Citrus Sinensis ID: 038096

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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-
Protein Sequence
LVPSPKHSFVPNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSRSDPVPMPVNGMEISHHSMRISVPRHYSSEEPPPPGVTLETNGYETHLNVTNYDYSRRVFGATLDSISRSRSGHYNSSNRHY
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHccccEEEEEccccccccccccEEEEEEccHHHHHHHHHHccccEEEccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccHHHHccccEEEEccccccccHHHHHHHHHHcccEEEEEcccccccccccEEEEEEEccHHHHHHHHHHHHccEEEccccEEEEEccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcHcEHcccccccccccccccccc
Coil and Loop (DISEMBL)
lvpspkhsfvpndvvsrnkrqimsgnsnsgcnvyignLDEKVNERVLYDILIQAGrvvdlyiprdketdkpkgfafVEYESEEIGHYAIKLFSGIVTLYNRTLRFalsgqdknaqnssmtttplssrksrsdpvpmpvngmeishhsmrisvprhysseeppppgvtletngyethlnvtnydysrrVFGATLDsisrsrsghynssnrhy
Flexible Loop (DISEMBL)
lvpspkhsfvpndvvsrnkrqimsgnsnsgcnvYIGNLDEKVNERVLYDILIQagrvvdlyiprdketdkpkGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAlsgqdknaqnssmtttplssrksrsdpvpMPVNGMEISHHSMRISVPRHYSSEEPPPPGVTLETNGYETHLNVTNYDYSRRVFGATLdsisrsrsghynssnrhy
Low Complexity Region (SEG)
LVPSPKHSFVPNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSRSDPVPMPVNGMEISHHSMRISVPRHYSSEEPPPPGVTLETNGYETHLNVTNYDYSRRVFGATLDSISRSRSGHYNSSNRHY
Disordered region (IsUnstruct)
*****************************GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL**************************************************************TNGYETHLNVTNYDYSRRVFGATL******************
Disordered Region (DISOPRED)
********************************VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR***********************************************************************************************************
Disordered Region (DISEMBL)
********FVPNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQ**********************PVPMPVNGMEISHHSMRISVP***********GVTLETNGYETHLNVTNYDYSRRVFGATLDSIS**************
Disordered Region (DISPRO)
LVPSPKHSFVPNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQ********MTTTPLS*******PVPMPVNGMEISHHSMRISVPRHYSSEEPPPPGVTLETNGYETHLNVTNYDYSRRVFGATLDSI***************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
LVPSPKHSFVPNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSRSDPVPMPVNGMEISHHSMRISVPRHYSSEEPPPPGVTLETNGYETHLNVTNYDYSRRVFGATLDSISRSRSGHYNSSNRHY
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	211	2.2.26 [Sep-21-2011]
Q15427	424	Splicing factor 3B subuni	yes	no	0.360	0.179	0.428	1e-13
Q6AYL5	424	Splicing factor 3B subuni	yes	no	0.360	0.179	0.428	2e-13
Q8QZY9	424	Splicing factor 3B subuni	yes	no	0.360	0.179	0.428	2e-13
Q09442	388	Splicing factor 3B subuni	yes	no	0.360	0.195	0.402	6e-13
O14102	335	Spliceosome-associated pr	yes	no	0.398	0.250	0.364	6e-12
Q9Y580	266	RNA-binding protein 7 OS=	no	no	0.407	0.323	0.393	1e-09
Q99181	213	Protein HSH49 OS=Saccharo	yes	no	0.511	0.507	0.313	1e-09
Q80YT9	238	Splicing regulator RBM11	no	no	0.464	0.411	0.346	2e-09
P57052	281	Splicing regulator RBM11	no	no	0.464	0.348	0.355	2e-09
Q3MHY8	262	RNA-binding protein 7 OS=	no	no	0.407	0.328	0.370	3e-09

>sp|Q15427|SF3B4_HUMAN Splicing factor 3B subunit 4 OS=Homo sapiens GN=SF3B4 PE=1 SV=1

 Score = 76.3 bits (186), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 33/77 (42%), Positives = 55/77 (71%), Gaps = 1/77 (1%)

Query: 28  NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
           N    VY+G LDEKV+E +L+++ +QAG VV+ ++P+D+ T + +G+ FVE+ SEE   Y
Sbjct: 10  NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 69

Query: 88  AIKLFSGIVTLYNRTLR 104
           AIK+ + ++ LY + +R
Sbjct: 70  AIKIMN-MIKLYGKPIR 85

Subunit of the splicing factor SF3B required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the 'E' complex. SF3B4 has been found in complex 'B' and 'C' as well. Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron.
Homo sapiens (taxid: 9606)

>sp|Q6AYL5|SF3B4_RAT Splicing factor 3B subunit 4 OS=Rattus norvegicus GN=Sf3b4 PE=2 SV=1

 Score = 75.9 bits (185), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 33/77 (42%), Positives = 55/77 (71%), Gaps = 1/77 (1%)

Query: 28  NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
           N    VY+G LDEKV+E +L+++ +QAG VV+ ++P+D+ T + +G+ FVE+ SEE   Y
Sbjct: 10  NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 69

Query: 88  AIKLFSGIVTLYNRTLR 104
           AIK+ + ++ LY + +R
Sbjct: 70  AIKIMN-MIKLYGKPIR 85

Subunit of the splicing factor SF3B required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the 'E' complex. SF3B4 has been found in complex 'B' and 'C' as well. Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron.

Rattus norvegicus (taxid: 10116)

>sp|Q8QZY9|SF3B4_MOUSE Splicing factor 3B subunit 4 OS=Mus musculus GN=Sf3b4 PE=2 SV=1

 Score = 75.9 bits (185), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 33/77 (42%), Positives = 55/77 (71%), Gaps = 1/77 (1%)

Query: 28  NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
           N    VY+G LDEKV+E +L+++ +QAG VV+ ++P+D+ T + +G+ FVE+ SEE   Y
Sbjct: 10  NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 69

Query: 88  AIKLFSGIVTLYNRTLR 104
           AIK+ + ++ LY + +R
Sbjct: 70  AIKIMN-MIKLYGKPIR 85

Subunit of the splicing factor SF3B required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the 'E' complex. SF3B4 has been found in complex 'B' and 'C' as well. Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron.

Mus musculus (taxid: 10090)

>sp|Q09442|SF3B4_CAEEL Splicing factor 3B subunit 4 OS=Caenorhabditis elegans GN=sap-49 PE=1 SV=2

 Score = 74.3 bits (181), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 31/77 (40%), Positives = 53/77 (68%), Gaps = 1/77 (1%)

Query: 28  NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
           N    +Y+G LDEKV+E +L+++++QAG VV + +P+D+ T   +GF FVE+  EE   Y
Sbjct: 10  NQDATIYVGGLDEKVSESILWELMVQAGPVVSVNMPKDRVTANHQGFGFVEFMGEEDADY 69

Query: 88  AIKLFSGIVTLYNRTLR 104
           AIK+ + ++ LY + ++
Sbjct: 70  AIKILN-MIKLYGKPIK 85

Subunit of the splicing factor SF3B required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the 'E' complex. SF3B4 has been found in complex 'B' and 'C' as well. Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron.

Caenorhabditis elegans (taxid: 6239)

>sp|O14102|SAP49_SCHPO Spliceosome-associated protein 49 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=sap49 PE=3 SV=2

 Score = 70.9 bits (172), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 31/85 (36%), Positives = 54/85 (63%), Gaps = 1/85 (1%)

Query: 28  NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
           N    +Y+GNLDEKV + +L+++ +QAG VV+++IPRD+  +   GF F E+  E+   Y
Sbjct: 8   NQDATIYLGNLDEKVTDSILFELCLQAGPVVNIHIPRDRVRNSHNGFGFCEFLHEQDVEY 67

Query: 88  AIKLFSGIVTLYNRTLRFALSGQDK 112
           A ++ +  V L+ + +R   + QD+
Sbjct: 68  ACQILNQ-VKLFGKPIRVNRASQDR 91

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q9Y580|RBM7_HUMAN RNA-binding protein 7 OS=Homo sapiens GN=RBM7 PE=1 SV=1

 Score = 63.5 bits (153), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 35/89 (39%), Positives = 56/89 (62%), Gaps = 3/89 (3%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +++GNL+ KV E +L+++  QAG V+ + IP+DK+  KPK FAFV ++ E    YA+ L 
Sbjct: 12  LFVGNLETKVTEELLFELFHQAGPVIKVKIPKDKDG-KPKQFAFVNFKHEVSVPYAMNLL 70

Query: 93  SGIVTLYNRTLRFAL-SGQDKNAQNSSMT 120
           +GI  LY R ++    SG     Q+ S++
Sbjct: 71  NGI-KLYGRPIKIQFRSGSSHAPQDVSLS 98

Possible involved in germ cell RNA processing and meiosis.

Homo sapiens (taxid: 9606)

>sp|Q99181|HSH49_YEAST Protein HSH49 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=HSH49 PE=1 SV=1

 Score = 63.2 bits (152), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 66/115 (57%), Gaps = 7/115 (6%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
           M+ +++SG  VY+GN+D ++ +  LY++ IQ   V+ +  P+DK     +G+AF+E+ ++
Sbjct: 1   MNYSADSGNTVYVGNIDPRITKEQLYELFIQINPVLRIKYPKDKVLQAYQGYAFIEFYNQ 60

Query: 83  EIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSRSDPVPMP 137
               YAIK+ +  V LY+R ++       +   NS+  TT L S  S+   +P+ 
Sbjct: 61  GDAQYAIKIMNNTVRLYDRLIKV------RQVTNST-GTTNLPSNISKDMILPIA 108

Possible SF3b-like factor.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q80YT9|RBM11_MOUSE Splicing regulator RBM11 OS=Mus musculus GN=Rbm11 PE=1 SV=1

 Score = 62.4 bits (150), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 36/104 (34%), Positives = 59/104 (56%), Gaps = 6/104 (5%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           V++GNL+ +V E +LY++ +QAG +  + + +D++  KPK F FV ++  E   YAI L 
Sbjct: 12  VFVGNLEARVREEILYELFLQAGPLTKVTLCKDRD-GKPKSFGFVCFKHPESVSYAIALL 70

Query: 93  SGIVTLYNRTL----RFALSGQDKNAQNSSMTTTPLSSRKSRSD 132
           +GI  LY R +    RF  S   + A  S  +   ++S   R+D
Sbjct: 71  NGI-RLYGRPINVQYRFGSSRSSEPANQSFESCAKINSHSFRND 113

Mus musculus (taxid: 10090)

>sp|P57052|RBM11_HUMAN Splicing regulator RBM11 OS=Homo sapiens GN=RBM11 PE=1 SV=1

 Score = 62.4 bits (150), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 37/104 (35%), Positives = 59/104 (56%), Gaps = 6/104 (5%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           V++GNL+ +V E +LY++ +QAG +  + I +D+E  KPK F FV ++  E   YAI L 
Sbjct: 12  VFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALL 70

Query: 93  SGIVTLYNRTL----RFALSGQDKNAQNSSMTTTPLSSRKSRSD 132
           +GI  LY R +    RF  S   + A  S  +   ++S   R++
Sbjct: 71  NGI-RLYGRPINVQYRFGSSRSSEPANQSFESCVKINSHNYRNE 113

Homo sapiens (taxid: 9606)

>sp|Q3MHY8|RBM7_BOVIN RNA-binding protein 7 OS=Bos taurus GN=RBM7 PE=2 SV=1

 Score = 62.0 bits (149), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 33/89 (37%), Positives = 56/89 (62%), Gaps = 3/89 (3%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +++GNL+ KV E +L+++  QAG V+ + IP+DK+  KPK FAFV ++ E    YA+ L 
Sbjct: 12  LFVGNLETKVTEELLFELFHQAGPVIKVKIPKDKDG-KPKQFAFVNFKHEVSVPYAMNLL 70

Query: 93  SGIVTLYNRTLRFAL-SGQDKNAQNSSMT 120
           +GI  L+ R ++    +G    +Q  S++
Sbjct: 71  NGI-KLFGRPIKIQFRAGSSHASQEVSLS 98

Possible involved in germ cell RNA processing and meiosis.

Bos taurus (taxid: 9913)

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	211
86156022	194	RNA recognition motif-containing protein	0.853	0.927	0.613	1e-55
356576175	196	PREDICTED: uncharacterized protein LOC10	0.867	0.933	0.578	1e-55
225460024	194	PREDICTED: 33 kDa ribonucleoprotein, chl	0.853	0.927	0.608	5e-55
356535691	186	PREDICTED: RNA-binding protein 7-like [G	0.805	0.913	0.581	8e-52
224127921	195	predicted protein [Populus trichocarpa]	0.872	0.943	0.575	2e-49
357443447	200	Peptidyl-prolyl cis-trans isomerase [Med	0.834	0.88	0.550	5e-49
217074838	218	unknown [Medicago truncatula]	0.834	0.807	0.541	9e-48
255564912	201	spliceosome associated protein, putative	0.805	0.845	0.558	7e-46
297813453	171	RNA recognition motif-containing protein	0.763	0.941	0.542	2e-44
30681329	173	RNA recognition motif-containing protein	0.777	0.947	0.528	3e-44

>gi|86156022|gb|ABC86742.1| RNA recognition motif-containing protein [Vitis pseudoreticulata]

 Score =  222 bits (565), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 116/189 (61%), Positives = 141/189 (74%), Gaps = 9/189 (4%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
           ++ SGC+VYIGNLDE+V++RVLYDILIQAGRVVDLYIPRDKETD+PKGFAF EYE+EEI 
Sbjct: 2   SAKSGCSVYIGNLDERVSDRVLYDILIQAGRVVDLYIPRDKETDRPKGFAFAEYETEEIA 61

Query: 86  HYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSRSDPVPMPVNGMEISH 145
            YA+KLFSG+VTLYNRTL+FA+SGQDK    SS   TP S+      P P+P N ME S 
Sbjct: 62  DYAVKLFSGLVTLYNRTLKFAISGQDK---PSSAAITPTSNSSLEPKPHPVPFNNMENSQ 118

Query: 146 HSMRISVPRHYSS-----EEPPPPGVTL-ETNGYETHLNVTNYDYSRRVFGATLDSISRS 199
           HSM +  P   ++      + P    TL + N Y + L+  +YDYSRRVFGATLDSISR+
Sbjct: 119 HSMGLRTPCRLAAHPVNYAQVPASSDTLHQPNRYSSQLDGHSYDYSRRVFGATLDSISRT 178

Query: 200 RSGHYNSSN 208
           RS +Y+SSN
Sbjct: 179 RSRYYDSSN 187

Source: Vitis pseudoreticulata

Species: Vitis pseudoreticulata

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356576175|ref|XP_003556209.1| PREDICTED: uncharacterized protein LOC100803118 [Glycine max]

 Score =  221 bits (564), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 110/190 (57%), Positives = 140/190 (73%), Gaps = 7/190 (3%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
           MSGNSN  C+VYIGNLDE+V +RVLYDILIQAGRVVDL+IP+DKE++KPKGFAF EYE+E
Sbjct: 1   MSGNSN--CSVYIGNLDERVTDRVLYDILIQAGRVVDLHIPKDKESEKPKGFAFAEYETE 58

Query: 83  EIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSRSDPVPMPVNGME 142
           EI  YA++LFSG++TLYNRTL+FA+SG+DK   N S    P  +   R  P P+P+N  E
Sbjct: 59  EIADYAVRLFSGLITLYNRTLKFAISGRDKTTSNGSTAIAPTLNSSQRPRPYPVPINNSE 118

Query: 143 ISHHSMRISVPRHYS-----SEEPPPPGVTLETNGYETHLNVTNYDYSRRVFGATLDSIS 197
              H  R+S P  +S     + +  P  VT +++GY +H +  NY+YSRR FGATLDSIS
Sbjct: 119 NFQHPARLSTPDRFSDYPVNNSQVLPSRVTDQSSGYGSHYSGNNYEYSRRAFGATLDSIS 178

Query: 198 RSRSGHYNSS 207
           RSRS H++ S
Sbjct: 179 RSRSRHFDKS 188

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225460024|ref|XP_002271789.1| PREDICTED: 33 kDa ribonucleoprotein, chloroplastic [Vitis vinifera] gi|297734803|emb|CBI17037.3| unnamed protein product [Vitis vinifera]

 Score =  219 bits (559), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 115/189 (60%), Positives = 141/189 (74%), Gaps = 9/189 (4%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
           ++ SGC+VYIGNLDE+V++RVLYDILIQAGRVVDLYIPRDKETD+PKGFAF EYE+EEI 
Sbjct: 2   SAKSGCSVYIGNLDERVSDRVLYDILIQAGRVVDLYIPRDKETDRPKGFAFAEYETEEIA 61

Query: 86  HYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSRSDPVPMPVNGMEISH 145
            YA+KLFSG+VTLYNRTL+FA+SGQDK    SS   TP S+      P P+P N ME S 
Sbjct: 62  DYAVKLFSGLVTLYNRTLKFAISGQDK---PSSAAITPTSNSSLEPKPHPVPFNNMENSQ 118

Query: 146 HSMRISVPRHYSSE-----EPPPPGVTL-ETNGYETHLNVTNYDYSRRVFGATLDSISRS 199
           HSM +  P   ++      + P    TL + N Y + L+  +YDYSRRVFGATLDSISR+
Sbjct: 119 HSMGLRTPCRLAAHPVNYAQVPASSDTLHQPNRYSSQLDGHSYDYSRRVFGATLDSISRT 178

Query: 200 RSGHYNSSN 208
           RS +++SSN
Sbjct: 179 RSRYHDSSN 187

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356535691|ref|XP_003536377.1| PREDICTED: RNA-binding protein 7-like [Glycine max]

 Score =  209 bits (531), Expect = 8e-52,   Method: Compositional matrix adjust.
 Identities = 103/177 (58%), Positives = 130/177 (73%), Gaps = 7/177 (3%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
           MSGNSN  C+VYIGNLDE+V +RVLYDILIQAGRVVDL+IP+DKE++KPKGFAF EYE+E
Sbjct: 1   MSGNSN--CSVYIGNLDERVTDRVLYDILIQAGRVVDLHIPKDKESEKPKGFAFAEYETE 58

Query: 83  EIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSRSDPVPMPVNGME 142
           EI  YA++LFSG++TLYNRTL+FA+SG+DK   N S   TP S+   R  P P+ +N  E
Sbjct: 59  EIADYAVRLFSGLITLYNRTLKFAISGRDKTTSNGSTAITPTSNSSQRPRPYPVSINNSE 118

Query: 143 ISHHSMRISVPRHYSS-----EEPPPPGVTLETNGYETHLNVTNYDYSRRVFGATLD 194
              HS R+S P  +S       +  P  VT +++GY +H +  NY+YSRR FGATLD
Sbjct: 119 NFQHSARLSTPDRFSDHPVNYSQVLPSRVTDQSSGYGSHYSGNNYEYSRRAFGATLD 175

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224127921|ref|XP_002329210.1| predicted protein [Populus trichocarpa] gi|222870991|gb|EEF08122.1| predicted protein [Populus trichocarpa]

 Score =  201 bits (511), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 110/191 (57%), Positives = 146/191 (76%), Gaps = 7/191 (3%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
           MSG S+  C++YIGNLDE+V++RVLYDILIQAGRVVDL+IPRD+ETDKPKG+AF EYE+E
Sbjct: 1   MSGPSS--CSIYIGNLDERVSDRVLYDILIQAGRVVDLHIPRDRETDKPKGYAFAEYETE 58

Query: 83  EIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSRSDPV-PMPVNGM 141
           EI  YA+KLFSG+VTLYNRTL+FA+SGQDK AQN+     P+ +  +R  P  P+ +N +
Sbjct: 59  EIADYAVKLFSGLVTLYNRTLKFAISGQDKLAQNNLNGVVPVPNSSNRQRPSHPVLINNL 118

Query: 142 EISHHSMRISVPRHYSS----EEPPPPGVTLETNGYETHLNVTNYDYSRRVFGATLDSIS 197
           EI +HSMR+S P   S+    +   PPGVT  +NGY ++ N  + D  RR+FG+ +++IS
Sbjct: 119 EIPNHSMRLSAPSRVSAYPANDSLAPPGVTNLSNGYGSNSNGNSNDSDRRLFGSAVNAIS 178

Query: 198 RSRSGHYNSSN 208
           RSRS  Y++SN
Sbjct: 179 RSRSRWYDTSN 189

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357443447|ref|XP_003592001.1| Peptidyl-prolyl cis-trans isomerase [Medicago truncatula] gi|355481049|gb|AES62252.1| Peptidyl-prolyl cis-trans isomerase [Medicago truncatula]

 Score =  199 bits (507), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 103/187 (55%), Positives = 129/187 (68%), Gaps = 11/187 (5%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
           MSGNS+  C VYIGNLDE+V +R+LYDILIQAGRVVDL+IP+DKE++KPKGFAF EYE+E
Sbjct: 1   MSGNSS--CTVYIGNLDERVTDRILYDILIQAGRVVDLHIPKDKESEKPKGFAFAEYETE 58

Query: 83  EIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSRSDPVPMPVNGME 142
           EI  YA++LFSG+VTLY RTL+FA+SG+DKN  NSS  TTP S+   R  P P+ +N  E
Sbjct: 59  EIADYAVRLFSGLVTLYKRTLKFAISGRDKNTPNSSTATTPSSNSSQRPRPYPVQINSSE 118

Query: 143 ISHHSMRISVPRHYSSEEPPPPGV---------TLETNGYETHLNVTNYDYSRRVFGATL 193
              HS R S+P  +S        V         T ++N Y +H    + D+SRR FG  L
Sbjct: 119 NFQHSARQSIPDRFSDRALNYSQVGELLGRNRATNQSNAYGSHFGGNHLDHSRRAFGEEL 178

