.34  Aligned_cols=70  Identities=29%  Similarity=0.284  Sum_probs=61.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~~~~   73 (223)
                      .+|||+|||+++++++|+++|++||+|+.+.|.  .+|||||+|.+.++|++||+.||+..    .++|.+....+
T Consensus        16 ~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~--~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~   89 (98)
T d1wg4a_          16 FRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ--KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYP   89 (98)
T ss_dssp             CEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE--TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhhccccccccc--ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCC
Confidence            479999999999999999999999999999886  47999999999999999999999987    35555555433

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.64  E-value=3.2e-16  Score=108.64  Aligned_cols=69  Identities=26%  Similarity=0.253  Sum_probs=60.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee---CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR---RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~---~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      |+|||+|||+++++++|+++|++||+|+.|.++.   ..++||||+|+++++|++|+. ||+..  +..|.|.+.
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            6899999999999999999999999999999975   345799999999999999995 88887  777777653

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=3.2e-16  Score=114.75  Aligned_cols=69  Identities=33%  Similarity=0.508  Sum_probs=61.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      .+|||+|||.++|+++|+++|++||+|.+|.|+.     .++|||||+|.+.++|++|++ ||+..  |..|.|..+
T Consensus        19 ~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a   94 (101)
T d2cq4a1          19 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQAS   94 (101)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEH
T ss_pred             CEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEEC
Confidence            4899999999999999999999999999999964     568999999999999999995 99987  666666654

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=5.8e-16  Score=111.74  Aligned_cols=73  Identities=23%  Similarity=0.348  Sum_probs=62.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--------cEEEEE
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--------GWRVEL   68 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--------g~~V~v   68 (223)
                      ++|||+|||+++|+++|+++|++||+|..+.++.     .++|||||+|.+.++|++|++.||+..        +..|.+
T Consensus         9 ~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v   88 (98)
T d1x4ha1           9 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKV   88 (98)
T ss_dssp             CCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEEE
Confidence            5899999999999999999999999999998863     368999999999999999999998542        567777


Q ss_pred             eeccCC
Q 041602           69 SHNSKG   74 (223)
Q Consensus        69 ~~~~~~   74 (223)
                      .++.++
T Consensus        89 ~~a~~k   94 (98)
T d1x4ha1          89 DLAVTR   94 (98)
T ss_dssp             ECCCCC
T ss_pred             EECCCC
Confidence            776543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=1.8e-16  Score=110.72  Aligned_cols=68  Identities=22%  Similarity=0.386  Sum_probs=59.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      ++|||+||+  +|+++|+++|++||+|.+|.+.. .++||||+|.+.++|++|+++||+..  +..|.+.+++
T Consensus         6 ~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~-~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           6 NTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP-PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET-TTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CEEEEECCC--CCHHHHHHHHhccCccceeeecc-CCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            689999986  89999999999999999999864 48999999999999999999999988  5555555554

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=1.8e-16  Score=109.15  Aligned_cols=67  Identities=21%  Similarity=0.388  Sum_probs=59.0

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEee
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSH   70 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~   70 (223)
                      +|||+|||+++||++|+++|++||.|..+.++.     .+++||||+|.+.++|++|++ +|+..  +..|+|.+
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~   74 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKK   74 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEE
Confidence            599999999999999999999999999988753     468999999999999999996 99887  66666554

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

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

Probab=99.63  E-value=5.8e-16  Score=110.06  Aligned_cols=70  Identities=21%  Similarity=0.332  Sum_probs=60.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe-eCCCCEEEEEEcCHHHHHHHHHHhCCCC---cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-RRPPGYAFVEFDDRRDAVDAIRALDGKN---GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~-~~~rGfaFV~F~~~e~A~~Al~~lng~~---g~~V~v~~~   71 (223)
                      ++|||+|||.++|+++|+++|++||+|..+.+. .+.++||||+|++.++|.+|+..|||..   +..|.+..+
T Consensus        11 ~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2          11 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            489999999999999999999999999877654 4568999999999999999999999875   455555554