Query: 194 DSISRSR 200
           D+ SRSR
Sbjct: 179 DNASRSR 185

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217074838|gb|ACJ85779.1| unknown [Medicago truncatula]

 Score =  195 bits (496), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 104/192 (54%), Positives = 129/192 (67%), Gaps = 16/192 (8%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
           MSGNS+  C VYIGNLDE+V +R+LYDILIQAGRVVDL+IP+DKE++KPKGFAF EYE+E
Sbjct: 1   MSGNSS--CTVYIGNLDERVTDRILYDILIQAGRVVDLHIPKDKESEKPKGFAFAEYETE 58

Query: 83  EIGHYAIKLFSGIVTLYNRTLRFA-----LSGQDKNAQNSSMTTTPLSSRKSRSDPVPMP 137
           EI  YA++LFSG+VTLY RTL+FA     LSG+DKN  NSS  TTP S+   R  P P+ 
Sbjct: 59  EIADYAVRLFSGLVTLYKRTLKFASANKQLSGRDKNTPNSSTATTPSSNSSQRPRPYPVQ 118

Query: 138 VNGMEISHHSMRISVPRHYSSEEPPPPGV---------TLETNGYETHLNVTNYDYSRRV 188
           +N  E   HS R S+P  +S        V         T ++N Y +H    + D+SRR 
Sbjct: 119 INSSENFQHSARQSIPDRFSDRALNYSQVGELLGRNRATNQSNAYGSHFGGNHLDHSRRA 178

Query: 189 FGATLDSISRSR 200
           FG  LD+ SRSR
Sbjct: 179 FGEELDNASRSR 190

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255564912|ref|XP_002523449.1| spliceosome associated protein, putative [Ricinus communis] gi|223537277|gb|EEF38908.1| spliceosome associated protein, putative [Ricinus communis]

 Score =  189 bits (480), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 100/179 (55%), Positives = 125/179 (69%), Gaps = 9/179 (5%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
           M G+S S C VYIGNLDE+V+ERVLYDILIQAGRVV+LYIPRDKETDK KG+AF EYESE
Sbjct: 1   MHGSSTS-CTVYIGNLDERVSERVLYDILIQAGRVVELYIPRDKETDKSKGYAFAEYESE 59

Query: 83  EIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSRSDPVPMPVNGME 142
           +I  YA+KLFSG+V L+NRTL+FA+SGQDK  QN S      S+  ++  P PMP+N ++
Sbjct: 60  QIADYAVKLFSGLVILHNRTLKFAISGQDKALQNVSSGAMHASNSSNKPRPYPMPMNNVD 119

Query: 143 ISHHSMRISVPRHYS------SEEPPPPGVTLETNGYETHLNVTNYD--YSRRVFGATL 193
            ++ SMR+S     S      S+ P   GVT   NG+ +  N  NYD    RRVFG++ 
Sbjct: 120 NTNQSMRLSASCRISAYPYNHSQVPVSSGVTHHHNGFGSQFNGVNYDNGIGRRVFGSSF 178

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297813453|ref|XP_002874610.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297320447|gb|EFH50869.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  184 bits (467), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 102/188 (54%), Positives = 125/188 (66%), Gaps = 27/188 (14%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
           ++NS C VYIGN+DE+V++RVLYDI+IQAGRV+DL+IPRDKETDKPKGFAF EYE+EEI 
Sbjct: 2   STNSNCTVYIGNVDERVSDRVLYDIMIQAGRVIDLHIPRDKETDKPKGFAFAEYETEEIA 61

Query: 86  HYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSRSDPVPMPVNGMEISH 145
            YA+KLFSG+V+LYNR L+FA+SGQDK   NS   T P S     SD       G    H
Sbjct: 62  DYAVKLFSGLVSLYNRNLKFAISGQDKLQANSGQRTRPQSLAFEHSD------RGYN-HH 114

Query: 146 HSMRIS---------VPRHYSSEEPPPPGVTLETNGYETHLNVTNYDYSRRVFGATLDSI 196
           HS R S         +P  Y ++EPPPPGV+          N  + +YSRRV G+ LDSI
Sbjct: 115 HSERFSSQLISPPSPLPLDY-TQEPPPPGVS----------NGASLEYSRRVLGSALDSI 163

Query: 197 SRSRSGHY 204
           + SR   Y
Sbjct: 164 NHSRPRRY 171

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30681329|ref|NP_192749.2| RNA recognition motif-containing protein [Arabidopsis thaliana] gi|26453246|dbj|BAC43696.1| unknown protein [Arabidopsis thaliana] gi|28372886|gb|AAO39925.1| At4g10100 [Arabidopsis thaliana] gi|332657441|gb|AEE82841.1| RNA recognition motif-containing protein [Arabidopsis thaliana]

 Score =  183 bits (465), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 101/191 (52%), Positives = 127/191 (66%), Gaps = 27/191 (14%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
           MSG SN  C VYIGN+DE+V++RVLYDI+IQAGRV+DL+IPRDKETDKPKGFAF EYE+E
Sbjct: 1   MSGTSN--CTVYIGNVDERVSDRVLYDIMIQAGRVIDLHIPRDKETDKPKGFAFAEYETE 58

Query: 83  EIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSRSDPVPMPVNGME 142
           EI  YA+KLFSG+V+LYNRTL+FA+SGQDK   NS+      S  ++R   +    +   
Sbjct: 59  EIADYAVKLFSGLVSLYNRTLKFAISGQDKLQSNSAN-----SGHRARPQSLAFEHSDRA 113

Query: 143 ISHHSMRIS---------VPRHYSSEEPPPPGVTLETNGYETHLNVTNYDYSRRVFGATL 193
             HH  R S         +P  Y ++EPPPPGV+          N  + +YSRRV G+ L
Sbjct: 114 AYHHLERFSSQLISPPSPLPLDY-TQEPPPPGVS----------NGASLEYSRRVLGSAL 162

Query: 194 DSISRSRSGHY 204
           DSI+ SR   Y
Sbjct: 163 DSINHSRPRRY 173

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	211
TAIR|locus:2124670	173	AT4G10110 [Arabidopsis thalian	0.786	0.959	0.555	3.5e-43
TAIR|locus:2046298	363	emb2444 "embryo defective 2444	0.426	0.247	0.362	3.5e-17
WB|WBGene00004723	388	sap-49 [Caenorhabditis elegans	0.402	0.219	0.390	6.4e-16
UNIPROTKB|Q09442	388	sap-49 "Splicing factor 3B sub	0.402	0.219	0.390	6.4e-16
ZFIN|ZDB-GENE-020419-22	400	sf3b4 "splicing factor 3b, sub	0.402	0.212	0.413	7.5e-16
UNIPROTKB|F1MWR2	424	SF3B4 "Uncharacterized protein	0.402	0.200	0.413	7.6e-16
UNIPROTKB|E2R5T2	424	SF3B4 "Uncharacterized protein	0.402	0.200	0.413	7.6e-16
UNIPROTKB|Q15427	424	SF3B4 "Splicing factor 3B subu	0.402	0.200	0.413	7.6e-16
UNIPROTKB|F1SDG0	424	SF3B4 "Uncharacterized protein	0.402	0.200	0.413	7.6e-16
MGI|MGI:109580	424	Sf3b4 "splicing factor 3b, sub	0.402	0.200	0.413	7.6e-16

TAIR|locus:2124670 AT4G10110 [Arabidopsis thaliana (taxid:3702)]

 Score = 456 (165.6 bits), Expect = 3.5e-43, P = 3.5e-43
 Identities = 105/189 (55%), Positives = 129/189 (68%)

Query:    23 MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
             MSG SN  C VYIGN+DE+V++RVLYDI+IQAGRV+DL+IPRDKETDKPKGFAF EYE+E
Sbjct:     1 MSGTSN--CTVYIGNVDERVSDRVLYDIMIQAGRVIDLHIPRDKETDKPKGFAFAEYETE 58

Query:    83 EIGHYAIKLFSGIVTLYNRTLRFALSGQDK---NAQNSSMTTTPLSSRKSRSDPVPMPVN 139
             EI  YA+KLFSG+V+LYNRTL+FA+SGQDK   N+ NS     P S     SD      +
Sbjct:    59 EIADYAVKLFSGLVSLYNRTLKFAISGQDKLQSNSANSGHRARPQSLAFEHSDRAAY--H 116

Query:   140 GMEISHHSMRIS----VPRHYSSEEPPPPGVTLETNGYETHLNVTNYDYSRRVFGATLDS 195
              +E    S  IS    +P  Y+ +EPPPPGV+   NG        + +YSRRV G+ LDS
Sbjct:   117 HLE-RFSSQLISPPSPLPLDYT-QEPPPPGVS---NG-------ASLEYSRRVLGSALDS 164

Query:   196 ISRSRSGHY 204
             I+ SR   Y
Sbjct:   165 INHSRPRRY 173

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2046298 emb2444 "embryo defective 2444" [Arabidopsis thaliana (taxid:3702)]

 Score = 187 (70.9 bits), Expect = 3.5e-17, Sum P(2) = 3.5e-17
 Identities = 33/91 (36%), Positives = 60/91 (65%)

Query:    24 SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
             S   N    VY+G LD +++E +L+++ +QAG VV++Y+P+D+ T+  + + F+EY SEE
Sbjct:    18 SAERNQDATVYVGGLDAQLSEELLWELFVQAGPVVNVYVPKDRVTNLHQNYGFIEYRSEE 77

Query:    84 IGHYAIKLFSGIVTLYNRTLRFALSGQDKNA 114
                YAIK+ + ++ L+ + +R   + QDK +
Sbjct:    78 DADYAIKVLN-MIKLHGKPIRVNKASQDKKS 107

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0009793 "embryo development ending in seed dormancy" evidence=NAS

GO:0005730 "nucleolus" evidence=IDA

WB|WBGene00004723 sap-49 [Caenorhabditis elegans (taxid:6239)]

 Score = 181 (68.8 bits), Expect = 6.4e-16, Sum P(2) = 6.4e-16
 Identities = 34/87 (39%), Positives = 57/87 (65%)

Query:    28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
             N    +Y+G LDEKV+E +L+++++QAG VV + +P+D+ T   +GF FVE+  EE   Y
Sbjct:    10 NQDATIYVGGLDEKVSESILWELMVQAGPVVSVNMPKDRVTANHQGFGFVEFMGEEDADY 69

Query:    88 AIKLFSGIVTLYNRTLRF-ALSGQDKN 113
             AIK+ + ++ LY + ++    S  +KN
Sbjct:    70 AIKILN-MIKLYGKPIKVNKASAHEKN 95

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0042127 "regulation of cell proliferation" evidence=IMP

GO:0040020 "regulation of meiosis" evidence=IMP

GO:0040022 "feminization of hermaphroditic germ-line" evidence=IMP

GO:0007281 "germ cell development" evidence=IMP

UNIPROTKB|Q09442 sap-49 "Splicing factor 3B subunit 4" [Caenorhabditis elegans (taxid:6239)]

 Score = 181 (68.8 bits), Expect = 6.4e-16, Sum P(2) = 6.4e-16
 Identities = 34/87 (39%), Positives = 57/87 (65%)

Query:    28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
             N    +Y+G LDEKV+E +L+++++QAG VV + +P+D+ T   +GF FVE+  EE   Y
Sbjct:    10 NQDATIYVGGLDEKVSESILWELMVQAGPVVSVNMPKDRVTANHQGFGFVEFMGEEDADY 69

Query:    88 AIKLFSGIVTLYNRTLRF-ALSGQDKN 113
             AIK+ + ++ LY + ++    S  +KN
Sbjct:    70 AIKILN-MIKLYGKPIKVNKASAHEKN 95

GO:0005515 "protein binding" evidence=IPI

ZFIN|ZDB-GENE-020419-22 sf3b4 "splicing factor 3b, subunit 4" [Danio rerio (taxid:7955)]

 Score = 181 (68.8 bits), Expect = 7.5e-16, Sum P(2) = 7.5e-16
 Identities = 36/87 (41%), Positives = 59/87 (67%)

Query:    28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
             N    VY+G LDEKV+E +L+++ +QAG VV+ ++P+D+ T + +G+ FVE+ SEE   Y
Sbjct:    10 NQDAAVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 69

Query:    88 AIKLFSGIVTLYNRTLRF-ALSGQDKN 113
             AIK+ + ++ LY + +R    S  +KN
Sbjct:    70 AIKIMN-MIKLYGKPIRVNKASAHNKN 95

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1MWR2 SF3B4 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 183 (69.5 bits), Expect = 7.6e-16, Sum P(2) = 7.6e-16
 Identities = 36/87 (41%), Positives = 59/87 (67%)

Query:    28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
             N    VY+G LDEKV+E +L+++ +QAG VV+ ++P+D+ T + +G+ FVE+ SEE   Y
Sbjct:    10 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 69

Query:    88 AIKLFSGIVTLYNRTLRF-ALSGQDKN 113
             AIK+ + ++ LY + +R    S  +KN
Sbjct:    70 AIKIMN-MIKLYGKPIRVNKASAHNKN 95

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2R5T2 SF3B4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 183 (69.5 bits), Expect = 7.6e-16, Sum P(2) = 7.6e-16
 Identities = 36/87 (41%), Positives = 59/87 (67%)

Query:    28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
             N    VY+G LDEKV+E +L+++ +QAG VV+ ++P+D+ T + +G+ FVE+ SEE   Y
Sbjct:    10 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 69

Query:    88 AIKLFSGIVTLYNRTLRF-ALSGQDKN 113
             AIK+ + ++ LY + +R    S  +KN
Sbjct:    70 AIKIMN-MIKLYGKPIRVNKASAHNKN 95

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q15427 SF3B4 "Splicing factor 3B subunit 4" [Homo sapiens (taxid:9606)]

 Score = 183 (69.5 bits), Expect = 7.6e-16, Sum P(2) = 7.6e-16
 Identities = 36/87 (41%), Positives = 59/87 (67%)

Query:    28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
             N    VY+G LDEKV+E +L+++ +QAG VV+ ++P+D+ T + +G+ FVE+ SEE   Y
Sbjct:    10 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 69

Query:    88 AIKLFSGIVTLYNRTLRF-ALSGQDKN 113
             AIK+ + ++ LY + +R    S  +KN
Sbjct:    70 AIKIMN-MIKLYGKPIRVNKASAHNKN 95

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005689 "U12-type spliceosomal complex" evidence=IDA

GO:0006397 "mRNA processing" evidence=TAS

GO:0000375 "RNA splicing, via transesterification reactions" evidence=TAS

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

GO:0005681 "spliceosomal complex" evidence=IDA

GO:0005654 "nucleoplasm" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|F1SDG0 SF3B4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 183 (69.5 bits), Expect = 7.6e-16, Sum P(2) = 7.6e-16
 Identities = 36/87 (41%), Positives = 59/87 (67%)

Query:    28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
             N    VY+G LDEKV+E +L+++ +QAG VV+ ++P+D+ T + +G+ FVE+ SEE   Y
Sbjct:    10 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 69

Query:    88 AIKLFSGIVTLYNRTLRF-ALSGQDKN 113
             AIK+ + ++ LY + +R    S  +KN
Sbjct:    70 AIKIMN-MIKLYGKPIRVNKASAHNKN 95

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:109580 Sf3b4 "splicing factor 3b, subunit 4" [Mus musculus (taxid:10090)]

 Score = 183 (69.5 bits), Expect = 7.6e-16, Sum P(2) = 7.6e-16
 Identities = 36/87 (41%), Positives = 59/87 (67%)

Query:    28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
             N    VY+G LDEKV+E +L+++ +QAG VV+ ++P+D+ T + +G+ FVE+ SEE   Y
Sbjct:    10 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 69

Query:    88 AIKLFSGIVTLYNRTLRF-ALSGQDKN 113
             AIK+ + ++ LY + +R    S  +KN
Sbjct:    70 AIKIMN-MIKLYGKPIRVNKASAHNKN 95

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=ISO

GO:0005689 "U12-type spliceosomal complex" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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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	211
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	3e-31
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	3e-22
smart00360	73	smart00360, RRM, RNA recognition motif	1e-18
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-15
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-15
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-14
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	2e-14
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	4e-13
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	7e-13
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	8e-13
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-12
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-11
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-10
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	5e-10
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	5e-10
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	8e-10
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	8e-10
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	9e-10
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-09
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	6e-09
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	1e-08
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	1e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-08
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-08
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-08
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	3e-08
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	5e-08
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	6e-08
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	6e-08
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	9e-08
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	1e-07
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-07
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-07
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-07
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-07
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	2e-07
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	3e-07
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	5e-07
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	5e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	1e-06
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-06
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	3e-06
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	4e-06
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	5e-06
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	7e-06
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	8e-06
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	8e-06
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-05
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-05
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	1e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-05
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-05
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	2e-05
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	2e-05
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	2e-05
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-05
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	3e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-05
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	4e-05
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	4e-05
cd12492	85	cd12492, RRM2_RBM46, RNA recognition motif 2 found	4e-05
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	4e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	4e-05
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	5e-05
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	5e-05
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	5e-05
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	5e-05
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	6e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	6e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	7e-05
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	7e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	1e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-04
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-04
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	1e-04
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	1e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-04
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	2e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-04
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-04
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	2e-04
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	2e-04
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-04
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	3e-04
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	3e-04
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	3e-04
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	3e-04
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	3e-04
cd12533	84	cd12533, RRM_EWS, RNA recognition motif in vertebr	4e-04
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	4e-04
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	5e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	5e-04
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	5e-04
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	6e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	6e-04
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	8e-04
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	8e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	0.001
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	0.001
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.001
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	0.001
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	0.001
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	0.001
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	0.001
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.001
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	0.001
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.002
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.002
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	0.002
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	0.002
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	0.002
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	0.002
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	0.002
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	0.002
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	0.003
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.003
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	0.003
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	0.003
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	0.003
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	0.003
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	0.003
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	0.003
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	0.003
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	0.004
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	0.004
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	0.004
cd12490	85	cd12490, RRM2_ACF, RNA recognition motif 2 in vert	0.004
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	0.004
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	0.004

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

 Score =  108 bits (273), Expect = 3e-31
 Identities = 36/73 (49%), Positives = 53/73 (72%), Gaps = 1/73 (1%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           VY+GNLDEKV E +L+++ IQAG VV+++IP+D+ T   +G+ FVE+ SEE   YAIK+ 
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 93  SGIVTLYNRTLRF 105
           + I  LY + +R 
Sbjct: 61  NMI-KLYGKPIRV 72

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

 Score = 85.4 bits (212), Expect = 3e-22
 Identities = 32/74 (43%), Positives = 48/74 (64%), Gaps = 2/74 (2%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
             +++GNLD +V E +LY++ +QAG +  + IP+D    KPK FAFV ++ E    YAI+
Sbjct: 2   RTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHEVSVPYAIQ 60

Query: 91  LFSGIVTLYNRTLR 104
           L +GI  L+ R LR
Sbjct: 61  LLNGI-RLFGRELR 73

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|214636 smart00360, RRM, RNA recognition motif

 Score = 76.5 bits (189), Expect = 1e-18
 Identities = 29/73 (39%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
            +++GNL     E  L ++  + G+V  + + RDKET K KGFAFVE+ESEE    A++ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 92  FSGIVTLYNRTLR 104
            +G   L  R L+
Sbjct: 61  LNGKE-LDGRPLK 72

Length = 73

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

 Score = 68.0 bits (167), Expect = 2e-15
 Identities = 25/51 (49%), Positives = 35/51 (68%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          +Y+G L E+V+E+VL+   I  G + D+ IP D ET K +GFAFVE+E  E
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPE 51

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 66.8 bits (164), Expect = 5e-15
 Identities = 28/72 (38%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +++GNL     E  L D+  + G +  + I RD ET + KGFAFVE+E EE    A++  
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 93  SGIVTLYNRTLR 104
           +G   L  R LR
Sbjct: 60  NGK-ELGGRELR 70

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

 Score = 65.6 bits (161), Expect = 2e-14
 Identities = 20/60 (33%), Positives = 34/60 (56%)

Query: 35 IGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSG 94
          + NL E  +E  L ++    G +  +Y+ +DKET + +GFAFV + + E    AI+  +G
Sbjct: 4  VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 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|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 65.3 bits (159), Expect = 2e-14
 Identities = 32/72 (44%), Positives = 49/72 (68%), Gaps = 2/72 (2%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +++GNLD KV E +++++ +QAG V+ + IP+DK+  KPK FAFV ++ E    YA+ L 
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKD-GKPKQFAFVNFKHEVSVPYAMNLL 62

Query: 93  SGIVTLYNRTLR 104
           +GI  LY R L 
Sbjct: 63  NGI-KLYGRPLN 73

This subfamily corresponds to the RRM of RBM7, a 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. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It 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. RBM7 contains 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. . Length = 75

>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 61.9 bits (150), Expect = 4e-13
 Identities = 30/72 (41%), Positives = 47/72 (65%), Gaps = 2/72 (2%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +++GNL+ +V E +LY++ +QAG +  + I +DKE  KPK F FV ++  E   YAI L 
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAIALL 62

Query: 93  SGIVTLYNRTLR 104
           +GI  LY R ++
Sbjct: 63  NGI-RLYGRPIK 73

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 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. RBM11 contains 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 of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>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 = 61.1 bits (149), Expect = 7e-13
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           V++GN+     E  L +I  + G VV   +  D++T KPKG+ F E+E  E    AI+  
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 93  SGIVTLYNRTLR 104
           +G      R LR
Sbjct: 61  NGY-EFNGRALR 71

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

 Score = 60.8 bits (148), Expect = 8e-13
 Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +++GNL     E  L ++  + G +  + I RDK   K KGFAFVE+ES E    A++  
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 93  SGIVTLYNRTLR 104
           +G   L  R L+
Sbjct: 60  NG-KELDGRKLK 70