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=1.7e-16  Score=116.33  Aligned_cols=71  Identities=31%  Similarity=0.631  Sum_probs=62.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      .+|||+|||.++|+++|+++|++||+|..|.|+.     .++|||||+|.+.++|++|++.||+..  +..|.+.++.
T Consensus         9 rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            4799999999999999999999999999999864     347899999999999999999999887  5555555553

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.63  E-value=3e-16  Score=111.32  Aligned_cols=71  Identities=20%  Similarity=0.355  Sum_probs=60.9

Q ss_pred             cEEEEecCCCCCC-HHHHHHHHHcCCCeEEEEEee------CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVS-ERDLEDEFRMFGVLRSVWVAR------RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~t-e~~L~~~F~~~G~I~~v~i~~------~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      .+|||+|||+++| |++|+++|++||+|..|.|+.      .++|||||+|.+.++|++|++ ||+..  +..|.|..+.
T Consensus         5 ~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a~   83 (86)
T d2ghpa3           5 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLAD   83 (86)
T ss_dssp             TEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEECC
T ss_pred             CEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEcC
Confidence            5899999999875 667999999999999999853      458899999999999999996 99887  7777777665


Q ss_pred             C
Q 041602           73 K   73 (223)
Q Consensus        73 ~   73 (223)
                      +
T Consensus        84 ~   84 (86)
T d2ghpa3          84 K   84 (86)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

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

Probab=99.62  E-value=2.4e-16  Score=112.73  Aligned_cols=68  Identities=25%  Similarity=0.462  Sum_probs=59.9

Q ss_pred             cEEEEecCCCCCCHHHH---HHHHHcCCCeEEEEEeeC--------CCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEE
Q 041602            2 SRVYVGNLDPRVSERDL---EDEFRMFGVLRSVWVARR--------PPGYAFVEFDDRRDAVDAIRALDGKN--GWRVEL   68 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L---~~~F~~~G~I~~v~i~~~--------~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v   68 (223)
                      ++|||+|||+++++++|   .++|++||+|..|.++.+        ++|||||+|.+.++|++|++.|||..  |..|++
T Consensus         9 n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lkv   88 (89)
T d2cpia1           9 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKA   88 (89)
T ss_dssp             SCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEEE
Confidence            46999999999999999   778999999999999642        34899999999999999999999987  777765


Q ss_pred             e
Q 041602           69 S   69 (223)
Q Consensus        69 ~   69 (223)
                      +
T Consensus        89 S   89 (89)
T d2cpia1          89 S   89 (89)
T ss_dssp             E
T ss_pred             C
Confidence            3

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=4.9e-16  Score=112.26  Aligned_cols=72  Identities=22%  Similarity=0.391  Sum_probs=61.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCC-eEEEEEee------CCCCEEEEEEcCHHHHHHHHHHhCCCC----cEEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGV-LRSVWVAR------RPPGYAFVEFDDRRDAVDAIRALDGKN----GWRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~-I~~v~i~~------~~rGfaFV~F~~~e~A~~Al~~lng~~----g~~V~v~~   70 (223)
                      |+|||+|||.++|+++|+++|++||+ |..+.++.      .++|||||+|.+.++|..|++.|++..    +..|.|.+
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            68999999999999999999999996 89998863      457899999999999999999997543    55556666


Q ss_pred             ccC
Q 041602           71 NSK   73 (223)
Q Consensus        71 ~~~   73 (223)
                      +.+
T Consensus        82 A~p   84 (96)
T d2disa1          82 AEP   84 (96)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            544

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=1.9e-16  Score=115.67  Aligned_cols=61  Identities=25%  Similarity=0.482  Sum_probs=56.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ++|||+|||.++|+++|+++|++||+|..+.+..    .++|||||+|.+.++|++|++.|||..
T Consensus        19 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~   83 (101)
T d1x5oa1          19 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKF   83 (101)
T ss_dssp             TEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCE
Confidence            6899999999999999999999999999988764    347899999999999999999999987

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.61  E-value=1.2e-16  Score=114.73  Aligned_cols=71  Identities=21%  Similarity=0.383  Sum_probs=62.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      .+|||+|||.++|+++|+++|++||+|..+.|+    +.++|||||+|.+.++|++||+ ||+..  +..|.|.++..
T Consensus        14 ~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~   90 (91)
T d1fjeb1          14 FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG   90 (91)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCC
T ss_pred             cEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCC
Confidence            479999999999999999999999998877664    4679999999999999999996 99887  78888877643

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=9e-16  Score=109.41  Aligned_cols=70  Identities=21%  Similarity=0.309  Sum_probs=58.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||++++++||+++|++|| ++.+.+ ...+|||||+|.+.++|++|++.||+.+  +..|.|..++.
T Consensus         6 ~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~-~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_           6 SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE-EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CEEEEeCCCCccChHHHHHHHHhcC-ceeeee-eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            5899999999999999999999999 222333 3458999999999999999999999998  66666666543

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

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

Probab=99.60  E-value=6e-16  Score=112.35  Aligned_cols=73  Identities=33%  Similarity=0.499  Sum_probs=62.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEE--------Ee-----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEE
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVW--------VA-----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRV   66 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~--------i~-----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V   66 (223)
                      ++|||+|||.++|+++|+++|++||+|..+.        +.     +.++|||||+|.+.++|++|++.||+..  +..|
T Consensus         9 ~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~i   88 (101)
T d2cpea1           9 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKL   88 (101)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECCEEE
Confidence            6899999999999999999999999986432        22     2457999999999999999999999998  7777


Q ss_pred             EEeeccCC
Q 041602           67 ELSHNSKG   74 (223)
Q Consensus        67 ~v~~~~~~   74 (223)
                      .|.++.++
T Consensus        89 ~V~~a~~~   96 (101)
T d2cpea1          89 KVSLARKK   96 (101)
T ss_dssp             EEECSSCC
T ss_pred             EEEEcCCC
Confidence            77777553

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=2e-15  Score=110.37  Aligned_cols=71  Identities=24%  Similarity=0.502  Sum_probs=59.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee------CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR------RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~------~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||+++|+++|+++|++|| |..+.++.      .++|||||+|.+.++|++|++ ||+..  +..|.|..+.+
T Consensus        16 ~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~a~~   93 (104)
T d1wi8a_          16 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVADQ   93 (104)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEECCC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEECCC
Confidence            5899999999999999999999999 66776642      357899999999999987774 99887  66677766654


Q ss_pred             C
Q 041602           74 G   74 (223)
Q Consensus        74 ~   74 (223)
                      +
T Consensus        94 ~   94 (104)
T d1wi8a_          94 A   94 (104)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.60  E-value=2.4e-15  Score=104.12  Aligned_cols=67  Identities=18%  Similarity=0.315  Sum_probs=57.8

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeecc
Q 041602            4 VYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNS   72 (223)
Q Consensus         4 LfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~   72 (223)
                      |||+|||+++++++|+++|++|| +..+.+ ..++|||||+|.+.++|++|++.||+..  |..|.|..+.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~-~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~   69 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQP   69 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECC
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee-cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeC
Confidence            79999999999999999999999 555544 4679999999999999999999999987  6666666653

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.4e-15  Score=108.93  Aligned_cols=72  Identities=25%  Similarity=0.505  Sum_probs=62.1

Q ss_pred             cEEEEecCCCCCCHHHHHH----HHHcCCCeEEEEEee--CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLED----EFRMFGVLRSVWVAR--RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~----~F~~~G~I~~v~i~~--~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||+++++++|++    +|++||+|..|.+..  +++|||||+|++.++|++|++.||+..  +..|.+.++..
T Consensus         4 ~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak~   83 (91)
T d1nu4a_           4 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT   83 (91)
T ss_dssp             SEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeCC
Confidence            5899999999999998864    689999999998864  468999999999999999999999987  66666666643