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 61.1 bits (149), Expect = 1e-12
 Identities = 28/72 (38%), Positives = 42/72 (58%), Gaps = 1/72 (1%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +YIG L  ++ E  +  +  Q G +VD+ + RDK+T K KGFAF+ YE +     A+   
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 93  SGIVTLYNRTLR 104
           +GI  L  RT+R
Sbjct: 72  NGI-KLLGRTIR 82

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

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

 Score = 57.6 bits (140), Expect = 2e-11
 Identities = 25/63 (39%), Positives = 36/63 (57%)

Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
          N+Y+GNL   V E  L D+  Q G V    +  D+ET + +GF FVE E+ E  + AI+ 
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 92 FSG 94
           +G
Sbjct: 61 LNG 63

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

 Score = 55.0 bits (133), Expect = 2e-10
 Identities = 28/66 (42%), Positives = 41/66 (62%), Gaps = 1/66 (1%)

Query: 30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDL-YIPRDKETDKPKGFAFVEYESEEIGHYA 88
          G N++IGNLD +V+E++LYD     G ++    I RD +T   KGFAF+ Y+S E    A
Sbjct: 1  GANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAA 60

Query: 89 IKLFSG 94
          I+  +G
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|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 = 53.8 bits (130), Expect = 5e-10
 Identities = 19/61 (31%), Positives = 34/61 (55%)

Query: 30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
          G  +++  L  +  E+ L  +  + GRV ++ + +D ET + +GF FV +ES E    AI
Sbjct: 1  GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60

Query: 90 K 90
          +
Sbjct: 61 R 61

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

 Score = 57.3 bits (137), Expect = 5e-10
 Identities = 33/106 (31%), Positives = 50/106 (47%), Gaps = 1/106 (0%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
           +      +++GNL   V E  L ++  + G V  + + RD+ET K +GFAFVE+ESEE  
Sbjct: 111 SKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESA 170

Query: 86  HYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSRS 131
             AI+  +G   L  R LR   +      ++        S  K  S
Sbjct: 171 EKAIEELNGKE-LEGRPLRVQKAQPASQPRSELSNNLDASFAKKLS 215

Length = 306

>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 52.9 bits (128), Expect = 8e-10
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           V++GNL   + E  L       G V  + I RD++T   KGF +V +++++    A+KL 
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL- 60

Query: 93  SGIVTLYNRTLR 104
           +GI  L  R +R
Sbjct: 61  NGI-KLKGRKIR 71

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

>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 = 52.9 bits (127), Expect = 8e-10
 Identities = 27/72 (37%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           V++GN+  +  E  L DI  + G VV   +  D+ET KPKG+ F EY+ +E    A++  
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 93  SGIVTLYNRTLR 104
           +G   L  R LR
Sbjct: 61  NG-YELNGRQLR 71

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

 Score = 52.9 bits (128), Expect = 9e-10
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +Y+GNL     E  +Y++  + G +  + +  D+ T  P GF FVEY + E    A+K  
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 93  SGIVTLYNRTLR 104
           +G   L +R +R
Sbjct: 61  NGT-KLDDRIIR 71

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

 Score = 52.6 bits (127), Expect = 1e-09
 Identities = 24/59 (40%), Positives = 36/59 (61%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
          V++  L  KV ER LY+   +AG+V D+ I RD+ + + KG A+VE+  EE    A+ L
Sbjct: 2  VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGL 60

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

 Score = 51.1 bits (123), Expect = 6e-09
 Identities = 20/65 (30%), Positives = 36/65 (55%)

Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
            V++GN+ E V++  +  +L + G+V+     +D  T K K F F E+E  E    A++
Sbjct: 1  TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 91 LFSGI 95
          L +G+
Sbjct: 61 LLNGL 65

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

 Score = 49.9 bits (120), Expect = 1e-08
 Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 5/48 (10%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE 80
          VY+GNL  +  +R L D   + G +  +++ R      P GFAFVE+E
Sbjct: 2  VYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFE 44

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|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 49.9 bits (120), Expect = 1e-08
 Identities = 24/52 (46%), Positives = 30/52 (57%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
          VYIG+L     E  L     Q G V  L + R K+T K KG+AFVE+ES E+
Sbjct: 2  VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEV 53

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|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 = 49.5 bits (119), Expect = 1e-08
 Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 6/59 (10%)

Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
            VY+GNL   + E  L       G + ++ + +D      KG+AFV +++ E    AI
Sbjct: 1  TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAI 53

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 49.5 bits (119), Expect = 1e-08
 Identities = 29/72 (40%), Positives = 42/72 (58%), Gaps = 3/72 (4%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +Y+ NL   V E  L +     G+V  + + R+K  D+P+GFAFVE+ S E    A+K  
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKL 58

Query: 93  SGIVTLYNRTLR 104
           +G+V L  RTLR
Sbjct: 59  NGLV-LDGRTLR 69

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

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

 Score = 49.8 bits (120), Expect = 2e-08
 Identities = 18/60 (30%), Positives = 33/60 (55%)

Query: 34 YIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFS 93
          Y+G+L   V E +LY+I   AG V+ + + RD  T +  G+A+V +++      A+   +
Sbjct: 3  YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

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

 Score = 49.1 bits (117), Expect = 3e-08
 Identities = 23/66 (34%), Positives = 43/66 (65%), Gaps = 1/66 (1%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
          +++G L+++  E+ + ++    GRV D+Y+ RD E  + +G AFV+Y S+E+   AIK  
Sbjct: 2  LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKAL 60

Query: 93 SGIVTL 98
          +G+ T+
Sbjct: 61 NGVYTM 66

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|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 = 5e-08
 Identities = 20/51 (39%), Positives = 33/51 (64%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          +++G L   VN+  L +I    G V D+ +P D+E + P+G+A+VE+ES E
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPE 51

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

 Score = 47.9 bits (115), Expect = 6e-08
 Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
           N++I NLD+ ++ + LYD     G ++   +  D E    KG+ FV +E+EE    AI
Sbjct: 3  GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRAI 60

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

 Score = 48.1 bits (115), Expect = 6e-08
 Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
             VY+ NL   +    L+ I  + G+VV + I +DKET K KG AF+ +   E  H  +K
Sbjct: 2   STVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVK 61

Query: 91  LFSGIVTLYNRTLR 104
             +    L+ RTL+
Sbjct: 62  ALNNKE-LFGRTLK 74

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

 Score = 47.4 bits (113), Expect = 9e-08
 Identities = 20/63 (31%), Positives = 34/63 (53%)

Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
           +++GNL   V++  L     + G VV   +  D+ET + +GF +V++ES E    AI+ 
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 92 FSG 94
            G
Sbjct: 61 MDG 63

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

 Score = 47.6 bits (114), Expect = 1e-07
 Identities = 19/62 (30%), Positives = 31/62 (50%)

Query: 34 YIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFS 93
          ++  L+    E  L     + G +  + + RDK+T KP+G+AF+E+E E     A K   
Sbjct: 5  FVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYAD 64

Query: 94 GI 95
          G 
Sbjct: 65 GK 66

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

 Score = 47.3 bits (113), Expect = 1e-07
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVD---LYIPRDKETDKPKGFAFVEYESEEIGHYA 88
            ++IGNLD ++ E  L  +  + G++     L+        +P+G+ FV +E++E    A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 89  IKLFSGIVTLYNRTL 103
           +K  +G  T   + L
Sbjct: 61  LKSLNG-KTALGKKL 74

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

 Score = 46.8 bits (112), Expect = 2e-07
 Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          NVY+ NL E +++  L ++  + G++    + +D +  K KGF FV +E+ E
Sbjct: 3  NVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHE 53

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

 Score = 46.9 bits (112), Expect = 2e-07
 Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 35 IGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSG 94
          + NL  K  E  L  +    G V ++ IPR     K KGFAFV++ S+     AIK  +G
Sbjct: 4  VRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKGVNG 62

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|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 = 46.4 bits (111), Expect = 2e-07
 Identities = 21/70 (30%), Positives = 38/70 (54%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +++G L +   E  +  +  + G + ++ I RDK+T + KG AFV++ S E    AI+  
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 93  SGIVTLYNRT 102
            G VT+   +
Sbjct: 62  HGKVTMPGAS 71

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

 Score = 46.6 bits (111), Expect = 2e-07
 Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +++ NLD KV  + L ++   AG+VV   I  DKE  K +G   V++E       AI +F
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISMF 59

Query: 93  SGIVTLYNRTLR 104
           +G + L++R +R
Sbjct: 60  NGQM-LFDRPMR 70

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|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 45.8 bits (109), Expect = 3e-07
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +++GNL    +E  +Y+   + G +  + +P D ++ +PKGF +VE+ S+E    A+   
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 93  SGIVTLYNRTLR 104
            G   L  R +R
Sbjct: 61  GG-TDLLGRPVR 71

This subfamily corresponds to the RRM2 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 = 73

>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 = 45.7 bits (109), Expect = 5e-07
 Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 2/66 (3%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGR--VVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
          +Y+GNL     +  L   L +AG   V  +     K   K KGFA+VE+ SE       +
Sbjct: 1  LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 91 LFSGIV 96
             G  
Sbjct: 61 KLEGRE 66

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

 Score = 45.4 bits (108), Expect = 5e-07
 Identities = 15/51 (29%), Positives = 27/51 (52%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          +++GN+D       L +     G +  + I  DK T +PKGFA++E+  + 
Sbjct: 2  IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKS 52

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

 Score = 48.6 bits (116), Expect = 6e-07
 Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
           N+++ NLD+ V+ + L+D   + G ++   +  D E  K +G+ FV +E EE    AI+ 
Sbjct: 90  NIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQK 148

Query: 92  FSGIV 96
            +G++
Sbjct: 149 VNGML 153

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

 Score = 44.6 bits (106), Expect = 1e-06
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 5/78 (6%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPK---GFAFVEYESEEIGHYAI 89
           +Y+ NLD K++E  L  I  + G V  + IP+ ++  + +   GFAFV ++       A+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 90  KLFSGIVTLYNRTLRFAL 107
           +L      L  R +  +L
Sbjct: 63  QLNG--TELGGRKISVSL 78

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|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 44.1 bits (104), Expect = 2e-06
 Identities = 23/65 (35%), Positives = 33/65 (50%)

Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
          N+Y+ NL  ++ E  L  I    G +V   + RDK T  P+G AFV Y+  E    AI  
Sbjct: 2  NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 92 FSGIV 96
           +G +
Sbjct: 62 LNGTI 66

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

 Score = 43.8 bits (104), Expect = 2e-06
 Identities = 18/55 (32%), Positives = 29/55 (52%)

Query: 35 IGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
          + NL  +     L  +  + G V D+YIPRD+ T + +GFAFV +  +     A+
Sbjct: 3  VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAM 57

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|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 43.5 bits (103), Expect = 3e-06
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 11/75 (14%)

Query: 34  YIGNL-DEKVN---ERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
           ++GNL    V    + +  D+ +++ R+V     RDKETDK KGF +VE+E  E    A+
Sbjct: 5   FVGNLPFNTVQGDLDAIFKDLSVKSVRLV-----RDKETDKFKGFCYVEFEDVESLKEAL 59

Query: 90  KLFSGIVTLYNRTLR 104
           +    +    +R+LR
Sbjct: 60  EYDGAL--FDDRSLR 72

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

 Score = 42.6 bits (101), Expect = 4e-06
 Identities = 16/50 (32%), Positives = 26/50 (52%)

Query: 34 YIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          Y+GNL   + E  L  I    G +  + + RD ET + KG+ F+++   E
Sbjct: 2  YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAE 51

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

 Score = 42.7 bits (101), Expect = 5e-06
 Identities = 17/52 (32%), Positives = 28/52 (53%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
          +++G L   V E  L     Q G V ++ +  D E  +P+GF F+ +ESE+ 
Sbjct: 5  IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDS 56

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|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 42.3 bits (100), Expect = 7e-06
 Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 5/54 (9%)

Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
            V++G L E + E  L     Q G V D+YIP+       + FAFV +   E+
Sbjct: 1  RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFADPEV 49

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

 Score = 42.2 bits (100), Expect = 8e-06
 Identities = 18/61 (29%), Positives = 35/61 (57%)

Query: 34 YIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFS 93
          ++G+L+  ++E  +Y    + G V  + I R+K+T K  G+ FVE+ + E    A++  +
Sbjct: 3  WMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLN 62

Query: 94 G 94
          G
Sbjct: 63 G 63

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|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 = 42.1 bits (99), Expect = 8e-06
 Identities = 15/51 (29%), Positives = 32/51 (62%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          ++IG L    NE+ L  +  + G++ ++ + +D+ET + +GF FV +E+ +
Sbjct: 3  LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPD 53

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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 45.0 bits (106), Expect = 1e-05
 Identities = 29/90 (32%), Positives = 43/90 (47%), Gaps = 5/90 (5%)

Query: 12  NDVVSRNKRQIMS-----GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDK 66
           N +  RNKR  +S     G S    N+Y+ NL   + +  L  I  + G++V   I RDK
Sbjct: 170 NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDK 229

Query: 67  ETDKPKGFAFVEYESEEIGHYAIKLFSGIV 96
            T  P+G AFV +   E    AI   + ++
Sbjct: 230 LTGTPRGVAFVRFNKREEAQEAISALNNVI 259

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). Length = 346

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

 Score = 41.9 bits (99), Expect = 1e-05
 Identities = 20/48 (41%), Positives = 28/48 (58%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE 80
          +++G L E V E  L +   Q G V  + I  DKET K +GFAFV ++
Sbjct: 2  LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFD 49

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

 Score = 41.8 bits (98), Expect = 1e-05
 Identities = 17/65 (26%), Positives = 32/65 (49%)

Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
          N+Y+  L + + ++ L  +  Q GR++   I RD+ T   +G  F+ ++       AIK 
Sbjct: 2  NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKG 61

Query: 92 FSGIV 96
           +G  
Sbjct: 62 LNGQK 66

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

 Score = 41.6 bits (98), Expect = 1e-05
 Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 3/61 (4%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
          ++I NL     E  L  +  + G + ++++P DK T KPKGFAFV Y   E   +A+K F
Sbjct: 5  LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPE---HAVKAF 61

Query: 93 S 93
          +
Sbjct: 62 A 62

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

 Score = 41.9 bits (99), Expect = 1e-05
 Identities = 18/52 (34%), Positives = 28/52 (53%)

Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
            +++G L  +  E  L ++  + G +  L + RD  T   KG+AFVEYE E
Sbjct: 4  LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHE 55

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|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 41.2 bits (97), Expect = 2e-05
 Identities = 17/50 (34%), Positives = 29/50 (58%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
          +++G L   V E    +   Q G+VVD  + +D +T + +GF FV ++SE
Sbjct: 2  IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSE 51

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 75

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

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 13/50 (26%), Positives = 25/50 (50%)

Query: 34 YIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           +GNL  +  +    +++   G V   ++   + T + KG+ FVEY S+ 
Sbjct: 3  CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKA 52

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

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 17/36 (47%), Positives = 25/36 (69%), Gaps = 1/36 (2%)

Query: 55 GRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
          G++V +Y+P D ET K KG+AFVE+ + E    A+K
Sbjct: 34 GKIVGIYMPVD-ETGKTKGYAFVEFATPEEAKEAVK 68

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|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 2/47 (4%)

Query: 37 NLDEKVNERVLYDILIQAGRVV--DLYIPRDKETDKPKGFAFVEYES 81
           LD    E  +   L     V   D+ + RDK T   +GFAFVE+ S
Sbjct: 9  GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPS 55

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 84

>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 41.3 bits (97), Expect = 2e-05
 Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
            VY+ ++D++V E  L  +    G+VVD  +  D   +    FAF+E+  EE    A+ 
Sbjct: 3  RTVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGD--PNSVLRFAFIEFTDEEGARAALS 60

Query: 91 L 91
          L
Sbjct: 61 L 61

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 40.8 bits (96), Expect = 3e-05
 Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 30  GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
           G  +++ NL    +E +L+ +    G V ++ + RD  T+K KG+ FV   + E  + AI
Sbjct: 1   GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60

Query: 90  KLFSGIVTLYNRTL 103
              +G   L  R L
Sbjct: 61  ASLNG-YRLGGRVL 73

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

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

 Score = 40.8 bits (96), Expect = 3e-05
 Identities = 14/26 (53%), Positives = 21/26 (80%)

Query: 55 GRVVDLYIPRDKETDKPKGFAFVEYE 80
          G +VD+YIP D  T +P+GFA+V++E
Sbjct: 25 GPIVDVYIPLDFYTRRPRGFAYVQFE 50

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 = 43.6 bits (103), Expect = 4e-05
 Identities = 22/85 (25%), Positives = 42/85 (49%), Gaps = 1/85 (1%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +Y+G+LD  V E  LYD+    G V+ + + RD  T +  G+ +V +++      A++  
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 93  SGIVTLYNRTLRFALSGQDKNAQNS 117
                L  + +R   S +D + + S
Sbjct: 63  -NFKRLGGKPIRIMWSQRDPSLRRS 86

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

 Score = 40.3 bits (95), Expect = 4e-05
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
          +++ NL   V  + L D+  + G V+   +  D +  + KGF  V +ES E    AI++F
Sbjct: 1  IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMF 59

Query: 93 SGI 95
          +G 
Sbjct: 60 NGY 62

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

 Score = 40.2 bits (95), Expect = 4e-05
 Identities = 14/51 (27%), Positives = 27/51 (52%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          +++G L   V E  L +   + G V D+ I + K+    +GFA+++  + E
Sbjct: 2  LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSE 52

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|240936 cd12492, RRM2_RBM46, RNA recognition motif 2 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 40.8 bits (95), Expect = 4e-05
 Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 3/79 (3%)

Query: 31  CNVYIGNL-DEKVNERVLYDILIQAGRVVDLYI-PRDKETDKPKGFAFVEYESEEIGHYA 88
           C ++IG++  EK  E +L ++      V+D+ + P   +  K +GFAFVEYES      A
Sbjct: 3   CRLFIGSIPKEKKKEEILEEMKKVTEGVMDVIVYPSATDRTKNRGFAFVEYESHRAAAMA 62

Query: 89  -IKLFSGIVTLYNRTLRFA 106
             KL  G   L+  T++  
Sbjct: 63  RRKLIPGTFQLWGHTIQVD 81

This subgroup corresponds to the RRM2 of RBM46, also termed cancer/testis antigen 68 (CT68). It 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 = 85

>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 40.5 bits (95), Expect = 4e-05
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
           N+ I  L + + +     + +  G V +  I RDK T    GF FV+Y+S E    AI+ 
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 92  FSGIVTLYNRTLRFALS 108
            +G+  L N+ ++ A +
Sbjct: 62  LNGL-QLQNKRIKVAYA 77

This subfamily corresponds to the RRM1 of 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 = 81

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 43.3 bits (102), Expect = 4e-05
 Identities = 29/107 (27%), Positives = 51/107 (47%), Gaps = 2/107 (1%)

Query: 17  RNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAF 76
           RN ++ ++        V++  L  K  ER LY+   + G+V D+   +D+ + + KG A+
Sbjct: 76  RNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAY 135

Query: 77  VEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTP 123
           VE+   E    A+ L +G + L  R +    S  +KN    + T  P
Sbjct: 136 VEFYDVESVIKALAL-TGQMLL-GRPIIVQSSQAEKNRAAKAATHQP 180

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|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 39.9 bits (94), Expect = 4e-05
 Identities = 19/59 (32%), Positives = 31/59 (52%)

Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
          NVYI  L     +  L  +    G+++      DK+T+K KG+ FV+++S E    AI+
Sbjct: 2  NVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60

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

 Score = 40.4 bits (95), Expect = 5e-05
 Identities = 15/72 (20%), Positives = 37/72 (51%), Gaps = 3/72 (4%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +++G L   V +  L +   + G+++++ +   K  +    FAF+++E E+    A++  
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVESE 63

Query: 93  SGIVTLYNRTLR 104
           +    L N+T+ 
Sbjct: 64  NH-SMLKNKTMH 74

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|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 = 40.0 bits (94), Expect = 5e-05
 Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 3/60 (5%)

Query: 34 YIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFS 93
          ++ NL     E  L ++    G + ++++P DKET + KGFAFV +   E   +A+K +S
Sbjct: 3  FVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPE---HAVKAYS 59

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

 Score = 39.8 bits (93), Expect = 5e-05
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 7/60 (11%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVV--DLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
          VY+GNL   + ER + D+  + G +V  DL +P      +P G+AF+E+E       AI+
Sbjct: 2  VYVGNLPGDIREREVEDLFYKYGPIVDIDLKLP-----PRPPGYAFIEFEDARDAEDAIR 56

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|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 40.0 bits (94), Expect = 5e-05
 Identities = 16/51 (31%), Positives = 33/51 (64%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          +++G L  +  E  + +   + G +V++ +P DK+T+K +GF F+ ++SEE
Sbjct: 2  IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEE 52

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 39.6 bits (93), Expect = 6e-05
 Identities = 17/51 (33%), Positives = 26/51 (50%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          +++GNL        L      AG    + +  DK+T K KG AFVE+++ E
Sbjct: 3  LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAE 53

This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing. . Length = 74

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 42.6 bits (100), Expect = 6e-05
 Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
           ++ +  +G  +++ NL    +E VL+ +    G V ++ I RD  T++ KG+ FV   + 
Sbjct: 262 IAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNY 321

Query: 83  EIGHYAIKLFSGIVTLYNRTLR 104
           +    AI   +G  TL NR L+
Sbjct: 322 DEAAMAILSLNG-YTLGNRVLQ 342

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|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 39.7 bits (93), Expect = 7e-05
 Identities = 15/29 (51%), Positives = 20/29 (68%)