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=4.1e-16  Score=106.75  Aligned_cols=59  Identities=29%  Similarity=0.515  Sum_probs=55.1

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            4 VYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         4 LfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      |||+|||.++|+++|+++|++||+|..+.+..     .++|||||+|.+.++|++|++.|||..
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~   64 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASG   64 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHT
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCE
Confidence            79999999999999999999999999998863     468999999999999999999999876

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

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

Probab=99.58  E-value=2.1e-15  Score=106.74  Aligned_cols=69  Identities=17%  Similarity=0.248  Sum_probs=60.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      .+|||+|||.++|+++|+++|++||+|..|.|..    .++|||||+|.++++|++||+ +++..  +..+.+.+.
T Consensus         7 rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~   81 (85)
T d1zh5a2           7 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   81 (85)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEG
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEc
Confidence            5899999999999999999999999999999874    347899999999999999996 67776  666666554

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

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

Probab=99.58  E-value=6.7e-15  Score=107.81  Aligned_cols=70  Identities=23%  Similarity=0.248  Sum_probs=58.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCC--CC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDG--KN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng--~~--g~~V~v~~~~   72 (223)
                      .+|||+|||..+||++|.++|++||+|+.+.+.. .+++|||+|++.++|++|++.|++  ..  +..|+|.++.
T Consensus        16 ~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~-~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~   89 (104)
T d1wexa_          16 PVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYST   89 (104)
T ss_dssp             SEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECS
T ss_pred             CEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe-cceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcC
Confidence            4799999999999999999999999999998864 589999999999999999998753  22  4445555543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=3.6e-15  Score=105.92  Aligned_cols=70  Identities=13%  Similarity=0.189  Sum_probs=60.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCC--C--cEEEEEeecc
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGK--N--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~--~--g~~V~v~~~~   72 (223)
                      .+|||+|||.++++++|+++|++||.|..+.+.. .++||||+|.+.++|++|++.+++.  .  +..|.+.++.
T Consensus         9 ~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~-~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk   82 (88)
T d2cq1a1           9 RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK-GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN   82 (88)
T ss_dssp             SEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhcccccccccccc-cceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECC
Confidence            5799999999999999999999999999998874 4799999999999999999977543  3  6666666654

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=8.4e-16  Score=111.86  Aligned_cols=72  Identities=29%  Similarity=0.452  Sum_probs=61.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe-----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~-----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      ++|||+|||.++++++|+++|++||.|..+.++     ++++|||||+|.+.++|++|++.||+..  +..|.|.++.+
T Consensus        19 ~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak~   97 (102)
T d2cpxa1          19 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN   97 (102)
T ss_dssp             SEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCCC
Confidence            589999999999999999999999998877664     3578999999999999999999999987  55555555543

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

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]

Probab=99.53  E-value=3e-15  Score=105.77  Aligned_cols=69  Identities=28%  Similarity=0.386  Sum_probs=59.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEE-EEEe----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRS-VWVA----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~-v~i~----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~   70 (223)
                      ++|||+|||.+++++||+++|+.||.|.. +.+.    +.++|+|||+|.+.++|++|++.||+..  +..|+|..
T Consensus        10 ~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1          10 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             EEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            57999999999999999999999998865 3443    2457899999999999999999999998  66666653

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=2.1e-14  Score=105.00  Aligned_cols=72  Identities=19%  Similarity=0.238  Sum_probs=59.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe-----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~-----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      .+|||+|||+++|++||+++|..+|.|..+.++     +.++|||||+|.++++|++|++ +|+..  +..|+|..+.+.
T Consensus        16 ~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~~~   94 (104)
T d1wg5a_          16 GFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRA   94 (104)
T ss_dssp             CEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEECTT
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECCHH
Confidence            369999999999999999999999988775443     2468999999999999999996 77776  666666665443