Query: 55 GRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          G VV + +PR K T   KGFAF+E+E+ E
Sbjct: 24 GTVVYVSLPRYKHTGDIKGFAFIEFETPE 52

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

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

 Score = 39.9 bits (94), Expect = 7e-05
 Identities = 19/51 (37%), Positives = 28/51 (54%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          V+I NL     E  L ++  Q G V    I +DK T   KG AFV+++++E
Sbjct: 3  VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKE 53

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

 Score = 42.1 bits (99), Expect = 1e-04
 Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 1/52 (1%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           N+Y+ NLD  VNE  L ++  + G +    + +D  + + +GFAFV +E  E
Sbjct: 180 NLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHE 230

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

 Score = 42.1 bits (99), Expect = 1e-04
 Identities = 27/157 (17%), Positives = 53/157 (33%), Gaps = 11/157 (7%)

Query: 17  RNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAF 76
             + Q        G N+Y+ NLD+ V +  L ++  + G +    +  D E    +GF F
Sbjct: 272 FEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGF 330

Query: 77  VEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSR-KSRSDPVP 135
           V + + E  + A+    G   +      +    Q K  + + +    +  + + R  P+ 
Sbjct: 331 VCFSNPEEANRAVTEMHG--RMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPRMRQLPMG 388

Query: 136 MPVNGMEISH-------HSMRISVPRHYSSEEPPPPG 165
            P+ G                   P  +      P  
Sbjct: 389 SPMGGAMGQPPYYGQGPQQQFNGQPLGWPRMSMMPTP 425

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

 Score = 39.3 bits (92), Expect = 1e-04
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
           ++++G+L  +++   L       G + D  + +D +T K KG+ FV +  +E    AI+ 
Sbjct: 1   HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 92  FSGIVTLYNRTLR 104
            +G   L  R +R
Sbjct: 61  MNG-QWLGGRAIR 72

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

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 7/74 (9%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
           C +++GNL   + E    ++  + G V ++++ ++      KGF F+  ++      A  
Sbjct: 2   CRLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKA 55

Query: 91  LFSGIVTLYNRTLR 104
              GI     R LR
Sbjct: 56  ELDGI-MRKGRQLR 68

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|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 38.7 bits (91), Expect = 1e-04
 Identities = 16/50 (32%), Positives = 23/50 (46%)

Query: 34 YIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          +IG L     E  L +   + G VVD  I +D  T + +GF FV +    
Sbjct: 2  FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPS 51

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes 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. 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). 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. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 38.9 bits (91), Expect = 1e-04
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
           C VY+G++  ++ E  +       G +  + +  D  T K KGFAFVEYE  E    A++
Sbjct: 1   CRVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALE 60

Query: 91  LFSGIVTLYNRTLR 104
             +G V L  R ++
Sbjct: 61  QMNG-VMLGGRNIK 73

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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 38.4 bits (90), Expect = 1e-04
 Identities = 18/51 (35%), Positives = 32/51 (62%), Gaps = 1/51 (1%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          V++ NLD  V E  L  +  + G + D+ + ++ +  K KG+A+VE+E+EE
Sbjct: 2  VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKG-KSKGYAYVEFENEE 51

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), 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 = 72

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
          +++GNL     +  L +   + G VVD+ I +D +  + KGF  VE+ +EE    A++ 
Sbjct: 2  LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEK 59

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|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 19/70 (27%), Positives = 29/70 (41%), Gaps = 9/70 (12%)

Query: 33 VYIGNL--DEKVNERVLYDILIQA---GRVVDLYIPRDKETDKPK---GFAFVEYESEEI 84
          V    L  DE+  E +L D+  +    G+V+ + IPR +         G  FVE+   E 
Sbjct: 10 VTPEELEDDEEYEE-ILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVED 68

Query: 85 GHYAIKLFSG 94
             A    +G
Sbjct: 69 AQKAQLALAG 78

This subfamily corresponds to the RRM3 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 = 89

>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 14/60 (23%), Positives = 28/60 (46%)

Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
            +++G L     +  L     Q G + +  +  D++T K +G+ FV ++ +E    A K
Sbjct: 1  TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 18/51 (35%), Positives = 28/51 (54%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          +++GNL   V  + L +   Q G+V    +P DKET   KG+ FV + S +
Sbjct: 2  LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRD 52

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 25/94 (26%), Positives = 38/94 (40%), Gaps = 1/94 (1%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           ++IG L    ++  L D     G VVD  +  D+ET + +GF FV +  E     AI   
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 93  SGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSS 126
            G   L  R +R   +    +A  +       S 
Sbjct: 97  DG-KELNGRHIRVNPANDRPSAPRAYGGGGGYSG 129

Length = 144

>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 38.5 bits (89), Expect = 2e-04
 Identities = 21/65 (32%), Positives = 34/65 (52%)

Query: 30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
          G  ++I NL +  +E +L+ +    G V ++ + RD  T+K KGF FV   + E    AI
Sbjct: 1  GWCIFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAI 60

Query: 90 KLFSG 94
             +G
Sbjct: 61 ASLNG 65

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), 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. 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. Like other Hu proteins, HuR 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 AU-rich RNA element (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 = 84

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

 Score = 38.0 bits (89), Expect = 2e-04
 Identities = 19/62 (30%), Positives = 32/62 (51%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
          ++I +L  +  ++ LY +    G V+   +  DK T + K F FV Y++ E    AIK  
Sbjct: 1  LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 93 SG 94
          +G
Sbjct: 61 NG 62

This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed 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. . Length = 73

>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 37.8 bits (88), Expect = 3e-04
 Identities = 26/74 (35%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           VYIGNL   + E  + +   +   +  + +  DKET + KGF  V++  EE    A+KL 
Sbjct: 2   VYIGNLAWDITEDDVRE-FFKGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKL- 59

Query: 93  SGIVTLYNRTLRFA 106
            G V L  R +R A
Sbjct: 60  DGTV-LCGRPIRIA 72

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 38.1 bits (88), Expect = 3e-04
 Identities = 21/85 (24%), Positives = 44/85 (51%), Gaps = 8/85 (9%)

Query: 33  VYIGNLDEKVNE----RVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
           +YI NL+EK+ +    + L+ I  + G+++D+ + R   + K +G AFV ++       A
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 62

Query: 89  IKLFSGIVTLYNRTLRFALSGQDKN 113
           ++   G    Y++ +R   +  D +
Sbjct: 63  LRSMQGF-PFYDKPMRIQYAKTDSD 86

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), 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 and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

>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 = 37.8 bits (88), Expect = 3e-04
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +++  L   V +  L  +  + G V  + +  ++ + KPKG A+VEYE+E     A+   
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVLKM 63

Query: 93  SGIVTLYNRTLRFALS 108
            G   +  +T+  A+S
Sbjct: 64  DGT-EIKEKTISVAIS 78

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

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 4/78 (5%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYI--PRDKETDKPKGF-AFVEYESEEIGHYA 88
           N+Y+GNL+ KV E VL     + G +  + I  PR +E  +      FV + +      A
Sbjct: 3   NLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERA 62

Query: 89  IKLFSGIVTLYNRTLRFA 106
           +    G   +    L+  
Sbjct: 63  LDELDGKD-VMGYELKLG 79

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 37.1 bits (87), Expect = 3e-04
 Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 10/64 (15%)

Query: 47  LYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGI--VTLYNRTLR 104
           LY +    G V  + + + K      GFAFVE+ +EE    A K    +  V    R LR
Sbjct: 1   LYKLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEE---AAEKAVQYLNGVLFGGRPLR 52

Query: 105 FALS 108
              S
Sbjct: 53  VDYS 56

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

 Score = 37.8 bits (88), Expect = 3e-04
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 3/50 (6%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
          +Y+GNL   + ER + D+  + G +  + +   K   +   FAFVE+E  
Sbjct: 2  IYVGNLPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFEDP 48

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|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma Protein (EWS)

 Score = 37.6 bits (87), Expect = 4e-04
 Identities = 24/72 (33%), Positives = 32/72 (44%), Gaps = 12/72 (16%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRV----------VDLYIPRDKETDKPKGFAFVEYESE 82
          +Y+  L++ V    L D     G V          V++Y   DKET KPKG A V YE  
Sbjct: 3  IYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYT--DKETGKPKGDATVSYEDP 60

Query: 83 EIGHYAIKLFSG 94
               A++ F G
Sbjct: 61 PSAKAAVEWFDG 72

This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, a member 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 multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene. . Length = 84

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 37.5 bits (88), Expect = 4e-04
 Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 8/75 (10%)

Query: 34  YIGNLDEKVN----ERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
           YI NL+EK+     +R LY +  Q G V+D+      +T K +G AFV ++  E    A+
Sbjct: 3   YINNLNEKIKKDELKRSLYALFSQFGPVLDIVA---SKTLKMRGQAFVVFKDVESATNAL 59

Query: 90  KLFSGIVTLYNRTLR 104
           +   G    Y++ +R
Sbjct: 60  RALQGF-PFYDKPMR 73

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains 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. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

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

 Score = 37.4 bits (87), Expect = 5e-04
 Identities = 12/51 (23%), Positives = 24/51 (47%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          +++GNL   + E  L +   + G V+++ I       +   F FV ++  E
Sbjct: 6  LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPE 56

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|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 37.0 bits (86), Expect = 5e-04
 Identities = 18/59 (30%), Positives = 32/59 (54%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
          +++GNL  +  E  L     + GR+  + +   +++ K KGFAFV++E  E    A+K 
Sbjct: 1  LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKG 59

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|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 37.2 bits (87), Expect = 5e-04
 Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           ++IG L   ++E  + ++L   G++    + +D  T   KG+AF EY    +   AI   
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 93  SGIVTLYNRTL 103
           +G+  L ++ L
Sbjct: 63  NGMQ-LGDKKL 72

This subfamily corresponds to the RRM2 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 = 77

>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 37.4 bits (86), Expect = 6e-04
 Identities = 27/85 (31%), Positives = 43/85 (50%), Gaps = 3/85 (3%)

Query: 30  GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
           G  +++ NL  + +E VL+ +    G V ++ + RD  T+K KGF FV   + +    AI
Sbjct: 1   GWCIFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAI 60

Query: 90  KLFSGIVTLYNRTLR--FALSGQDK 112
              +G   L +R L+  F  S Q K
Sbjct: 61  ASLNG-YRLGDRVLQVSFKTSKQHK 84

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC 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 AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. 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 = 85

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

 Score = 37.1 bits (86), Expect = 6e-04
 Identities = 17/62 (27%), Positives = 31/62 (50%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
          +YIG+L     E+ L     Q G V ++ + R K+T   K + F+++ + E+   A K  
Sbjct: 2  IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 93 SG 94
          + 
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|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 36.9 bits (85), Expect = 8e-04
 Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           V++ NLD KV  + L ++   AG VV   I  DK+  K +G   V +E       AI +F
Sbjct: 3   VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKD-GKSRGIGTVTFEQPIEAVQAISMF 61

Query: 93  SGIVTLYNRTLRFAL 107
           +G + L++R +   +
Sbjct: 62  NGQL-LFDRPMHVKM 75

This subgroup corresponds to the RRM2 of hnRNP M, a 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). . Length = 76

>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 36.8 bits (86), Expect = 8e-04
 Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          G N+Y+ NLD+ +++  L +     G +    +  D E  + KGF FV + S E
Sbjct: 1  GVNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPE 53

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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 38.8 bits (90), Expect = 0.001
 Identities = 27/80 (33%), Positives = 43/80 (53%), Gaps = 1/80 (1%)

Query: 25  GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
             +NSG N+ +  L + + +R LY +    G +    I RD +T    G+AFV++ SE  
Sbjct: 102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEAD 161

Query: 85  GHYAIKLFSGIVTLYNRTLR 104
              AIK  +GI T+ N+ L+
Sbjct: 162 SQRAIKNLNGI-TVRNKRLK 180

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). Length = 346

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 14/47 (29%), Positives = 25/47 (53%)

Query: 37 NLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           L     ER L ++  + G +  + +  D++T + +GF FV +ES E
Sbjct: 6  GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVE 52

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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 36.4 bits (84), Expect = 0.001
 Identities = 16/51 (31%), Positives = 27/51 (52%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          +++G L   V E  L +   Q G V    +  DK+T K +GF FV +++ +
Sbjct: 2  LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHD 52

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

 Score = 36.1 bits (84), Expect = 0.001
 Identities = 13/63 (20%), Positives = 29/63 (46%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
          +++ NL     +  L +   + G +   ++ +DK + K +GF +V +  EE    A++  
Sbjct: 2  LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 93 SGI 95
             
Sbjct: 62 KKT 64

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

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 12/26 (46%), Positives = 21/26 (80%)

Query: 55 GRVVDLYIPRDKETDKPKGFAFVEYE 80
          G +VD+Y+P D  T +P+GFA++++E
Sbjct: 25 GPIVDVYVPLDFYTRRPRGFAYIQFE 50

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|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 36.2 bits (84), Expect = 0.001
 Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
          N+YI NL   ++E+ L  +L   G+V+   I RD +    +G  F   ES E     I  
Sbjct: 2  NLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQS-RGVGFARMESREKCEDIISK 60

Query: 92 FSG 94
          F+G
Sbjct: 61 FNG 63

This subfamily corresponds to the RRM2 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, they 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 = 79

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 36.2 bits (84), Expect = 0.001
 Identities = 14/49 (28%), Positives = 25/49 (51%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYES 81
          ++IG L  +  +  L +   Q G + D  + +D  T + +GF FV + S
Sbjct: 2  LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFAS 50

This subfamily corresponds to the RRM1 in 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 = 78

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

 Score = 36.0 bits (83), Expect = 0.001
 Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
          +Y+GNLD +V E +L  I    G V ++ I  DK  +K   + FVEY        A++  
Sbjct: 1  LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 93 SG 94
          +G
Sbjct: 60 NG 61

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|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 36.1 bits (84), Expect = 0.001
 Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 9/70 (12%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRV-VD-------LYIPRDKETDKPKGFAFVEYESEEI 84
          +YI  L + V E  L ++    G +  D       + I  DKET +PKG A V Y+    
Sbjct: 1  IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKET-EPKGEATVTYDDPSA 59

Query: 85 GHYAIKLFSG 94
             AI+ F+G
Sbjct: 60 AQAAIEWFNG 69

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 38.0 bits (88), Expect = 0.002
 Identities = 20/62 (32%), Positives = 35/62 (56%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +Y+GNL   + E+ L  I    G + D+ + RD ET + KGF F+++   E    A+++ 
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248

Query: 93  SG 94
           +G
Sbjct: 249 NG 250

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

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
           N+ +  L + + +  L  +    G +    I RD+ T +  G+ FV+Y  E     AI  
Sbjct: 2   NLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINT 61

Query: 92  FSGIVTLYNRTLRFAL 107
            +G   + N+ L+ + 
Sbjct: 62  LNGF-EIRNKRLKVSY 76

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|241083 cd12639, RRM3_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 = 36.0 bits (83), Expect = 0.002
 Identities = 17/65 (26%), Positives = 35/65 (53%)

Query: 30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
          GCN++I +L ++  +  L  + +  G V+   +  D+ T++ K F FV +++      AI
Sbjct: 4  GCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAI 63

Query: 90 KLFSG 94
          +  +G
Sbjct: 64 QAMNG 68

This subgroup corresponds to the RRM3 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, 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 contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. 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, 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 an 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 = 79

>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 35.7 bits (82), Expect = 0.002
 Identities = 19/65 (29%), Positives = 35/65 (53%)

Query: 30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
          GCN++I +L ++  +  L    +  G V+   +  DK+T+  K F FV Y++ +    AI
Sbjct: 4  GCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAI 63

Query: 90 KLFSG 94
          +  +G
Sbjct: 64 QAMNG 68

This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 79

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 16/62 (25%), Positives = 36/62 (58%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
          +++  + E+  E  ++D   + G + +L++  D+ T   KG+A +EYE+++    AI+  
Sbjct: 9  IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 93 SG 94
          +G
Sbjct: 69 NG 70

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

 Score = 34.9 bits (81), Expect = 0.002
 Identities = 16/60 (26%), Positives = 35/60 (58%), Gaps = 9/60 (15%)

Query: 31 CNVYIGNLD-EKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
            V++GNL+ +KV++  L +I  + G+++ + +         KG+ FV++++EE    A+
Sbjct: 1  SRVFVGNLNTDKVSKEDLEEIFSKYGKILGISLH--------KGYGFVQFDNEEDARAAV 52

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|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 35.1 bits (81), Expect = 0.002
 Identities = 17/52 (32%), Positives = 30/52 (57%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
          +++G L     E  +     Q G+V D  +  DK+T++ +GF FV +ESE++
Sbjct: 2  IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDV 53

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 35.5 bits (81), Expect = 0.002
 Identities = 19/66 (28%), Positives = 34/66 (51%)

Query: 29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
          +G  +++ NL    +E +L+ +    G V ++ + RD  T+K KGF FV   + +    A
Sbjct: 2  TGWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMA 61

Query: 89 IKLFSG 94
          I   +G
Sbjct: 62 IASLNG 67

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB 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 AU-rich RNA element (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 = 86

>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 14/48 (29%), Positives = 26/48 (54%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE 80
          ++IG L+ +  +  L +   Q G V D  + RD  T + +GF F+ ++
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFK 48

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 38.0 bits (88), Expect = 0.003
 Identities = 25/90 (27%), Positives = 43/90 (47%), Gaps = 5/90 (5%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +YIGNL   + E  + ++L   G +    + +D  T   KG+AF EY+   +   AI   
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL 357

Query: 93  SGIVTLYNR-TLRFALSGQDKNAQNSSMTT 121
           +G  T  N+  ++ A  G    A  +++ T
Sbjct: 358 NGKDTGDNKLHVQRACVG----ANQATIDT 383

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

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

 Score = 37.7 bits (87), Expect = 0.003
 Identities = 25/85 (29%), Positives = 39/85 (45%), Gaps = 1/85 (1%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
           C VY+G++  ++ E  +       G +  + +  D  T K KGFAFVEYE  E    A++
Sbjct: 108 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALE 167

Query: 91  LFSGIVTLYNRTLRFALSGQDKNAQ 115
             +G   L  R ++         AQ
Sbjct: 168 QMNG-QMLGGRNIKVGRPSNMPQAQ 191

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

 Score = 35.5 bits (82), Expect = 0.003
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 8/70 (11%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRV-VD-------LYIPRDKETDKPKGFAFVEYESEEI 84
          V++ NL     E+ L +     G + +D       +++ +DK+T +PKG A V Y+    
Sbjct: 1  VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 85 GHYAIKLFSG 94
             AI+ F+ 
Sbjct: 61 ASAAIEWFNN 70

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

 Score = 35.2 bits (81), Expect = 0.003
 Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
           N+++G+L  +V +  L+          D  +  D ++ + +G+ FV + S++    AI  
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 92  FSGIVTLYNRTLR 104
            +G   L +R +R
Sbjct: 61  MNG-KWLGSRPIR 72

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

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 13/26 (50%), Positives = 21/26 (80%)

Query: 55 GRVVDLYIPRDKETDKPKGFAFVEYE 80
          G +VD+Y+P D  T +P+GFA+V++E
Sbjct: 25 GPIVDVYVPLDFYTRRPRGFAYVQFE 50

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|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 34.9 bits (80), Expect = 0.003
 Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 7/74 (9%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
           C +++GNL   + E     +  + G   +++I RD      +GF F+  ES  +   A  
Sbjct: 2   CRLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD------RGFGFIRLESRTLAEIAKA 55

Query: 91  LFSGIVTLYNRTLR 104
              G + L NR LR
Sbjct: 56  ELDGTI-LKNRPLR 68

This subgroup corresponds to the RRM1 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. Its cellular function remains unknown currently, however, 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 = 71

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 34.9 bits (80), Expect = 0.003
 Identities = 16/64 (25%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
          GC V++G +   + E  L  +  +AG++ +  +  +   +  +G+AFV Y ++E    AI
Sbjct: 1  GCEVFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGEN-RGYAFVMYTTKEEAQLAI 59

Query: 90 KLFS 93
          ++ +
Sbjct: 60 RILN 63

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), 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 = 78

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

 Score = 34.9 bits (81), Expect = 0.003
 Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          +++G +     E  L D   + G V D+ I  D+     KG+ FV +E++E
Sbjct: 5  IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQE 54

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

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 3/73 (4%)

Query: 31  CNVYIGNL-DEKVNERVLYDILIQAGRVVDLYIPRD-KETDKPKGFAFVEYESEEIGHYA 88
           C +++G +   K  E +L +       VVD+ + R   + +K +GFAFVEYES      A
Sbjct: 2   CRLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMA 61

Query: 89  I-KLFSGIVTLYN 100
             KL  G + L+ 
Sbjct: 62  RRKLVPGRILLWG 74

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

 Score = 34.7 bits (80), Expect = 0.004
 Identities = 19/63 (30%), Positives = 27/63 (42%), Gaps = 6/63 (9%)

Query: 34 YIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFS 93
          YIGNL   VNE  L  +  +        IP      K  G+AFV+   +     AI+  +
Sbjct: 2  YIGNLSSDVNESDLRQLFEEHK------IPVSSVLVKKGGYAFVDCPDQSWADKAIEKLN 55

Query: 94 GIV 96
          G +
Sbjct: 56 GKI 58

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

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 14/45 (31%), Positives = 23/45 (51%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFV 77
          +++G+L  +V + VL     +        + RDK T K KG+ FV
Sbjct: 9  IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFV 53