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=1.5e-14  Score=105.51  Aligned_cols=71  Identities=34%  Similarity=0.336  Sum_probs=57.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      .+|||+|||+++||++|+++|+.+|.+ .|.++.    ..+|||||+|.+.++|++|++ ||+..  +..|+|.++...
T Consensus        16 ~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~~~   92 (102)
T d1weza_          16 HCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTA   92 (102)
T ss_dssp             CEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcCCC
Confidence            379999999999999999999999854 555543    347899999999999999986 88887  665666555443

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.50  E-value=1.4e-14  Score=105.32  Aligned_cols=70  Identities=19%  Similarity=0.262  Sum_probs=58.2

Q ss_pred             cEEEEecCCCC-CCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHH--hCCCC--cEEEEEeecc
Q 041602            2 SRVYVGNLDPR-VSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRA--LDGKN--GWRVELSHNS   72 (223)
Q Consensus         2 ttLfVgnLp~~-~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~--lng~~--g~~V~v~~~~   72 (223)
                      ++|||+|||.+ +|+++|.++|++||+|..+.++. .+|+|||+|++.++|.+|++.  +++..  |..|.|..+.
T Consensus        19 ~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~-~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~   93 (99)
T d1x4fa1          19 RVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSE   93 (99)
T ss_dssp             CEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET-TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEEC
T ss_pred             CEEEEeCCcCCccCHHHHHhhhccccceeEEEEee-cCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcC
Confidence            47999999985 89999999999999999999874 489999999999999999984  56544  5545555543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=2.8e-14  Score=104.18  Aligned_cols=60  Identities=20%  Similarity=0.361  Sum_probs=54.8

Q ss_pred             cEEEEe--cCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            2 SRVYVG--NLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         2 ttLfVg--nLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      .+|||.  |||.++|+++|+++|++||+|+.|.++.+ ++||||+|.+.++|++|++.|||..
T Consensus        19 ~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-k~~aFV~f~~~e~A~~A~~~lng~~   80 (101)
T d2cq2a1          19 QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-KPYSFARYRTTEESKRAYVTLNGKE   80 (101)
T ss_dssp             SEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-CSCEEEEESSHHHHHHHHHHTTTCE
T ss_pred             ceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-ccEEEEEECCHHHHHHHHHHhCCCC
Confidence            468885  59999999999999999999999988754 8899999999999999999999986

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=8.5e-16  Score=109.62  Aligned_cols=70  Identities=26%  Similarity=0.418  Sum_probs=59.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe----------eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEe
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA----------RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELS   69 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~----------~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~   69 (223)
                      -+|||+|||.++||++|+++|++||.|..+.+.          ..++|||||+|.+.++|++|++ |||..  |..|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            379999999999999999999999987665542          2568999999999999999995 99998  7777776


Q ss_pred             ecc
Q 041602           70 HNS   72 (223)
Q Consensus        70 ~~~   72 (223)
                      ++.
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.47  E-value=3.4e-14  Score=101.32  Aligned_cols=69  Identities=19%  Similarity=0.196  Sum_probs=59.0

Q ss_pred             EEEEecCCCC-CCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhC--CCC--cEEEEEeecc
Q 041602            3 RVYVGNLDPR-VSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALD--GKN--GWRVELSHNS   72 (223)
Q Consensus         3 tLfVgnLp~~-~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~ln--g~~--g~~V~v~~~~   72 (223)
                      +|||+|||.. +|++||.++|++||+|..|.+..+ +++|||+|++.++|++|++.|+  +..  |..|.|.++.
T Consensus        10 ~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~   83 (89)
T d1x4da1          10 VVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQ   83 (89)
T ss_dssp             EEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEEC
T ss_pred             EEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECC
Confidence            6999999986 889999999999999999999754 7899999999999999999764  443  6666666654

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.47  E-value=5.5e-14  Score=104.47  Aligned_cols=68  Identities=18%  Similarity=0.280  Sum_probs=58.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCH-HHHHHHHHHhCCCC----cEEEEEee
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDR-RDAVDAIRALDGKN----GWRVELSH   70 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~-e~A~~Al~~lng~~----g~~V~v~~   70 (223)
                      ..+||||||..+|+++|+++|++||+|..|.|+. .+|||||.|.++ ++|.+|+..|++..    .+.|.+..
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~-~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR-GAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT-TCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEec-CCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            3579999999999999999999999999999984 489999999996 68999999999875    44555544