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|240934 cd12490, RRM2_ACF, RNA recognition motif 2 in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 35.0 bits (80), Expect = 0.004
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 31 CNVYIGNLDE-KVNERVLYDILIQAGRVVDLYI-PRDKETDKPKGFAFVEYESEEIGHYA 88
          C +++G + + K  E +L ++      V+D+ + P   +  K +GFAFVEYES      A
Sbjct: 3  CRLFVGGIPKTKKREEILAEMKKVTDGVLDVIVYPSAADKAKNRGFAFVEYESHRAAAMA 62

Query: 89 -IKLFSGIVTLY 99
            KL  G + L+
Sbjct: 63 RRKLLPGRIQLW 74

This subgroup corresponds to the RRM2 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 = 85

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 34.7 bits (80), Expect = 0.004
 Identities = 14/37 (37%), Positives = 24/37 (64%)

Query: 55 GRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
          G +  + IP D+ET   KGFA++E++S +    A++L
Sbjct: 28 GEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALEL 64

This subfamily corresponds to the RRM2 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 = 79

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

 Score = 34.6 bits (79), Expect = 0.004
 Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 6/82 (7%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
           C VY+GNL    N+  L       G +  +++ R+     P GFAFVE+E       A++
Sbjct: 5   CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVR 59

Query: 91  LFSGIVTLYNRTLRFALSGQDK 112
              G  TL    +R  LS  +K
Sbjct: 60  ELDG-RTLCGCRVRVELSNGEK 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	211
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.85
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.81
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.78
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.77
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.76
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.73
KOG0122	270	consensus Translation initiation factor 3, subunit	99.73
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.72
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.71
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.68
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.68
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.68
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.67
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.67
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.66
PLN03120	260	nucleic acid binding protein; Provisional	99.65
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.64
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.64
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.63
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.63
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.63
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.63
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.63
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.62
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.62
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.62
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.62
PLN03213	759	repressor of silencing 3; Provisional	99.62
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.62
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.62
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.62
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.6
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.59
smart00362	72	RRM_2 RNA recognition motif.	99.58
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.58
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.58
smart00360	71	RRM RNA recognition motif.	99.56
PLN03121	243	nucleic acid binding protein; Provisional	99.56
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.54
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.51
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.51
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.51
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.48
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.48
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.48
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.46
smart00361	70	RRM_1 RNA recognition motif.	99.46
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.45
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.45
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.43
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.42
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.41
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.4
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.4
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.4
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.38
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.37
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.35
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.29
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.29
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.26
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.26
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.25
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.23
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.22
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.21
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.17
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.16
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.11
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.08
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.07
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.07
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.06
KOG0151	877	consensus Predicted splicing regulator, contains R	99.03
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.0
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.98
KOG0226	290	consensus RNA-binding proteins [General function p	98.96
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.94
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.9
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.89
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.88
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.86
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.84
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.74
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.7
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.67
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.6
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.41
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.38
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.33
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.32
KOG4210	285	consensus Nuclear localization sequence binding pr	98.11
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.08
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.01
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.98
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.97
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.97
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.94
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	97.94
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.87
KOG2314	698	consensus Translation initiation factor 3, subunit	97.73
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.7
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.62
KOG3152	278	consensus TBP-binding protein, activator of basal	97.61
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.6
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.6
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.56
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.53
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.52
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.4
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.3
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.3
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.26
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	97.25
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.2
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.1
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.04
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.01
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.88
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.84
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.77
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.75
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.61
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.41
KOG2068	327	consensus MOT2 transcription factor [Transcription	96.33
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.16
KOG2591	684	consensus c-Mpl binding protein, contains La domai	96.03
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.92
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	95.89
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	95.87
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.82
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	95.47
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.25
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.08
KOG2135	526	consensus Proteins containing the RNA recognition	94.38
KOG4210	285	consensus Nuclear localization sequence binding pr	93.96
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	93.69
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	93.45
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	93.36
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	92.54
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	91.93
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	91.45
KOG4660	549	consensus Protein Mei2, essential for commitment t	91.21
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	91.14
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	86.44
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	82.67
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	81.03

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.85  E-value=1.3e-20  Score=143.62  Aligned_cols=84  Identities=27%  Similarity=0.444  Sum_probs=79.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ...+++|||+||+++++|++|+++|++||.|.+|.|+.|+.|++++|||||+|.+.++|++||+.||+. .|+|+.|+|+
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~-~i~Gr~l~V~  109 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGK-ELNGRHIRVN  109 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCC-EECCEEEEEE
Confidence            345789999999999999999999999999999999999999999999999999999999999999998 9999999999


Q ss_pred             ecCCC
Q 038096          107 LSGQD  111 (211)
Q Consensus       107 ~a~~~  111 (211)
                      |+...
T Consensus       110 ~a~~~  114 (144)
T PLN03134        110 PANDR  114 (144)
T ss_pred             eCCcC
Confidence            98643

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.81  E-value=1.9e-19  Score=143.26  Aligned_cols=79  Identities=23%  Similarity=0.347  Sum_probs=74.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      -++||||||+|++..++|+++|++||+|++..|+.|+.||++||||||+|.+.++|++|++..|-  .|+||+..|.+|.
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~p--iIdGR~aNcnlA~   89 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNP--IIDGRKANCNLAS   89 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCC--cccccccccchhh
Confidence            47899999999999999999999999999999999999999999999999999999999998875  6999999998876


Q ss_pred             C
Q 038096          110 Q  110 (211)
Q Consensus       110 ~  110 (211)
                      -
T Consensus        90 l   90 (247)
T KOG0149|consen   90 L   90 (247)
T ss_pred             h
Confidence            4

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.78  E-value=1.4e-18  Score=150.09  Aligned_cols=81  Identities=30%  Similarity=0.460  Sum_probs=77.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      +.+|||+|||+++++++|+++|++||.|.+++|++|..||.+||||||+|.+.++|.+||..|||. .|+|+.|+|.|+.
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~-~~~gr~i~V~~~~  347 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGY-TLGNRVLQVSFKT  347 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCC-EECCeEEEEEEcc
Confidence            457999999999999999999999999999999999999999999999999999999999999998 9999999999976


Q ss_pred             CC
Q 038096          110 QD  111 (211)
Q Consensus       110 ~~  111 (211)
                      .+
T Consensus       348 ~~  349 (352)
T TIGR01661       348 NK  349 (352)
T ss_pred             CC
Confidence            54

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.77  E-value=2.5e-18  Score=148.41  Aligned_cols=83  Identities=22%  Similarity=0.408  Sum_probs=79.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +.++|||+|||.+++|++|+++|++||+|.+|+|++|+.+|+++|||||+|.+.++|++||+.|||. .|.|+.|+|.|+
T Consensus         2 ~~~~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   80 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGL-RLQNKTIKVSYA   80 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccE-EECCeeEEEEee
Confidence            3689999999999999999999999999999999999999999999999999999999999999998 999999999998


Q ss_pred             CCCc
Q 038096          109 GQDK  112 (211)
Q Consensus       109 ~~~~  112 (211)
                      ++..
T Consensus        81 ~~~~   84 (352)
T TIGR01661        81 RPSS   84 (352)
T ss_pred             cccc
Confidence            7654

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.76  E-value=3e-18  Score=147.77  Aligned_cols=84  Identities=32%  Similarity=0.498  Sum_probs=79.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ...++|||+|||++++|++|+++|+.||.|++|+|++|+.|++++|||||+|.++++|++||+.||+. .|.+++|+|.+
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~-~l~gr~i~V~~  183 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGI-TVRNKRLKVSY  183 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCC-ccCCceeeeec
Confidence            45899999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cCCCc
Q 038096          108 SGQDK  112 (211)
Q Consensus       108 a~~~~  112 (211)
                      +++..
T Consensus       184 a~p~~  188 (346)
T TIGR01659       184 ARPGG  188 (346)
T ss_pred             ccccc
Confidence            87643

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).

>PF00076 RRM_1: RNA recognition motif

Probab=99.73  E-value=2e-17  Score=109.80  Aligned_cols=70  Identities=37%  Similarity=0.644  Sum_probs=66.8

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEE
Q 038096           33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR  104 (211)
Q Consensus        33 lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~  104 (211)
                      |||+|||.++++++|+++|++||.|..+.+..+ .++..+|+|||+|.+.++|++|++.++|. .++|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~-~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGK-KINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTE-EETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCC-EECccCcC
Confidence            799999999999999999999999999999987 56899999999999999999999999998 99999885

(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 ....

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

Probab=99.73  E-value=2e-17  Score=132.40  Aligned_cols=85  Identities=33%  Similarity=0.468  Sum_probs=80.2

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEE
Q 038096           26 NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRF  105 (211)
Q Consensus        26 ~s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v  105 (211)
                      ...+.++|-|.||+.+++|++|+++|..||.|.++.|.+|+.||.+||||||.|.++++|++||+.|||. -++.-.|+|
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~-gyd~LILrv  263 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGY-GYDNLILRV  263 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCc-ccceEEEEE
Confidence            3457899999999999999999999999999999999999999999999999999999999999999997 888889999


Q ss_pred             EecCCC
Q 038096          106 ALSGQD  111 (211)
Q Consensus       106 ~~a~~~  111 (211)
                      +|+++.
T Consensus       264 EwskP~  269 (270)
T KOG0122|consen  264 EWSKPS  269 (270)
T ss_pred             EecCCC
Confidence            999764

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

Probab=99.72  E-value=7.3e-18  Score=144.06  Aligned_cols=112  Identities=21%  Similarity=0.337  Sum_probs=101.1

Q ss_pred             CCCCCCCCCCCccccccccccCCCC--CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeC
Q 038096            3 PSPKHSFVPNDVVSRNKRQIMSGNS--NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE   80 (211)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~s--~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~   80 (211)
                      .|+++.+.+..+.+.+.|..+.|..  .+.++||||.|+..++|+|++++|++||.|++|.|++|.+ +.+||||||.|.
T Consensus        95 Alhn~ktlpG~~~pvqvk~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~-~~sRGcaFV~fs  173 (510)
T KOG0144|consen   95 ALHNQKTLPGMHHPVQVKYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD-GLSRGCAFVKFS  173 (510)
T ss_pred             HhhcccccCCCCcceeecccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheeccc-ccccceeEEEEe
Confidence            4678888999999999887666654  3589999999999999999999999999999999999986 999999999999


Q ss_pred             CHHHHHHHHHHcCCCeeeCCe--EEEEEecCCCccCC
Q 038096           81 SEEIGHYAIKLFSGIVTLYNR--TLRFALSGQDKNAQ  115 (211)
Q Consensus        81 ~~~~A~~Ai~~lng~~~i~gr--~l~v~~a~~~~~~~  115 (211)
                      +++.|..||+.|||...+.|.  +|.|+||+.++.+.
T Consensus       174 tke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~  210 (510)
T KOG0144|consen  174 TKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKD  210 (510)
T ss_pred             hHHHHHHHHHhhccceeeccCCCceEEEecccCCCch
Confidence            999999999999999888885  89999999887764

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.71  E-value=7.1e-17  Score=139.25  Aligned_cols=85  Identities=28%  Similarity=0.440  Sum_probs=78.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCC--eEEEEE
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYN--RTLRFA  106 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~g--r~l~v~  106 (211)
                      ..++|||+|||++++|++|+++|++||.|+.|+|++|+.|++++|||||+|.+.++|++||+.||+. .+.+  +.|+|.
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~-~~~g~~~~l~V~  270 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNV-IPEGGSQPLTVR  270 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCC-ccCCCceeEEEE
Confidence            4678999999999999999999999999999999999999999999999999999999999999998 7766  689999


Q ss_pred             ecCCCccC
Q 038096          107 LSGQDKNA  114 (211)
Q Consensus       107 ~a~~~~~~  114 (211)
                      +++.....
T Consensus       271 ~a~~~~~~  278 (346)
T TIGR01659       271 LAEEHGKA  278 (346)
T ss_pred             ECCccccc
Confidence            99865443

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).

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

Probab=99.68  E-value=1.4e-16  Score=121.72  Aligned_cols=79  Identities=28%  Similarity=0.542  Sum_probs=72.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      -.++||||||+..+++.||+..|..||.|..|+|...     +.|||||+|++..+|+.|+..|+|+ .|+|..|+|+++
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~-~~cG~r~rVE~S   82 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGK-DICGSRIRVELS   82 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCc-cccCceEEEEee
Confidence            3799999999999999999999999999999999764     4699999999999999999999999 999999999998


Q ss_pred             CCCcc
Q 038096          109 GQDKN  113 (211)
Q Consensus       109 ~~~~~  113 (211)
                      .....
T Consensus        83 ~G~~r   87 (195)
T KOG0107|consen   83 TGRPR   87 (195)
T ss_pred             cCCcc
Confidence            76544

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

Probab=99.68  E-value=1.2e-16  Score=116.35  Aligned_cols=81  Identities=30%  Similarity=0.579  Sum_probs=77.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .++++||||||.+.++|++|.++|++.|+|..|.+-.|+.+..+-|||||+|.+.++|+.|++.++|. .++.+.|++.|
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~Alryisgt-rLddr~ir~D~  112 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGT-RLDDRPIRIDW  112 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccC-cccccceeeec
Confidence            34899999999999999999999999999999999999999999999999999999999999999999 99999999999


Q ss_pred             cC
Q 038096          108 SG  109 (211)
Q Consensus       108 a~  109 (211)
                      .-
T Consensus       113 D~  114 (153)
T KOG0121|consen  113 DA  114 (153)
T ss_pred             cc
Confidence            53

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

Probab=99.68  E-value=4.8e-17  Score=128.52  Aligned_cols=93  Identities=34%  Similarity=0.554  Sum_probs=85.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ...++||||+|..+++|..|...|..||.|.+|.|+.|-+++++||||||+|...|+|.+||..||+. +|.||.|+|.+
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnes-EL~GrtirVN~   86 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNES-ELFGRTIRVNL   86 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchh-hhcceeEEEee
Confidence            34789999999999999999999999999999999999999999999999999999999999999999 99999999999


Q ss_pred             cCCCccCCCCCccc
Q 038096          108 SGQDKNAQNSSMTT  121 (211)
Q Consensus       108 a~~~~~~~~~~~~~  121 (211)
                      |++.+-+....-++
T Consensus        87 AkP~kikegsqkPv  100 (298)
T KOG0111|consen   87 AKPEKIKEGSQKPV  100 (298)
T ss_pred             cCCccccCCCCCCc
Confidence            99887665444344

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

Probab=99.67  E-value=4.4e-16  Score=141.77  Aligned_cols=82  Identities=18%  Similarity=0.273  Sum_probs=78.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+||+.++++++|+++|+.||.|.+|+|.+|+.+++++|||||+|.+.++|.+||+.||+. .|+|+.|+|.++.
T Consensus       204 ~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~-elgGr~LrV~kAi  282 (612)
T TIGR01645       204 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLF-DLGGQYLRVGKCV  282 (612)
T ss_pred             cceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCC-eeCCeEEEEEecC
Confidence            579999999999999999999999999999999999999999999999999999999999999998 9999999999987


Q ss_pred             CCc
Q 038096          110 QDK  112 (211)
Q Consensus       110 ~~~  112 (211)
                      ...
T Consensus       283 ~pP  285 (612)
T TIGR01645       283 TPP  285 (612)
T ss_pred             CCc
Confidence            543

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.

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

Probab=99.67  E-value=2.7e-16  Score=143.11  Aligned_cols=80  Identities=29%  Similarity=0.494  Sum_probs=76.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ..++||||||++++++++|+++|.+||.|.+|.|++|+.||+++|||||+|.+.++|++||+.|||. .|+|+.|+|.+.
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~-~i~GR~IkV~rp  184 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQ-MLGGRNIKVGRP  184 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCe-EEecceeeeccc
Confidence            3689999999999999999999999999999999999999999999999999999999999999998 999999999864


Q ss_pred             C
Q 038096          109 G  109 (211)
Q Consensus       109 ~  109 (211)
                      .
T Consensus       185 ~  185 (612)
T TIGR01645       185 S  185 (612)
T ss_pred             c
Confidence            3

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.

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.66  E-value=5.5e-16  Score=103.39  Aligned_cols=70  Identities=36%  Similarity=0.591  Sum_probs=65.0

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEE
Q 038096           33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR  104 (211)
Q Consensus        33 lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~  104 (211)
                      |||+|||+++++++|+++|+.||.|..+.+..+++ +..+|+|||+|.+.++|.+|++.+++. .++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~-~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGK-EIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTE-EETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCc-EECCEEcC
Confidence            79999999999999999999999999999999987 899999999999999999999999987 99999885

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 ....

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.65  E-value=9.5e-16  Score=125.56  Aligned_cols=76  Identities=17%  Similarity=0.289  Sum_probs=70.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+||++.++|++|+++|+.||.|.+|.|+.|..   .+|||||+|.+.++|+.||. |||. .|+|+.|.|.++.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~-~l~gr~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGA-TIVDQSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCC-eeCCceEEEEecc
Confidence            58999999999999999999999999999999998863   57999999999999999995 8998 9999999999975


Q ss_pred             C
Q 038096          110 Q  110 (211)
Q Consensus       110 ~  110 (211)
                      .
T Consensus        79 ~   79 (260)
T PLN03120         79 D   79 (260)
T ss_pred             C
Confidence            4

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

Probab=99.64  E-value=1.2e-15  Score=139.84  Aligned_cols=79  Identities=27%  Similarity=0.495  Sum_probs=76.0

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCCC
Q 038096           32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQD  111 (211)
Q Consensus        32 ~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~~  111 (211)
                      +|||||||.+++|++|+++|++||.|.+|+|.+|+.|++++|||||+|.+.++|++||+.+|+. .|.|+.|+|.|+..+
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~-~i~gk~i~i~~s~~~   80 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFK-RLGGKPIRIMWSQRD   80 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCC-EECCeeEEeeccccc
Confidence            7999999999999999999999999999999999999999999999999999999999999998 899999999998644

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

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

Probab=99.64  E-value=3.7e-16  Score=122.44  Aligned_cols=83  Identities=29%  Similarity=0.486  Sum_probs=78.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      -..|-|-||.+.++.++|+.+|++||.|-+|.|++|+.|+.++|||||.|.+..+|+.|++.|+|. .|+|+.|.|+.|+
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~-~ldgRelrVq~ar   91 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGA-VLDGRELRVQMAR   91 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcce-eeccceeeehhhh
Confidence            577999999999999999999999999999999999999999999999999999999999999998 9999999999887


Q ss_pred             CCcc
Q 038096          110 QDKN  113 (211)
Q Consensus       110 ~~~~  113 (211)
                      -...
T Consensus        92 ygr~   95 (256)
T KOG4207|consen   92 YGRP   95 (256)
T ss_pred             cCCC
Confidence            5544

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.63  E-value=2e-15  Score=125.34  Aligned_cols=82  Identities=18%  Similarity=0.261  Sum_probs=75.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ++..++|+|.|||+...|-||+.+|++||.|.+|.|+.+.  .-+||||||+|++.++|++|-++|+|. .+.||+|.|.
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt-~VEGRkIEVn  169 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGT-VVEGRKIEVN  169 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcc-eeeceEEEEe
Confidence            3456899999999999999999999999999999999875  468999999999999999999999999 9999999999


Q ss_pred             ecCCC
Q 038096          107 LSGQD  111 (211)
Q Consensus       107 ~a~~~  111 (211)
                      .|...
T Consensus       170 ~ATar  174 (376)
T KOG0125|consen  170 NATAR  174 (376)
T ss_pred             ccchh
Confidence            87643

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.63  E-value=2.4e-15  Score=135.93  Aligned_cols=83  Identities=25%  Similarity=0.370  Sum_probs=78.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ..++|||||||+.+++++|+++|+.||.|..+.|+++..+|.++|||||+|.+.++|..||+.|||. .|+|+.|.|.+|
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~-~~~~~~l~v~~a  372 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGK-DTGDNKLHVQRA  372 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCC-EECCeEEEEEEC
Confidence            4689999999999999999999999999999999999999999999999999999999999999998 999999999998


Q ss_pred             CCCc
Q 038096          109 GQDK  112 (211)
Q Consensus       109 ~~~~  112 (211)
                      ....
T Consensus       373 ~~~~  376 (509)
T TIGR01642       373 CVGA  376 (509)
T ss_pred             ccCC
Confidence            6543

Members of this subfamily are found in plants, metazoa and fungi.

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

Probab=99.63  E-value=1.1e-15  Score=131.21  Aligned_cols=88  Identities=23%  Similarity=0.390  Sum_probs=79.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee-CCeEEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL-YNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i-~gr~l~v~  106 (211)
                      +-+|.||||.||.++.|++|..+|++.|+|-+++|++|+.+|.+||||||+|.+.++|++||+.||+. +| .|+.|.|+
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~-Eir~GK~igvc  159 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNY-EIRPGKLLGVC  159 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCc-cccCCCEeEEE
Confidence            44899999999999999999999999999999999999999999999999999999999999999998 55 68999998


Q ss_pred             ecCCCccCCC
Q 038096          107 LSGQDKNAQN  116 (211)
Q Consensus       107 ~a~~~~~~~~  116 (211)
                      .+..+.....
T Consensus       160 ~Svan~RLFi  169 (506)
T KOG0117|consen  160 VSVANCRLFI  169 (506)
T ss_pred             EeeecceeEe
Confidence            8765544433

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

Probab=99.63  E-value=6.2e-16  Score=125.52  Aligned_cols=82  Identities=28%  Similarity=0.473  Sum_probs=78.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQ  110 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~  110 (211)
                      --+|||-|..+++-++|++.|..||+|.+++|++|..|+++||||||.|-+.++|+.||..|||. .|++|.|+-.||..
T Consensus        63 fhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGq-WlG~R~IRTNWATR  141 (321)
T KOG0148|consen   63 FHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQ-WLGRRTIRTNWATR  141 (321)
T ss_pred             eeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCe-eeccceeecccccc
Confidence            45999999999999999999999999999999999999999999999999999999999999999 89999999999977


Q ss_pred             Ccc
Q 038096          111 DKN  113 (211)
Q Consensus       111 ~~~  113 (211)
                      +..
T Consensus       142 Kp~  144 (321)
T KOG0148|consen  142 KPS  144 (321)
T ss_pred             Ccc
Confidence            653

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

Probab=99.63  E-value=6.9e-16  Score=118.68  Aligned_cols=83  Identities=46%  Similarity=0.832  Sum_probs=79.0

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEE
Q 038096           26 NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRF  105 (211)
Q Consensus        26 ~s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v  105 (211)
                      ..+...+||||||+..++++.|.++|-+.|+|+.+.|++|+.|+..+||||++|.++++|+-||+.||. |.+.|++|+|
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~-VkLYgrpIrv   83 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNM-VKLYGRPIRV   83 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHH-HHhcCceeEE
Confidence            345689999999999999999999999999999999999999999999999999999999999999996 5999999999


Q ss_pred             EecC
Q 038096          106 ALSG  109 (211)
Q Consensus       106 ~~a~  109 (211)
                      ..+.
T Consensus        84 ~kas   87 (203)
T KOG0131|consen   84 NKAS   87 (203)
T ss_pred             Eecc
Confidence            9987

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

Probab=99.62  E-value=1.8e-15  Score=124.27  Aligned_cols=81  Identities=27%  Similarity=0.374  Sum_probs=77.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ++-++|||+-|+.+++|..|+..|+.||.|+.|.|++|+.||+++|||||+|+++.+..+|.+..+|. .|+|+.|.|.+
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~-~Idgrri~VDv  177 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGI-KIDGRRILVDV  177 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCc-eecCcEEEEEe
Confidence            56799999999999999999999999999999999999999999999999999999999999999998 99999999987


Q ss_pred             cC
Q 038096          108 SG  109 (211)
Q Consensus       108 a~  109 (211)
                      -.
T Consensus       178 ER  179 (335)
T KOG0113|consen  178 ER  179 (335)
T ss_pred             cc
Confidence            43

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

Probab=99.62  E-value=4.9e-17  Score=124.98  Aligned_cols=79  Identities=34%  Similarity=0.567  Sum_probs=75.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ++.-|||||||+++||.||..+|++||+|+.|.+++|+.||+++||||+.|++..+..-|+.-|||. .|.||.|+|...
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGi-ki~gRtirVDHv  112 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGI-KILGRTIRVDHV  112 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCc-eecceeEEeeec
Confidence            4677999999999999999999999999999999999999999999999999999999999999997 999999999764

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

Probab=99.62  E-value=1.4e-15  Score=122.92  Aligned_cols=100  Identities=20%  Similarity=0.373  Sum_probs=88.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ..++|.|.-||..+++|||+.+|...|+|++|++++|+-||.+.|||||.|.++++|++||..|||. .+..++|+|++|
T Consensus        40 skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGL-rLQ~KTIKVSyA  118 (360)
T KOG0145|consen   40 SKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGL-RLQNKTIKVSYA  118 (360)
T ss_pred             ccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcce-eeccceEEEEec
Confidence            3678999999999999999999999999999999999999999999999999999999999999997 999999999999


Q ss_pred             CCCccC-CCCCcccCCCCCCCC
Q 038096          109 GQDKNA-QNSSMTTTPLSSRKS  129 (211)
Q Consensus       109 ~~~~~~-~~~~~~~~p~~~~~~  129 (211)
                      ++.... +..+.++...+..+.
T Consensus       119 RPSs~~Ik~aNLYvSGlPktMt  140 (360)
T KOG0145|consen  119 RPSSDSIKDANLYVSGLPKTMT  140 (360)
T ss_pred             cCChhhhcccceEEecCCccch
Confidence            877654 344555555554443

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.62  E-value=2.7e-15  Score=134.01  Aligned_cols=80  Identities=28%  Similarity=0.534  Sum_probs=77.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||..+++++|+++|+.||.|..|.|+.+..+|.++|||||+|.+.++|.+|++.|||. .|.|+.|+|.|+.
T Consensus       186 ~~~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       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGF-ELAGRPIKVGYAQ  264 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCc-EECCEEEEEEEcc
Confidence            689999999999999999999999999999999999999999999999999999999999999997 9999999999986


Q ss_pred             C
Q 038096          110 Q  110 (211)
Q Consensus       110 ~  110 (211)
                      .
T Consensus       265 ~  265 (457)
T TIGR01622       265 D  265 (457)
T ss_pred             C
Confidence            3

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.

>PLN03213 repressor of silencing 3; Provisional

Probab=99.62  E-value=1.7e-15  Score=131.72  Aligned_cols=77  Identities=19%  Similarity=0.355  Sum_probs=71.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCH--HHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE--EIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~--~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      +.+||||||++.+++++|+.+|+.||.|.+|.|++  +||  ||||||+|.+.  .++.+||..|||. .+.|+.|+|..
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGA-EWKGR~LKVNK   84 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGC-VWKGGRLRLEK   84 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCC-eecCceeEEee
Confidence            68999999999999999999999999999999994  567  89999999987  7899999999999 99999999999


Q ss_pred             cCCC
Q 038096          108 SGQD  111 (211)
Q Consensus       108 a~~~  111 (211)
                      |++.
T Consensus        85 AKP~   88 (759)
T PLN03213         85 AKEH   88 (759)
T ss_pred             ccHH
Confidence            8753

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

Probab=99.62  E-value=2.6e-15  Score=137.56  Aligned_cols=84  Identities=26%  Similarity=0.477  Sum_probs=78.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ..+++|||+||++++++++|+++|++||.|.+|+|+.| .+|.++|||||+|.+.++|.+|+..|||. .++|+.|.|.+
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~-~~~gk~l~V~~  360 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGR-MLGGKPLYVAL  360 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCC-eeCCceeEEEe
Confidence            34788999999999999999999999999999999999 57999999999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      |..+..
T Consensus       361 a~~k~~  366 (562)
T TIGR01628       361 AQRKEQ  366 (562)
T ss_pred             ccCcHH
Confidence            986543

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

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

Probab=99.62  E-value=1.1e-14  Score=118.27  Aligned_cols=82  Identities=21%  Similarity=0.426  Sum_probs=76.0

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEE
Q 038096           25 GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR  104 (211)
Q Consensus        25 ~~s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~  104 (211)
                      ..++++|+|||||++..++|++|++.|+.||.|.+|++.+|+      ||+||.|++.|.|..||..+|+. +|+|..++
T Consensus       159 Qssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q------GYaFVrF~tkEaAahAIv~mNnt-ei~G~~Vk  231 (321)
T KOG0148|consen  159 QSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ------GYAFVRFETKEAAAHAIVQMNNT-EIGGQLVR  231 (321)
T ss_pred             cCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc------ceEEEEecchhhHHHHHHHhcCc-eeCceEEE
Confidence            456889999999999999999999999999999999998875      99999999999999999999999 99999999


Q ss_pred             EEecCCCcc
Q 038096          105 FALSGQDKN  113 (211)
Q Consensus       105 v~~a~~~~~  113 (211)
                      |.|.+....
T Consensus       232 CsWGKe~~~  240 (321)
T KOG0148|consen  232 CSWGKEGDD  240 (321)
T ss_pred             EeccccCCC
Confidence            999875443

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.62  E-value=2.3e-15  Score=136.73  Aligned_cols=81  Identities=26%  Similarity=0.497  Sum_probs=73.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee-CCeEEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL-YNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i-~gr~l~v~  106 (211)
                      ...++|||+|||++++|++|+++|++||.|.+|+|++| .+|+++|||||+|.+.++|++||+.||+. .| .|+.|.|.
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~-~i~~Gr~l~V~  133 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNY-EIRPGRLLGVC  133 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCC-eecCCcccccc
Confidence            34799999999999999999999999999999999999 78999999999999999999999999998 66 47888777


Q ss_pred             ecCC
Q 038096          107 LSGQ  110 (211)
Q Consensus       107 ~a~~  110 (211)
                      ++..
T Consensus       134 ~S~~  137 (578)
T TIGR01648       134 ISVD  137 (578)
T ss_pred             cccc
Confidence            6643

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.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.60  E-value=6.6e-15  Score=131.50  Aligned_cols=82  Identities=28%  Similarity=0.438  Sum_probs=76.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +.++|||+|||..+++++|+++|++||.|..|.|++|+.+++++|||||+|.+.++|++||. |+|. .+.|+.|.|.++
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~-~~~g~~i~v~~~  165 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQ-MLLGRPIIVQSS  165 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCC-EECCeeeEEeec
Confidence            47899999999999999999999999999999999999999999999999999999999997 7898 899999999887


Q ss_pred             CCCc
Q 038096          109 GQDK  112 (211)
Q Consensus       109 ~~~~  112 (211)
                      ....
T Consensus       166 ~~~~  169 (457)
T TIGR01622       166 QAEK  169 (457)
T ss_pred             chhh
Confidence            5443

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.

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

Probab=99.59  E-value=2.3e-15  Score=110.62  Aligned_cols=83  Identities=23%  Similarity=0.378  Sum_probs=79.1

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEE
Q 038096           26 NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRF  105 (211)
Q Consensus        26 ~s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v  105 (211)
                      .|.+++.|||.++...++|+++.+.|..||+|+.+.+..|+.||-.||||+|+|++.++|++||..+||. .|.|..|.|
T Consensus        68 rSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~-~ll~q~v~V  146 (170)
T KOG0130|consen   68 RSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGA-ELLGQNVSV  146 (170)
T ss_pred             cceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccch-hhhCCceeE
Confidence            3556889999999999999999999999999999999999999999999999999999999999999998 999999999


Q ss_pred             EecC
Q 038096          106 ALSG  109 (211)
Q Consensus       106 ~~a~  109 (211)
                      .|+-
T Consensus       147 Dw~F  150 (170)
T KOG0130|consen  147 DWCF  150 (170)
T ss_pred             EEEE
Confidence            9974

>smart00362 RRM_2 RNA recognition motif

Probab=99.58  E-value=1.9e-14  Score=94.55  Aligned_cols=72  Identities=40%  Similarity=0.656  Sum_probs=67.2

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        32 ~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      +|||+|||..+++++|+++|..||.|..+.+..+.  +.++|+|||+|.+.++|++|++.+++. .+.|+.|.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~-~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGT-KLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCc-EECCEEEeeC
Confidence            58999999999999999999999999999998876  778999999999999999999999997 8999998863

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

Probab=99.58  E-value=6.9e-15  Score=129.25  Aligned_cols=83  Identities=35%  Similarity=0.587  Sum_probs=79.8

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQ  110 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~  110 (211)
                      +.|||||+|++++|++|.++|+..|.|.+++++.|++||+.+||||++|.+.++|+.|++.|||. ++.|++|+|.|+..
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 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGA-EFNGRKLRVNYASN   97 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCc-ccCCceEEeecccc
Confidence            89999999999999999999999999999999999999999999999999999999999999998 99999999999876


Q ss_pred             CccC
Q 038096          111 DKNA  114 (211)
Q Consensus       111 ~~~~  114 (211)
                      .+.+
T Consensus        98 ~~~~  101 (435)
T KOG0108|consen   98 RKNA  101 (435)
T ss_pred             cchh
Confidence            6553

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

Probab=99.58  E-value=1.3e-14  Score=118.49  Aligned_cols=80  Identities=38%  Similarity=0.564  Sum_probs=76.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++||||||++++++++|+++|..||.|..+.+..|+.++.++|||||+|.+.++|..|++.++|. .|.|+.|.|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~-~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGK-ELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCC-eECCceeEeeccc
Confidence            599999999999999999999999999999999999989999999999999999999999999998 9999999999965


Q ss_pred             C
Q 038096          110 Q  110 (211)
Q Consensus       110 ~  110 (211)
                      .
T Consensus       194 ~  194 (306)
T COG0724         194 P  194 (306)
T ss_pred             c
Confidence            3

>smart00360 RRM RNA recognition motif

Probab=99.56  E-value=2.4e-14  Score=93.67  Aligned_cols=71  Identities=39%  Similarity=0.634  Sum_probs=66.8

Q ss_pred             EcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           35 IGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        35 VgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      |+|||..+++++|+++|.+||.|..+.+..++.++.++|+|||+|.+.++|.+|++.+++. .++|+.|.|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~-~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGK-ELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCC-eeCCcEEEeC
Confidence            6899999999999999999999999999998888999999999999999999999999987 8999998873

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.56  E-value=2.8e-14  Score=115.34  Aligned_cols=76  Identities=24%  Similarity=0.361  Sum_probs=69.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      .+.+|||+||++.++|++|+++|+.||.|.+|.|++|.   ..+|||||+|.++++|+.|+ .|+|. .|.++.|.|..+
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAl-lLnGa-~l~d~~I~It~~   78 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAV-LLSGA-TIVDQRVCITRW   78 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHH-hcCCC-eeCCceEEEEeC
Confidence            47899999999999999999999999999999999984   45689999999999999999 58998 999999998775


Q ss_pred             C
Q 038096          109 G  109 (211)
Q Consensus       109 ~  109 (211)
                      .
T Consensus        79 ~   79 (243)
T PLN03121         79 G   79 (243)
T ss_pred             c
Confidence            4

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

Probab=99.54  E-value=2.2e-14  Score=122.98  Aligned_cols=87  Identities=21%  Similarity=0.399  Sum_probs=79.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCe--EEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNR--TLRF  105 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr--~l~v  105 (211)
                      .+.-++|||.+|..++|.||+++|++||.|.+|.|++|+.|+.++|||||.|.+.++|.+|+..|++...|-|-  .|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            34678999999999999999999999999999999999999999999999999999999999999888677774  8899


Q ss_pred             EecCCCccC
Q 038096          106 ALSGQDKNA  114 (211)
Q Consensus       106 ~~a~~~~~~  114 (211)
                      ++|+.++++
T Consensus       112 k~Ad~E~er  120 (510)
T KOG0144|consen  112 KYADGERER  120 (510)
T ss_pred             cccchhhhc
Confidence            998866655

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.51  E-value=9.7e-14  Score=125.04  Aligned_cols=78  Identities=24%  Similarity=0.412  Sum_probs=72.1

Q ss_pred             CCCCeEEEcCCCC-CCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           28 NSGCNVYIGNLDE-KVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~-~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      +++++|||+||++ .+++++|+++|+.||.|.+|+|++++     +|||||+|.+.++|+.||..|||. .|.|+.|+|.
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~-~l~g~~l~v~  346 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGV-KLFGKPLRVC  346 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCC-EECCceEEEE
Confidence            4578999999997 69999999999999999999998864     599999999999999999999998 9999999999


Q ss_pred             ecCCC
Q 038096          107 LSGQD  111 (211)
Q Consensus       107 ~a~~~  111 (211)
                      +++..
T Consensus       347 ~s~~~  351 (481)
T TIGR01649       347 PSKQQ  351 (481)
T ss_pred             Ecccc
Confidence            98654

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).

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.51  E-value=1.1e-13  Score=125.83  Aligned_cols=75  Identities=21%  Similarity=0.292  Sum_probs=69.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcC--CCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQA--GRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~--G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .++|||+||++++++++|+++|++|  |.|++|.+++        +||||+|.+.++|++||+.||+. +|+|+.|+|.|
T Consensus       233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG~-~i~Gr~I~V~~  303 (578)
T TIGR01648       233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMDELNGK-ELEGSEIEVTL  303 (578)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCCC-EECCEEEEEEE
Confidence            5789999999999999999999999  9999997753        69999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      |++...
T Consensus       304 Akp~~~  309 (578)
T TIGR01648       304 AKPVDK  309 (578)
T ss_pred             ccCCCc
Confidence            987543

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.

>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=99.51  E-value=2.5e-13  Score=89.62  Aligned_cols=74  Identities=41%  Similarity=0.650  Sum_probs=68.6

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        32 ~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      +|+|+|||..+++++|+++|+.+|.|..+.+..+..+ ..+|+|||+|.+.++|..|++.+++. .++|+.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~-~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGK-ELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCC-eECCeEEEEeC
Confidence            4899999999999999999999999999999987764 77899999999999999999999998 89999998864

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).

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.48  E-value=2e-13  Score=123.01  Aligned_cols=75  Identities=27%  Similarity=0.274  Sum_probs=68.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHc--CCCeeeCCeEEEEEe
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF--SGIVTLYNRTLRFAL  107 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~l--ng~~~i~gr~l~v~~  107 (211)
                      ++.|||+|||++++|++|+++|++||.|.+|.|+++      +|||||+|.+.++|++||+.+  ++. .|+|+.|.|.|
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~-~l~g~~l~v~~   74 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPI-YIRGQPAFFNY   74 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCc-eEcCeEEEEEe
Confidence            689999999999999999999999999999999864      489999999999999999874  676 89999999999


Q ss_pred             cCCC
Q 038096          108 SGQD  111 (211)
Q Consensus       108 a~~~  111 (211)
                      +..+
T Consensus        75 s~~~   78 (481)
T TIGR01649        75 STSQ   78 (481)
T ss_pred             cCCc
Confidence            8643

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).

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

Probab=99.48  E-value=2.7e-13  Score=95.51  Aligned_cols=78  Identities=29%  Similarity=0.352  Sum_probs=71.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      .++.|||.|||+++|.++..++|.+||.|..|+|-.+++   .+|-|||.|++..+|.+|++.|+|. .++++-|.|-+-
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~-n~~~ryl~vlyy   92 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGY-NVDNRYLVVLYY   92 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhccc-ccCCceEEEEec
Confidence            378899999999999999999999999999999987654   5799999999999999999999998 999999998875


Q ss_pred             CC
Q 038096          109 GQ  110 (211)
Q Consensus       109 ~~  110 (211)
                      .+
T Consensus        93 q~   94 (124)
T KOG0114|consen   93 QP   94 (124)
T ss_pred             CH
Confidence            43

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

Probab=99.48  E-value=1.6e-13  Score=120.74  Aligned_cols=81  Identities=26%  Similarity=0.443  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +.++|+|.||||.+.+.+|+.+|+.||.|.+|.|++..+++.+ |||||+|....+|..||+.+|+. +|+||+|.|.||
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklc-GFaFV~fk~~~dA~~Al~~~N~~-~i~gR~VAVDWA  193 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLC-GFAFVQFKEKKDAEKALEFFNGN-KIDGRPVAVDWA  193 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCcc-ceEEEEEeeHHHHHHHHHhccCc-eecCceeEEeee
Confidence            3789999999999999999999999999999999988875555 99999999999999999999998 999999999998


Q ss_pred             CCC
Q 038096          109 GQD  111 (211)
Q Consensus       109 ~~~  111 (211)
                      -.+
T Consensus       194 V~K  196 (678)
T KOG0127|consen  194 VDK  196 (678)
T ss_pred             ccc
Confidence            654

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

Probab=99.46  E-value=1.8e-13  Score=105.78  Aligned_cols=80  Identities=25%  Similarity=0.421  Sum_probs=72.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      +++|||||||.++.|.+|+++|.+||.|.+|.|..-   -....||||+|++..+|+.||..-+|. -++|..|+|++++
T Consensus         6 ~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGY-dydg~rLRVEfpr   81 (241)
T KOG0105|consen    6 SRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGY-DYDGCRLRVEFPR   81 (241)
T ss_pred             cceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhccccc-ccCcceEEEEecc
Confidence            799999999999999999999999999999988543   234689999999999999999999998 9999999999988


Q ss_pred             CCcc
Q 038096          110 QDKN  113 (211)
Q Consensus       110 ~~~~  113 (211)
                      ....
T Consensus        82 ggr~   85 (241)
T KOG0105|consen   82 GGRS   85 (241)
T ss_pred             CCCc
Confidence            6653

>smart00361 RRM_1 RNA recognition motif

Probab=99.46  E-value=4.3e-13  Score=89.78  Aligned_cols=61  Identities=20%  Similarity=0.224  Sum_probs=55.9

Q ss_pred             HHHHHHHHh----cCCCeEEEE-EccCCCC--CCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEE
Q 038096           44 ERVLYDILI----QAGRVVDLY-IPRDKET--DKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRF  105 (211)
Q Consensus        44 e~~L~~~F~----~~G~i~~v~-i~~d~~t--g~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v  105 (211)
                      +++|+++|+    .||.|.++. |..++.+  +.++|||||+|.+.++|.+|++.|||. .++|+.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~-~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGR-YFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCC-EECCEEEEe
Confidence            678999998    999999995 7777766  899999999999999999999999999 999999986

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

Probab=99.45  E-value=4.6e-13  Score=108.49  Aligned_cols=80  Identities=28%  Similarity=0.460  Sum_probs=76.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      .+++|||=||..+++|..|.++|..||.|..++|++|..|.+.||||||++.+-++|..||..|||. .++++.|.|.+.
T Consensus       277 ~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy-~lg~rvLQVsFK  355 (360)
T KOG0145|consen  277 GGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGY-RLGDRVLQVSFK  355 (360)
T ss_pred             CeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCc-cccceEEEEEEe
Confidence            3789999999999999999999999999999999999999999999999999999999999999998 999999999985


Q ss_pred             C
Q 038096          109 G  109 (211)
Q Consensus       109 ~  109 (211)
                      .
T Consensus       356 t  356 (360)
T KOG0145|consen  356 T  356 (360)
T ss_pred             c
Confidence            3

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

Probab=99.45  E-value=8.5e-14  Score=113.11  Aligned_cols=85  Identities=22%  Similarity=0.469  Sum_probs=80.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      -+++|+|||=.||.+..+.||-.+|-.||.|++.++..|+.|+.+|.||||.|.+..+|++||..|||. .|+-++|+|.
T Consensus       282 GPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGF-QIGMKRLKVQ  360 (371)
T KOG0146|consen  282 GPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGF-QIGMKRLKVQ  360 (371)
T ss_pred             CCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcch-hhhhhhhhhh
Confidence            367999999999999999999999999999999999999999999999999999999999999999997 9999999999


Q ss_pred             ecCCCc
Q 038096          107 LSGQDK  112 (211)
Q Consensus       107 ~a~~~~  112 (211)
                      ..+++.
T Consensus       361 LKRPkd  366 (371)
T KOG0146|consen  361 LKRPKD  366 (371)
T ss_pred             hcCccc
Confidence            876654

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

Probab=99.43  E-value=9.8e-14  Score=117.01  Aligned_cols=77  Identities=30%  Similarity=0.517  Sum_probs=74.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      -|+||||.+.+++.|+.|+..|..||.|++|.+-+|..|+++||||||+|+-+|.|+-|++.|||. +++||.|+|..
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~-mlGGRNiKVgr  189 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQ-MLGGRNIKVGR  189 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccc-cccCccccccC
Confidence            489999999999999999999999999999999999999999999999999999999999999998 99999999974

>PF13893 RRM_5: RNA recognition motif

Probab=99.42  E-value=1.7e-12  Score=82.88  Aligned_cols=56  Identities=34%  Similarity=0.574  Sum_probs=50.9

Q ss_pred             HHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           47 LYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        47 L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      |+++|++||.|.++.+..+.     +++|||+|.+.++|+.|++.|||. .++|++|+|.||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~-~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGR-QFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTS-EETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCC-EECCcEEEEEEC
Confidence            68899999999999997654     699999999999999999999998 899999999986

(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 ....