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=2.4e-14  Score=104.43  Aligned_cols=69  Identities=22%  Similarity=0.210  Sum_probs=58.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEE-EEEe----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRS-VWVA----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~-v~i~----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|||+|||+++|+++|+++|..||.|.. +.+.    +.++|||||+|.+.++|++||+ +|+..  +..|.|..+
T Consensus         9 ~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           9 VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             CEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             eEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            46999999999999999999999998876 4443    2568999999999999999996 88886  777777665

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.46  E-value=6.6e-14  Score=102.72  Aligned_cols=72  Identities=19%  Similarity=0.157  Sum_probs=61.8

Q ss_pred             cEEEEecCCCCC-CH----HHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccCC
Q 041602            2 SRVYVGNLDPRV-SE----RDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSKG   74 (223)
Q Consensus         2 ttLfVgnLp~~~-te----~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~~   74 (223)
                      ++|||+||+.++ ++    ++|+++|++||+|..+.+. +.+++|||+|.+.++|++|++.|||..  +..|++.+++..
T Consensus         6 ~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~-k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   84 (104)
T d1weya_           6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL   84 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE-TTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCS
T ss_pred             ceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEe-cCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecccC
Confidence            689999999875 33    5799999999999999887 458899999999999999999999998  777777766443

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=7e-14  Score=103.62  Aligned_cols=69  Identities=17%  Similarity=0.248  Sum_probs=57.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEe-----eCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVA-----RRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~-----~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      .+|||+|||+++|+++|+++|+.+|.|..+.++     +.++|||||+|.+.++|++|++ ||+..  +..|+|..+
T Consensus        19 ~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          19 FCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             eEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEc
Confidence            479999999999999999999999988654332     2457899999999999999996 89887  666666554

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=1e-12  Score=103.80  Aligned_cols=71  Identities=23%  Similarity=0.474  Sum_probs=61.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeeccC
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHNSK   73 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~~~   73 (223)
                      .+|||+|||..+|+++|+++|+.||+|..+.++.     .++|||||+|.+.++|++|++ +++..  |..|.|.++.+
T Consensus        98 ~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~  175 (183)
T d1u1qa_          98 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALS  175 (183)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCC
T ss_pred             ceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCC
Confidence            5899999999999999999999999999998874     357899999999999999997 66655  77788776643

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.32  E-value=1.7e-12  Score=90.93  Aligned_cols=67  Identities=13%  Similarity=0.184  Sum_probs=55.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--c-EEEEEeec
Q 041602            2 SRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--G-WRVELSHN   71 (223)
Q Consensus         2 ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g-~~V~v~~~   71 (223)
                      +.|+|+|+|++++++.| ++|++||+|.++.+. ..++||||+|.++++|++||+ +||..  + ..|.+...
T Consensus         5 ~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~-~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           5 TWVTVFGFPQASASYIL-LQFAQYGNILKHVMS-NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC-SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             cEEEEECCChHHHHHHH-HHHHhhhhhheEEec-CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeC
Confidence            57999999999987666 579999999999875 448999999999999999996 89887  4 44555544

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=1.2e-13  Score=101.36  Aligned_cols=68  Identities=18%  Similarity=0.214  Sum_probs=58.1

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee----CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEee
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR----RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSH   70 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~----~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~   70 (223)
                      .++|.+++.+++|++|+++|++||+|+.|.|+.    +++|||||+|.+.++|++|++.|||..  |..|.+..
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~  102 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL  102 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEE
Confidence            355667777788999999999999999999964    568999999999999999999999998  66666544

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.28  E-value=3.1e-12  Score=100.94  Aligned_cols=70  Identities=26%  Similarity=0.485  Sum_probs=58.3