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

Probab=99.41  E-value=4.2e-13  Score=109.11  Aligned_cols=86  Identities=21%  Similarity=0.368  Sum_probs=79.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCC--eEEEEE
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYN--RTLRFA  106 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~g--r~l~v~  106 (211)
                      +.++||||.|...-.|||++.+|..||.|.+|.+++..+ |.+||+|||.|.+..+|++||..|+|...+-|  ..|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~d-g~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPD-GNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCC-CCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            689999999999999999999999999999999999886 99999999999999999999999999866666  479999


Q ss_pred             ecCCCccCC
Q 038096          107 LSGQDKNAQ  115 (211)
Q Consensus       107 ~a~~~~~~~  115 (211)
                      +++.++++.
T Consensus        97 ~ADTdkER~  105 (371)
T KOG0146|consen   97 FADTDKERT  105 (371)
T ss_pred             eccchHHHH
Confidence            999888764

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

Probab=99.40  E-value=5.2e-13  Score=102.89  Aligned_cols=87  Identities=34%  Similarity=0.596  Sum_probs=79.2

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEE-EEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDL-YIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRF  105 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v-~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v  105 (211)
                      .+.+.+||||||.++++|..|.+.|+.||.|... .|++|..||.++|||||.|.+.+.+.+|++.+||. .++.++|.|
T Consensus        93 l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq-~l~nr~itv  171 (203)
T KOG0131|consen   93 LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQ-YLCNRPITV  171 (203)
T ss_pred             ccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccc-hhcCCceEE
Confidence            3557899999999999999999999999999774 89999999999999999999999999999999998 899999999


Q ss_pred             EecCCCccC
Q 038096          106 ALSGQDKNA  114 (211)
Q Consensus       106 ~~a~~~~~~  114 (211)
                      .++..+...
T Consensus       172 ~ya~k~~~k  180 (203)
T KOG0131|consen  172 SYAFKKDTK  180 (203)
T ss_pred             EEEEecCCC
Confidence            998654443

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

Probab=99.40  E-value=1.3e-12  Score=115.03  Aligned_cols=83  Identities=29%  Similarity=0.394  Sum_probs=75.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHc-----CCCeeeCCeEE
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF-----SGIVTLYNRTL  103 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~l-----ng~~~i~gr~l  103 (211)
                      .+.+|||.|||++++|++|.+.|++||.|..+.|+.++.|+.++|.|||.|.+..+|+.||...     .|.+.|+||.|
T Consensus       291 ~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~L  370 (678)
T KOG0127|consen  291 EGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLL  370 (678)
T ss_pred             ccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEE
Confidence            4689999999999999999999999999999999999999999999999999999999999876     34368999999


Q ss_pred             EEEecCCC
Q 038096          104 RFALSGQD  111 (211)
Q Consensus       104 ~v~~a~~~  111 (211)
                      +|..|-..
T Consensus       371 kv~~Av~R  378 (678)
T KOG0127|consen  371 KVTLAVTR  378 (678)
T ss_pred             eeeeccch
Confidence            99887543

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

Probab=99.40  E-value=5.8e-13  Score=109.32  Aligned_cols=74  Identities=26%  Similarity=0.425  Sum_probs=69.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQ  110 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~  110 (211)
                      .+|||||||..+++.+|+.+|++||+|++|+|++        .||||..++...|+.||..|+|. .|+|..|.|+-++.
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvK--------NYgFVHiEdktaaedairNLhgY-tLhg~nInVeaSks   73 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVK--------NYGFVHIEDKTAAEDAIRNLHGY-TLHGVNINVEASKS   73 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeec--------ccceEEeecccccHHHHhhcccc-eecceEEEEEeccc
Confidence            4799999999999999999999999999999987        59999999999999999999998 99999999999877


Q ss_pred             Ccc
Q 038096          111 DKN  113 (211)
Q Consensus       111 ~~~  113 (211)
                      +.+
T Consensus        74 Ksk   76 (346)
T KOG0109|consen   74 KSK   76 (346)
T ss_pred             cCC
Confidence            633

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.38  E-value=6.2e-13  Score=117.08  Aligned_cols=78  Identities=26%  Similarity=0.536  Sum_probs=73.8

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      ..||||||.++++|++|+.+|+.||.|..|.+.+|.+||.++|||||+|.+.++|.+|++.|||. +|-|+.|+|..-.
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngf-elAGr~ikV~~v~  356 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGF-ELAGRLIKVSVVT  356 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccc-eecCceEEEEEee
Confidence            34999999999999999999999999999999999999999999999999999999999999995 9999999987643

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

Probab=99.37  E-value=1.6e-12  Score=112.12  Aligned_cols=77  Identities=25%  Similarity=0.339  Sum_probs=70.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      -+.|||.||+.++||+.|+++|.+||.|.+|+.++        .||||.|.++++|.+|++.+||+ +|+|..|.|.+|+
T Consensus       259 VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~r--------DYaFVHf~eR~davkAm~~~ngk-eldG~~iEvtLAK  329 (506)
T KOG0117|consen  259 VKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPR--------DYAFVHFAEREDAVKAMKETNGK-ELDGSPIEVTLAK  329 (506)
T ss_pred             eeeeeeeccchhhhHHHHHHHHHhccceEEeeccc--------ceeEEeecchHHHHHHHHHhcCc-eecCceEEEEecC
Confidence            46799999999999999999999999999998775        49999999999999999999999 9999999999999


Q ss_pred             CCccCC
Q 038096          110 QDKNAQ  115 (211)
Q Consensus       110 ~~~~~~  115 (211)
                      +..+.+
T Consensus       330 P~~k~k  335 (506)
T KOG0117|consen  330 PVDKKK  335 (506)
T ss_pred             Chhhhc
Confidence            765543

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

Probab=99.35  E-value=2.4e-12  Score=108.93  Aligned_cols=109  Identities=23%  Similarity=0.312  Sum_probs=94.0

Q ss_pred             CCCCCCCCCCccccccccccCCCCCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHH
Q 038096            4 SPKHSFVPNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE   83 (211)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~   83 (211)
                      +....++++++.+++........ ....+||||+|+.++++++|++.|.+||.|..+.++.|..+.+.+||+||+|.+++
T Consensus        72 ~dgr~ve~k~av~r~~~~~~~~~-~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~  150 (311)
T KOG4205|consen   72 LDGRSVEPKRAVSREDQTKVGRH-LRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSED  150 (311)
T ss_pred             cCCccccceeccCcccccccccc-cceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEecccc
Confidence            34557899999999888665544 35789999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHcCCCeeeCCeEEEEEecCCCccCC
Q 038096           84 IGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQ  115 (211)
Q Consensus        84 ~A~~Ai~~lng~~~i~gr~l~v~~a~~~~~~~  115 (211)
                      .+.+++..- - ..|+|+.+.|..|.++....
T Consensus       151 sVdkv~~~~-f-~~~~gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  151 SVDKVTLQK-F-HDFNGKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             ccceecccc-e-eeecCceeeEeeccchhhcc
Confidence            999998652 2 48999999999998765544

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.29  E-value=5.9e-12  Score=105.93  Aligned_cols=83  Identities=19%  Similarity=0.322  Sum_probs=79.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      .++.+.|||--|.+-+++++|+-+|+.||.|..|.+++|..||.+..||||+|++.+++++|.-.|++. .|++++|.|.
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNv-LIDDrRIHVD  314 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNV-LIDDRRIHVD  314 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcce-eeccceEEee
Confidence            477899999999999999999999999999999999999999999999999999999999999999996 9999999999


Q ss_pred             ecCC
Q 038096          107 LSGQ  110 (211)
Q Consensus       107 ~a~~  110 (211)
                      ++..
T Consensus       315 FSQS  318 (479)
T KOG0415|consen  315 FSQS  318 (479)
T ss_pred             hhhh
Confidence            8754

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

Probab=99.29  E-value=3.3e-12  Score=108.09  Aligned_cols=82  Identities=23%  Similarity=0.343  Sum_probs=74.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +.++||||+|+|+++++.|++.|.+||+|.+|.+++|+.|++++||+||+|.+.+...++|..-..  .|+|+.|.+..|
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h--~~dgr~ve~k~a   82 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTH--KLDGRSVEPKRA   82 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeeccccc--ccCCccccceec
Confidence            589999999999999999999999999999999999999999999999999999999999877554  699999888776


Q ss_pred             CCCc
Q 038096          109 GQDK  112 (211)
Q Consensus       109 ~~~~  112 (211)
                      .+..
T Consensus        83 v~r~   86 (311)
T KOG4205|consen   83 VSRE   86 (311)
T ss_pred             cCcc
Confidence            5443

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.26  E-value=2.4e-11  Score=109.98  Aligned_cols=74  Identities=23%  Similarity=0.405  Sum_probs=62.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcC------------CCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCC
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQA------------GRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGI   95 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~------------G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~   95 (211)
                      ...++|||||||+.+++++|+++|..+            +.|..+.+      +..+|||||+|.+.++|..||. |+|.
T Consensus       173 ~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~-l~g~  245 (509)
T TIGR01642       173 RQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMA-LDSI  245 (509)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhc-CCCe
Confidence            447899999999999999999999974            34444554      4557999999999999999995 8997


Q ss_pred             eeeCCeEEEEEecC
Q 038096           96 VTLYNRTLRFALSG  109 (211)
Q Consensus        96 ~~i~gr~l~v~~a~  109 (211)
                       .|.|+.|+|....
T Consensus       246 -~~~g~~l~v~r~~  258 (509)
T TIGR01642       246 -IYSNVFLKIRRPH  258 (509)
T ss_pred             -EeeCceeEecCcc
Confidence             9999999997654

Members of this subfamily are found in plants, metazoa and fungi.

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.26  E-value=1.9e-11  Score=96.08  Aligned_cols=82  Identities=27%  Similarity=0.422  Sum_probs=75.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcC-CCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQA-GRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~-G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ...-+||+.+|.-+.+.++..+|.++ |.+..+++-+++.||.++|||||+|++.+.|.-|.+.||+. .+.++.|.|.+
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNY-Ll~e~lL~c~v  126 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNY-LLMEHLLECHV  126 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhh-hhhhheeeeEE
Confidence            35668999999999999999999988 78888899999999999999999999999999999999998 89999999988


Q ss_pred             cCCC
Q 038096          108 SGQD  111 (211)
Q Consensus       108 a~~~  111 (211)
                      -.++
T Consensus       127 mppe  130 (214)
T KOG4208|consen  127 MPPE  130 (214)
T ss_pred             eCch
Confidence            7665

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

Probab=99.25  E-value=2e-11  Score=106.21  Aligned_cols=79  Identities=30%  Similarity=0.582  Sum_probs=72.6

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQ  110 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~  110 (211)
                      ..|||.||+.+++.++|.++|+.||.|++|++.+|.. | ++|| ||+|+++++|.+||+.+||. .+.|++|.|.....
T Consensus        77 ~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~-ll~~kki~vg~~~~  152 (369)
T KOG0123|consen   77 SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGM-LLNGKKIYVGLFER  152 (369)
T ss_pred             ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCc-ccCCCeeEEeeccc
Confidence            3399999999999999999999999999999999986 5 9999 99999999999999999998 89999999988765


Q ss_pred             Ccc
Q 038096          111 DKN  113 (211)
Q Consensus       111 ~~~  113 (211)
                      +..
T Consensus       153 ~~e  155 (369)
T KOG0123|consen  153 KEE  155 (369)
T ss_pred             hhh
Confidence            544

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.23  E-value=3e-11  Score=104.18  Aligned_cols=79  Identities=22%  Similarity=0.254  Sum_probs=72.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHH-hcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           30 GCNVYIGNLDEKVNERVLYDIL-IQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F-~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      .+.+||.|||+++.|.+|+++| ++.|+|+.|.++.|.. |++||+|.|+|+++|.+++|++.||.. .+.||.|+|+-.
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~-GK~rGcavVEFk~~E~~qKa~E~lnk~-~~~GR~l~vKEd  121 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDES-GKARGCAVVEFKDPENVQKALEKLNKY-EVNGRELVVKED  121 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccC-CCcCCceEEEeeCHHHHHHHHHHhhhc-cccCceEEEecc
Confidence            4569999999999999999999 4799999999999975 999999999999999999999999997 999999999875


Q ss_pred             CC
Q 038096          109 GQ  110 (211)
Q Consensus       109 ~~  110 (211)
                      ..
T Consensus       122 ~d  123 (608)
T KOG4212|consen  122 HD  123 (608)
T ss_pred             Cc
Confidence            44

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

Probab=99.22  E-value=7.1e-11  Score=99.17  Aligned_cols=77  Identities=23%  Similarity=0.320  Sum_probs=68.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++||||+|...++|.+|+++|.+||+|+++.+...+      ++|||+|.+.++|+.|.+..-..+.|+|++|+|.|++
T Consensus       228 I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~  301 (377)
T KOG0153|consen  228 IKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGR  301 (377)
T ss_pred             eeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCC
Confidence            6789999999999999999999999999999987643      7999999999999999866655669999999999998


Q ss_pred             CCc
Q 038096          110 QDK  112 (211)
Q Consensus       110 ~~~  112 (211)
                      +.+
T Consensus       302 ~~~  304 (377)
T KOG0153|consen  302 PKQ  304 (377)
T ss_pred             Ccc
Confidence            843

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

Probab=99.21  E-value=5.8e-11  Score=94.60  Aligned_cols=81  Identities=27%  Similarity=0.525  Sum_probs=73.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHH----HHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEE
Q 038096           30 GCNVYIGNLDEKVNERVLYD----ILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRF  105 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~----~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v  105 (211)
                      ..+|||.||+..+..++|+.    +|++||.|.+|...+   |.+.||-|||.|.+.+.|..|+..|+|. .+.|+.+++
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gf-pFygK~mri   84 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGF-PFYGKPMRI   84 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCC-cccCchhhe
Confidence            45999999999999999988    999999999998765   5789999999999999999999999998 999999999


Q ss_pred             EecCCCccC
Q 038096          106 ALSGQDKNA  114 (211)
Q Consensus       106 ~~a~~~~~~  114 (211)
                      ++|+.+...
T Consensus        85 qyA~s~sdi   93 (221)
T KOG4206|consen   85 QYAKSDSDI   93 (221)
T ss_pred             ecccCccch
Confidence            999876553

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

Probab=99.17  E-value=3.1e-11  Score=99.25  Aligned_cols=76  Identities=18%  Similarity=0.312  Sum_probs=70.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      .+++|+||||.+.++..||+..|++||.|.+|+|++        +|+||.|.-.++|..|++.|++. ++.|++++|+.+
T Consensus        77 ~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk--------dy~fvh~d~~eda~~air~l~~~-~~~gk~m~vq~s  147 (346)
T KOG0109|consen   77 ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK--------DYAFVHFDRAEDAVEAIRGLDNT-EFQGKRMHVQLS  147 (346)
T ss_pred             CccccccCCCCccccCHHHhhhhcccCCceeeeeec--------ceeEEEEeeccchHHHHhccccc-ccccceeeeeee
Confidence            478999999999999999999999999999999986        69999999999999999999999 999999999987


Q ss_pred             CCCcc
Q 038096          109 GQDKN  113 (211)
Q Consensus       109 ~~~~~  113 (211)
                      .....
T Consensus       148 tsrlr  152 (346)
T KOG0109|consen  148 TSRLR  152 (346)
T ss_pred             ccccc
Confidence            54433

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

Probab=99.16  E-value=7.4e-11  Score=107.62  Aligned_cols=74  Identities=18%  Similarity=0.406  Sum_probs=68.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      +++||||+|+..++|.||.++|+.||.|.+|.++.      ++|+|||.+....+|++|+..|+.. .+.++.|+|.||.
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n~-kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNV-KVADKTIKIAWAV  493 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcc-cccceeeEEeeec
Confidence            58999999999999999999999999999998864      4699999999999999999999986 9999999999975


Q ss_pred             C
Q 038096          110 Q  110 (211)
Q Consensus       110 ~  110 (211)
                      .
T Consensus       494 g  494 (894)
T KOG0132|consen  494 G  494 (894)
T ss_pred             c
Confidence            3

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.11  E-value=6.9e-11  Score=106.96  Aligned_cols=83  Identities=18%  Similarity=0.409  Sum_probs=76.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|+|.|||+..+-.+++.+|..||.+.+|+|+.-...+.++|||||+|.++.+|..|++.|..+ -+.||.|.++||.
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~ST-HlyGRrLVLEwA~  691 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGST-HLYGRRLVLEWAK  691 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhccc-ceechhhheehhc
Confidence            579999999999999999999999999999999987666788999999999999999999999987 8999999999998


Q ss_pred             CCcc
Q 038096          110 QDKN  113 (211)
Q Consensus       110 ~~~~  113 (211)
                      .+..
T Consensus       692 ~d~~  695 (725)
T KOG0110|consen  692 SDNT  695 (725)
T ss_pred             cchH
Confidence            6643

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

Probab=99.08  E-value=3.6e-10  Score=98.40  Aligned_cols=76  Identities=26%  Similarity=0.477  Sum_probs=71.0

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQ  110 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~  110 (211)
                      ..||||   ++++|..|.++|+.+|.++++++.+|. |  +-|||||.|.+.++|++||+.+|.. .+.|+.|++.|+..
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~-~~~~~~~rim~s~r   74 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFD-VLKGKPIRIMWSQR   74 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCc-ccCCcEEEeehhcc
Confidence            468999   899999999999999999999999998 6  9999999999999999999999998 99999999999876


Q ss_pred             Ccc
Q 038096          111 DKN  113 (211)
Q Consensus       111 ~~~  113 (211)
                      +..
T Consensus        75 d~~   77 (369)
T KOG0123|consen   75 DPS   77 (369)
T ss_pred             CCc
Confidence            543

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.07  E-value=3.1e-10  Score=97.95  Aligned_cols=75  Identities=27%  Similarity=0.358  Sum_probs=69.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      +.+.|+|||.|||+++||..|++-|..||.|..+.|+.   .|+++|  .|.|.++++|+.|+..|+|. .++|+.|+|.
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs-~l~Gr~I~V~  606 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGS-RLDGRNIKVT  606 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccC-cccCceeeee
Confidence            45689999999999999999999999999999999953   378887  89999999999999999999 9999999997


Q ss_pred             e
Q 038096          107 L  107 (211)
Q Consensus       107 ~  107 (211)
                      +
T Consensus       607 y  607 (608)
T KOG4212|consen  607 Y  607 (608)
T ss_pred             e
Confidence            6

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

Probab=99.07  E-value=3.1e-10  Score=96.07  Aligned_cols=79  Identities=19%  Similarity=0.289  Sum_probs=74.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      -.+|||..+..+++|+||+..|+.||+|+.|.+-++..++.+|||||++|.+..+...||..||-. -++|.-|+|..+-
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlF-DLGGQyLRVGk~v  288 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLF-DLGGQYLRVGKCV  288 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchh-hcccceEeccccc
Confidence            478999999999999999999999999999999999988999999999999999999999999976 9999999997754

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

Probab=99.06  E-value=4.9e-10  Score=99.52  Aligned_cols=83  Identities=14%  Similarity=0.278  Sum_probs=77.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .-+++|||.+|...+...+|+.+|++||.|+-.+++++..+--.++||||++.+.++|.+||+.|+.+ +|.|+.|.|..
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrT-ELHGrmISVEk  481 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRT-ELHGRMISVEK  481 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhh-hhcceeeeeee
Confidence            34789999999999999999999999999999999999888888999999999999999999999998 99999999998


Q ss_pred             cCCC
Q 038096          108 SGQD  111 (211)
Q Consensus       108 a~~~  111 (211)
                      ++..
T Consensus       482 aKNE  485 (940)
T KOG4661|consen  482 AKNE  485 (940)
T ss_pred             cccC
Confidence            8643

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

Probab=99.03  E-value=1.4e-09  Score=98.60  Aligned_cols=82  Identities=21%  Similarity=0.379  Sum_probs=74.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCC---CCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDK---ETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR  104 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~---~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~  104 (211)
                      +.+++||||||+..++++.|...|+.||+|..++|+.-+   +..+.+-+|||.|.+..+|++|++.|+|. ++.+..++
T Consensus       172 P~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~-iv~~~e~K  250 (877)
T KOG0151|consen  172 PQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGI-IVMEYEMK  250 (877)
T ss_pred             CcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcce-eeeeeeee
Confidence            457899999999999999999999999999999988754   34567889999999999999999999997 99999999