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-----CCCCEEEEEEcCHHHHHHHHHHhCCCC-cEEEEEee
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-----RPPGYAFVEFDDRRDAVDAIRALDGKN-GWRVELSH   70 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-----~~rGfaFV~F~~~e~A~~Al~~lng~~-g~~V~v~~   70 (223)
                      +.+|||+|||+++|+++|+++|++||+|..+.++.     .++|||||+|.+.++|++|+..++... ...+.+..
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~   81 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR   81 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhh
Confidence            35899999999999999999999999999999864     457899999999999999998665554 34444443

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.10  E-value=8.5e-11  Score=84.89  Aligned_cols=72  Identities=28%  Similarity=0.396  Sum_probs=59.4

Q ss_pred             cEEEEecC--CCCCC---------HHHHHHHHHcCCCeEEEEEee-CCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEE
Q 041602            2 SRVYVGNL--DPRVS---------ERDLEDEFRMFGVLRSVWVAR-RPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVE   67 (223)
Q Consensus         2 ttLfVgnL--p~~~t---------e~~L~~~F~~~G~I~~v~i~~-~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~   67 (223)
                      .+|+|.||  |.++.         ++||++.|++||+|..|.+.. +++|||||+|++.++|.+|++.|||..  +..|.
T Consensus         9 r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~i~   88 (99)
T d2dita1           9 RVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT   88 (99)
T ss_dssp             CEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTEECE
T ss_pred             cEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECCEEEE
Confidence            46899998  54321         368999999999999998864 568999999999999999999999998  77777


Q ss_pred             EeeccC
Q 041602           68 LSHNSK   73 (223)
Q Consensus        68 v~~~~~   73 (223)
                      +....+
T Consensus        89 v~~~~g   94 (99)
T d2dita1          89 AQAWDG   94 (99)
T ss_dssp             EEECCS
T ss_pred             EEEeCC
Confidence            776543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.89  E-value=7.8e-10  Score=80.28  Aligned_cols=69  Identities=25%  Similarity=0.360  Sum_probs=55.3

Q ss_pred             EEEEecC--CCCCC--------HHHHHHHHHcCCCeEEEEEee-------CCCCEEEEEEcCHHHHHHHHHHhCCCC--c
Q 041602            3 RVYVGNL--DPRVS--------ERDLEDEFRMFGVLRSVWVAR-------RPPGYAFVEFDDRRDAVDAIRALDGKN--G   63 (223)
Q Consensus         3 tLfVgnL--p~~~t--------e~~L~~~F~~~G~I~~v~i~~-------~~rGfaFV~F~~~e~A~~Al~~lng~~--g   63 (223)
                      .|.|.|+  +.++.        .+||++.|++||+|++|.|+.       ...|++||+|.+.++|.+|++.|||..  |
T Consensus         6 vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f~g   85 (104)
T d1o0pa_           6 VLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFAN   85 (104)
T ss_dssp             EEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCSSS
T ss_pred             EEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            4777898  44432        357899999999999999864       235899999999999999999999998  6


Q ss_pred             EEEEEeec
Q 041602           64 WRVELSHN   71 (223)
Q Consensus        64 ~~V~v~~~   71 (223)
                      +.|.+...
T Consensus        86 R~v~v~f~   93 (104)
T d1o0pa_          86 RVVVTKYC   93 (104)
T ss_dssp             SCCEEEEE
T ss_pred             eEEEEEEc
Confidence            66666554

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.36  E-value=0.00053  Score=47.71  Aligned_cols=62  Identities=16%  Similarity=0.263  Sum_probs=53.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeEEEEEee-C------CCCEEEEEEcCHHHHHHHHHHhCCCC
Q 041602            1 MSRVYVGNLDPRVSERDLEDEFRMFGVLRSVWVAR-R------PPGYAFVEFDDRRDAVDAIRALDGKN   62 (223)
Q Consensus         1 ~ttLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~-~------~rGfaFV~F~~~e~A~~Al~~lng~~   62 (223)
                      ||+|.|..||+..||+++.+.+...|++....... +      .-.-|+|.|.+.+++..-.+..+|..
T Consensus         1 ~tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~   69 (91)
T d1uw4a_           1 LSKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYV   69 (91)
T ss_dssp             CCEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCE
T ss_pred             CceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcE
Confidence            78999999999999999999999899888776642 1      13489999999999999999999875

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.17  E-value=0.0055  Score=42.26  Aligned_cols=52  Identities=25%  Similarity=0.469  Sum_probs=44.2

Q ss_pred             HHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602           16 RDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus        16 ~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      ++|-+.|++||+|.-|+++   .+-..|+|.+-..|.+|++ +++.+  +..+++.-.
T Consensus        39 ~~Llq~l~~~GeViLvRFv---~d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRIN---QGQMLVTFADSHSALSVLD-VDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEE---TTEEEEECSCSHHHHHHHH-GGGSEETTEEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEe---CCeEEEEECCcHHHHHHhc-cCCeEEcceEEEEecC
Confidence            3678889999999999998   5689999999999999997 88887  777777644

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.58  E-value=0.036  Score=36.25  Aligned_cols=60  Identities=23%  Similarity=0.382  Sum_probs=46.6

Q ss_pred             CCCHHH----HHHHHHcCCCeEEEEEeeCCCC--EEEEEEcCHHHHHHHHHHhCCCC--cEEEEEeec
Q 041602           12 RVSERD----LEDEFRMFGVLRSVWVARRPPG--YAFVEFDDRRDAVDAIRALDGKN--GWRVELSHN   71 (223)
Q Consensus        12 ~~te~~----L~~~F~~~G~I~~v~i~~~~rG--faFV~F~~~e~A~~Al~~lng~~--g~~V~v~~~   71 (223)
                      .+++++    |.+.|.++|+|..+.+.-.+.|  .|-|...+..+|.-|+..|+...  ..+|.++.+
T Consensus         3 ~L~~kelqq~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~   70 (73)
T d2dgxa1           3 RLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLA   70 (73)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             cCCHHHHHHHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEe
Confidence            445544    5567899999999998644443  89999999999999999999776  456666654

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=93.49  E-value=0.1  Score=36.15  Aligned_cols=54  Identities=20%  Similarity=0.312  Sum_probs=44.5

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeEEEEEeeCCCCEEEEEEcCHHHHHHHHHHhC
Q 041602            3 RVYVGNLDPRVSERDLEDEFRMFGVLRSVWVARRPPGYAFVEFDDRRDAVDAIRALD   59 (223)
Q Consensus         3 tLfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~~~rGfaFV~F~~~e~A~~Al~~ln   59 (223)
                      .||.-.+|..+...||.++|+.||.|.--.| .  .--|||...+.++|+.+++.++
T Consensus        17 HVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-d--dTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          17 HVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-D--DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-E--TTEEEEECSCHHHHHHHHHHHH
T ss_pred             eeEEEeCCcccchhHHHHHhcCCCceEEEEe-c--CceEEEEecCHHHHHHHHHHhc
Confidence            3678899999999999999999998744333 2  3379999999999999987665

>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Zinc finger protein ncp10
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=81.90  E-value=1.9  Score=24.14  Aligned_cols=26  Identities=31%  Similarity=0.670  Sum_probs=21.1

Q ss_pred             CCCCCCCCCcCCCCCCCCCCCCCCCC
Q 041602           83 RGGGEDLKCYECGEPGHFARECRLRI  108 (223)
Q Consensus        83 ~~~~~~~~~~~~g~~G~~~r~~~~~~  108 (223)
                      +..-+.+.|--|...|||.++||...
T Consensus         5 r~~L~kDQCAyCke~GHW~~dCPkkp   30 (40)
T d1a6bb_           5 RSQLDRDQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             CCSCCSSSCSSSCCTTCCTTSCSSSC
T ss_pred             cCcccchhhHHHhhcCchhhhCccCC
Confidence            33456678889999999999999874