Q ss_pred             EEecCC
Q 038096          105 FALSGQ  110 (211)
Q Consensus       105 v~~a~~  110 (211)
                      +.|++.
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            999854

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.00  E-value=1.3e-09  Score=98.77  Aligned_cols=78  Identities=26%  Similarity=0.442  Sum_probs=70.3

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCC---CCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKET---DKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~t---g~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ++|||.||+++++.++|...|...|.|..+.|.+-++.   -.+.|||||+|.+.++|+.|++.|+|+ .|+|+.|.|++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgt-vldGH~l~lk~  594 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGT-VLDGHKLELKI  594 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCc-eecCceEEEEe
Confidence            44999999999999999999999999999988776542   125599999999999999999999999 89999999999


Q ss_pred             cC
Q 038096          108 SG  109 (211)
Q Consensus       108 a~  109 (211)
                      +.
T Consensus       595 S~  596 (725)
T KOG0110|consen  595 SE  596 (725)
T ss_pred             cc
Confidence            87

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

Probab=98.98  E-value=1.3e-08  Score=81.14  Aligned_cols=87  Identities=16%  Similarity=0.290  Sum_probs=70.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEcc-CCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeC---CeEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPR-DKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLY---NRTL  103 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~-d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~---gr~l  103 (211)
                      ..-++|||.+||.++...+|..+|..|-..+.+.|.. ++...-.+-+|||+|.+..+|++|++.|||. .|+   +..|
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGv-rFDpE~~stL  110 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGV-RFDPETGSTL  110 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCe-eeccccCcee
Confidence            3468999999999999999999999987777765544 3322335689999999999999999999996 787   4689


Q ss_pred             EEEecCCCccCC
Q 038096          104 RFALSGQDKNAQ  115 (211)
Q Consensus       104 ~v~~a~~~~~~~  115 (211)
                      ++++|+...+.+
T Consensus       111 hiElAKSNtK~k  122 (284)
T KOG1457|consen  111 HIELAKSNTKRK  122 (284)
T ss_pred             EeeehhcCcccc
Confidence            999987655544

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.96  E-value=6.4e-10  Score=90.01  Aligned_cols=81  Identities=23%  Similarity=0.368  Sum_probs=75.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+..+||+|.|..+++++.|-..|.+|-.-...++++|+.||+++||+||.|.+..++..|+.+|+|+ .++.+.|++..
T Consensus       188 ~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gk-yVgsrpiklRk  266 (290)
T KOG0226|consen  188 EDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGK-YVGSRPIKLRK  266 (290)
T ss_pred             cccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhccc-ccccchhHhhh
Confidence            45678999999999999999999999998888999999999999999999999999999999999999 89999998865


Q ss_pred             cC
Q 038096          108 SG  109 (211)
Q Consensus       108 a~  109 (211)
                      +.
T Consensus       267 S~  268 (290)
T KOG0226|consen  267 SE  268 (290)
T ss_pred             hh
Confidence            44

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.94  E-value=4.4e-10  Score=89.20  Aligned_cols=77  Identities=27%  Similarity=0.373  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      +..++|||+||...++|+-|.++|.+.|.|.++.|..+++ ++.| ||||.|.++..+.-|++++||. .+.++.+.+.+
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~-~l~~~e~q~~~   83 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGD-DLEEDEEQRTL   83 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccc-hhccchhhccc
Confidence            3478999999999999999999999999999999999987 6777 9999999999999999999997 99998877765

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

Probab=98.90  E-value=1.3e-09  Score=87.46  Aligned_cols=72  Identities=26%  Similarity=0.385  Sum_probs=66.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQ  110 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~  110 (211)
                      ..+|||+|++.+.+.+|+.+|..||.|..+.+..        ||+||+|.+..+|..||..+|++ +|+|-++.|+|+..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~-~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGK-ELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCc-eecceeeeeecccc
Confidence            4799999999999999999999999999997754        89999999999999999999999 89998899999875


Q ss_pred             C
Q 038096          111 D  111 (211)
Q Consensus       111 ~  111 (211)
                      .
T Consensus        73 ~   73 (216)
T KOG0106|consen   73 K   73 (216)
T ss_pred             c
Confidence            3

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.89  E-value=7.6e-09  Score=84.66  Aligned_cols=80  Identities=19%  Similarity=0.331  Sum_probs=73.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      ..+|+|.||+..+.++||+++|..||.+..+.+.+|+. |.+.|.|-|.|...++|.+|++.+||. .++|+.+++....
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~-G~s~Gta~v~~~r~~DA~~avk~~~gv-~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRA-GRSLGTADVSFNRRDDAERAVKKYNGV-ALDGRPMKIEIIS  160 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCC-CCCCccceeeecchHhHHHHHHHhcCc-ccCCceeeeEEec
Confidence            37899999999999999999999999999999999875 999999999999999999999999995 9999999988764


Q ss_pred             CC
Q 038096          110 QD  111 (211)
Q Consensus       110 ~~  111 (211)
                      ..
T Consensus       161 ~~  162 (243)
T KOG0533|consen  161 SP  162 (243)
T ss_pred             Cc
Confidence            43

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

Probab=98.88  E-value=2.8e-09  Score=87.12  Aligned_cols=81  Identities=27%  Similarity=0.408  Sum_probs=75.6

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+...+||||+.+.++.++++..|+.||.|..+.|+.|+.++.++||+||+|.+.+.++.|+. |+|. .|.|+.+.|.
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs-~i~~~~i~vt  175 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGS-EIPGPAIEVT  175 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCc-ccccccceee
Confidence            3457889999999999999999999999999999999999999999999999999999999999 8998 9999999998


Q ss_pred             ecC
Q 038096          107 LSG  109 (211)
Q Consensus       107 ~a~  109 (211)
                      +.+
T Consensus       176 ~~r  178 (231)
T KOG4209|consen  176 LKR  178 (231)
T ss_pred             eee
Confidence            853

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.86  E-value=1.5e-08  Score=85.27  Aligned_cols=82  Identities=22%  Similarity=0.314  Sum_probs=74.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEE--------EEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCe
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVD--------LYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNR  101 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~--------v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr  101 (211)
                      ++.|||.|||.++|.+++.++|+++|.|..        |+|-++.+ |.-+|=|.+.|...++++-|++.|++. .+.|+
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~-~~rg~  211 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDED-ELRGK  211 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCcc-cccCc
Confidence            567999999999999999999999998864        88888877 999999999999999999999999999 99999


Q ss_pred             EEEEEecCCCcc
Q 038096          102 TLRFALSGQDKN  113 (211)
Q Consensus       102 ~l~v~~a~~~~~  113 (211)
                      .|+|+.|+-+.+
T Consensus       212 ~~rVerAkfq~K  223 (382)
T KOG1548|consen  212 KLRVERAKFQMK  223 (382)
T ss_pred             EEEEehhhhhhc
Confidence            999999874443

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

Probab=98.84  E-value=6.3e-09  Score=91.38  Aligned_cols=79  Identities=22%  Similarity=0.267  Sum_probs=66.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      ...|||+|||.++++++|+++|..||.|+...|..-.-.++..+||||+|.+.++++.||+.-  .+.|++++|.|+--+
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As--p~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS--PLEIGGRKLNVEEKR  365 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC--ccccCCeeEEEEecc
Confidence            456999999999999999999999999999777654322444599999999999999999885  358999999998744


Q ss_pred             C
Q 038096          110 Q  110 (211)
Q Consensus       110 ~  110 (211)
                      .
T Consensus       366 ~  366 (419)
T KOG0116|consen  366 P  366 (419)
T ss_pred             c
Confidence            3

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

Probab=98.74  E-value=1.4e-08  Score=90.44  Aligned_cols=87  Identities=23%  Similarity=0.357  Sum_probs=81.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ...+++|||+||..++++++++++..||.+....+..|..+|.++||||.+|.+......|+..|||. .++++.|.|..
T Consensus       287 ~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm-~lgd~~lvvq~  365 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGM-QLGDKKLVVQR  365 (500)
T ss_pred             cccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchh-hhcCceeEeeh
Confidence            44688999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cCCCccCC
Q 038096          108 SGQDKNAQ  115 (211)
Q Consensus       108 a~~~~~~~  115 (211)
                      |-......
T Consensus       366 A~~g~~~~  373 (500)
T KOG0120|consen  366 AIVGASNA  373 (500)
T ss_pred             hhccchhc
Confidence            87766554

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

Probab=98.70  E-value=1e-08  Score=90.93  Aligned_cols=74  Identities=18%  Similarity=0.265  Sum_probs=65.9

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEE
Q 038096           25 GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR  104 (211)
Q Consensus        25 ~~s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~  104 (211)
                      ++.....+|+|-|||..+++++|+++|+.||+|+.++.     |-..+|..||+|.|..+|++|++.||+. .|.|+.|+
T Consensus        70 ~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~-~~~~~~~k  143 (549)
T KOG4660|consen   70 EKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRR-EIAGKRIK  143 (549)
T ss_pred             cccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHH-Hhhhhhhc
Confidence            33445789999999999999999999999999999654     3455799999999999999999999998 99999888

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=98.67  E-value=8.4e-09  Score=91.33  Aligned_cols=94  Identities=28%  Similarity=0.380  Sum_probs=81.6

Q ss_pred             cccccCCCCCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee
Q 038096           19 KRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL   98 (211)
Q Consensus        19 ~~~~~~~~s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i   98 (211)
                      ...+.....-+.+++|+-.|...+++.+|.+||+.+|.|..|.|+.|+.++.++|.|||+|.+.+.+..||. |.|. .+
T Consensus       168 ~~~~l~~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGq-rl  245 (549)
T KOG0147|consen  168 ASRILSPEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQ-RL  245 (549)
T ss_pred             ccccCCchHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCC-cc
Confidence            333444444557889999999999999999999999999999999999999999999999999999999995 6888 89


Q ss_pred             CCeEEEEEecCCCccC
Q 038096           99 YNRTLRFALSGQDKNA  114 (211)
Q Consensus        99 ~gr~l~v~~a~~~~~~  114 (211)
                      .|..|.|......+..
T Consensus       246 lg~pv~vq~sEaeknr  261 (549)
T KOG0147|consen  246 LGVPVIVQLSEAEKNR  261 (549)
T ss_pred             cCceeEecccHHHHHH
Confidence            9999999987665554

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.60  E-value=4.5e-07  Score=64.21  Aligned_cols=80  Identities=24%  Similarity=0.360  Sum_probs=68.8

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhc--CCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeC----CeEEE
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQ--AGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLY----NRTLR  104 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~--~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~----gr~l~  104 (211)
                      ++|-|.|||...+.++|.+++..  .|....+.++.|..++.+.|||||.|.+.+.|.+-.+.++|. .+.    .+.+.
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~-~w~~~~s~Kvc~   80 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGK-KWPNFNSKKVCE   80 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCC-ccccCCCCcEEE
Confidence            68999999999999999988854  467777899999999999999999999999999999999998 665    35677


Q ss_pred             EEecCCC
Q 038096          105 FALSGQD  111 (211)
Q Consensus       105 v~~a~~~  111 (211)
                      |.||+-+
T Consensus        81 i~yAriQ   87 (97)
T PF04059_consen   81 ISYARIQ   87 (97)
T ss_pred             EehhHhh
Confidence            8887543

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.41  E-value=2.4e-07  Score=78.55  Aligned_cols=84  Identities=27%  Similarity=0.407  Sum_probs=76.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEE--------EEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeC
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVD--------LYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLY   99 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~--------v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~   99 (211)
                      ....+|||-+|+..+++++|.++|.++|.|..        |.|-+|++|+..||-|.|.|.+...|++||..++++ .+.
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agk-df~  142 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGK-DFC  142 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccc-ccc
Confidence            44678999999999999999999999998853        788899999999999999999999999999999999 999


Q ss_pred             CeEEEEEecCCCc
Q 038096          100 NRTLRFALSGQDK  112 (211)
Q Consensus       100 gr~l~v~~a~~~~  112 (211)
                      +.+|+|..|....
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999998876443

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.38  E-value=1.6e-06  Score=74.74  Aligned_cols=75  Identities=25%  Similarity=0.410  Sum_probs=68.6

Q ss_pred             CCeEEEcCCC-CCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           30 GCNVYIGNLD-EKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        30 ~~~lfVgnLp-~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ++.|-|.||. ..+|.+.|..+|+.||.|.+|+|+.++.     .-|+|+|.+...|+-|++.|+|. .+.|++|+|.++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~-~l~gk~lrvt~S  370 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGH-KLYGKKLRVTLS  370 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcc-eecCceEEEeec
Confidence            5788999997 5699999999999999999999998763     67999999999999999999998 999999999998


Q ss_pred             CC
Q 038096          109 GQ  110 (211)
Q Consensus       109 ~~  110 (211)
                      +-
T Consensus       371 KH  372 (492)
T KOG1190|consen  371 KH  372 (492)
T ss_pred             cC
Confidence            63

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

Probab=98.33  E-value=2.4e-06  Score=75.24  Aligned_cols=75  Identities=28%  Similarity=0.423  Sum_probs=63.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      ..-|-+.+|||++|++||.+||+.++ |..+.+.+  .+|+..|-|||+|.+.+++++|++. +.. .+..|-|.|-.+.
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~Alkk-dR~-~mg~RYIEVf~~~   84 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR--RNGRPSGEAYVEFTSEEDVEKALKK-DRE-SMGHRYIEVFTAG   84 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec--cCCCcCcceEEEeechHHHHHHHHh-hHH-HhCCceEEEEccC
Confidence            45677889999999999999999986 77766665  4699999999999999999999987 443 6788888887664

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.32  E-value=7.2e-06  Score=69.56  Aligned_cols=70  Identities=19%  Similarity=0.328  Sum_probs=63.1

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCC--CeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCe
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAG--RVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNR  101 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G--~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr  101 (211)
                      -.+|||||-|++|++||.+.+..-|  .+.++++..++..|.+||||+|...+..+..+.++.|-.+ +|.|+
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k-~iHGQ  152 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTK-TIHGQ  152 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccc-eecCC
Confidence            3589999999999999999998877  4677888888888999999999999999999999999988 89887

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.11  E-value=3.5e-06  Score=71.08  Aligned_cols=82  Identities=21%  Similarity=0.442  Sum_probs=73.7

Q ss_pred             CCeEE-EcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           30 GCNVY-IGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        30 ~~~lf-VgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ..++| |++|++.+++++|+.+|..+|.|..+++..+..++..+|||+|.|.+...+..++.. +.. .+.++.+.+...
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~-~~~~~~~~~~~~  261 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTR-SIGGRPLRLEED  261 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccC-cccCcccccccC
Confidence            45555 999999999999999999999999999999999999999999999999999999987 665 899999999887


Q ss_pred             CCCcc
Q 038096          109 GQDKN  113 (211)
Q Consensus       109 ~~~~~  113 (211)
                      .+...
T Consensus       262 ~~~~~  266 (285)
T KOG4210|consen  262 EPRPK  266 (285)
T ss_pred             CCCcc
Confidence            65544

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

Probab=98.08  E-value=4.3e-06  Score=66.99  Aligned_cols=61  Identities=23%  Similarity=0.257  Sum_probs=52.4

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGI   95 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~   95 (211)
                      .+|||.||..+++|++|+.+|+.|-....++|..    ...-..||++|++.+.|..|+..|+|.
T Consensus       211 stlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~----~~g~~vaf~~~~~~~~at~am~~lqg~  271 (284)
T KOG1457|consen  211 STLFIANLGPNCTEDELKQLLSRYPGFHILKIRA----RGGMPVAFADFEEIEQATDAMNHLQGN  271 (284)
T ss_pred             hhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec----CCCcceEeecHHHHHHHHHHHHHhhcc
Confidence            4699999999999999999999998777777643    223368999999999999999999987

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

Probab=98.01  E-value=3.5e-06  Score=67.79  Aligned_cols=69  Identities=26%  Similarity=0.347  Sum_probs=62.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.|+|.++...+.+.+|.+.|..+|.+....+        ..+++||+|...++|..||..+++. .+.++.|.+..
T Consensus        99 ~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~-~~~~~~l~~~~  167 (216)
T KOG0106|consen   99 HFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGK-KLNGRRISVEK  167 (216)
T ss_pred             cceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccch-hhcCceeeecc
Confidence            688999999999999999999999999955444        3489999999999999999999999 99999999944

>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=97.98  E-value=3.4e-05  Score=52.76  Aligned_cols=70  Identities=17%  Similarity=0.366  Sum_probs=47.0

Q ss_pred             CeEEEcCCCCCCcHHHH----HHHHhcCC-CeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEE
Q 038096           31 CNVYIGNLDEKVNERVL----YDILIQAG-RVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRF  105 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L----~~~F~~~G-~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v  105 (211)
                      .-|+|.|||.+.+...+    +.++.-+| .|..|.          .+-|+|.|.+.+.|++|.+.|+|. .+.|.+|.|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegE-dVfG~kI~v   71 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGE-DVFGNKISV   71 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT---SSSS--EE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhccc-ccccceEEE
Confidence            46899999998887655    45555565 555552          278999999999999999999997 899999999


Q ss_pred             EecCCC
Q 038096          106 ALSGQD  111 (211)
Q Consensus       106 ~~a~~~  111 (211)
                      ++....
T Consensus        72 ~~~~~~   77 (90)
T PF11608_consen   72 SFSPKN   77 (90)
T ss_dssp             ESS--S
T ss_pred             EEcCCc
Confidence            997433

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

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

Probab=97.97  E-value=2.6e-05  Score=68.76  Aligned_cols=78  Identities=23%  Similarity=0.322  Sum_probs=64.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEE-EEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVD-LYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~-v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ....|-+.+||+.|+++||.+||+..-.+.. +.++.|.. +++.|-|||+|++.+.|++||..-..  .|+-|-|.|-.
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~r-gR~tGEAfVqF~sqe~ae~Al~rhre--~iGhRYIEvF~  178 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQR-GRPTGEAFVQFESQESAEIALGRHRE--NIGHRYIEVFR  178 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCC-CCcccceEEEecCHHHHHHHHHHHHH--hhccceEEeeh
Confidence            3567888999999999999999998765544 66777765 78999999999999999999987443  68888888876


Q ss_pred             cC
Q 038096          108 SG  109 (211)
Q Consensus       108 a~  109 (211)
                      +.
T Consensus       179 Ss  180 (510)
T KOG4211|consen  179 SS  180 (510)
T ss_pred             hH
Confidence            54

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.97  E-value=2e-05  Score=66.69  Aligned_cols=78  Identities=18%  Similarity=0.273  Sum_probs=60.9

Q ss_pred             CCeEEEcCCCCCCcHHH----H--HHHHhcCCCeEEEEEccCCCCCC-Ccc-E-EEEEeCCHHHHHHHHHHcCCCeeeCC
Q 038096           30 GCNVYIGNLDEKVNERV----L--YDILIQAGRVVDLYIPRDKETDK-PKG-F-AFVEYESEEIGHYAIKLFSGIVTLYN  100 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~----L--~~~F~~~G~i~~v~i~~d~~tg~-~rg-~-aFV~f~~~~~A~~Ai~~lng~~~i~g  100 (211)
                      ..-+||-+|+..+-.++    |  .++|++||.|..|.+-+-.-+.. ..+ + .||+|.+.++|..||...+|. .++|
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs-~~DG  192 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGS-LLDG  192 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccc-cccC
Confidence            45689999997766554    3  58999999999998765431111 112 2 399999999999999999999 8999


Q ss_pred             eEEEEEec
Q 038096          101 RTLRFALS  108 (211)
Q Consensus       101 r~l~v~~a  108 (211)
                      |.|+..+.
T Consensus       193 r~lkatYG  200 (480)
T COG5175         193 RVLKATYG  200 (480)
T ss_pred             ceEeeecC
Confidence            99999874

>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=97.94  E-value=2.8e-05  Score=56.03  Aligned_cols=71  Identities=15%  Similarity=0.312  Sum_probs=43.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCC----CeeeCCeEEEE
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSG----IVTLYNRTLRF  105 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng----~~~i~gr~l~v  105 (211)
                      ++.|.|.++...++.++|++.|+.||.|..|.+...-      .-|+|.|.+.+.|++|++.+..    .+.+.+..+.+
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~   74 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTL   74 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEE
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEE
Confidence            3678899999999999999999999999999986643      5899999999999999976532    13455555544


Q ss_pred             E
Q 038096          106 A  106 (211)
Q Consensus       106 ~  106 (211)
                      .
T Consensus        75 ~   75 (105)
T PF08777_consen   75 E   75 (105)
T ss_dssp             E
T ss_pred             E
Confidence            4

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

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

Probab=97.94  E-value=4.8e-05  Score=61.03  Aligned_cols=77  Identities=17%  Similarity=0.328  Sum_probs=66.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeC-CeEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLY-NRTLRF  105 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~-gr~l~v  105 (211)
                      .++...+|+.|||.+++.+.|..+|.+|..-.+++++...     ++.|||+|.+...|..|...+++. .|- ...+.|
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~-~it~~~~m~i  216 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGF-KITKKNTMQI  216 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccc-eeccCceEEe
Confidence            4668899999999999999999999999999999887654     489999999999999999999887 665 567777


Q ss_pred             EecC
Q 038096          106 ALSG  109 (211)
Q Consensus       106 ~~a~  109 (211)
                      .+++
T Consensus       217 ~~a~  220 (221)
T KOG4206|consen  217 TFAK  220 (221)
T ss_pred             cccC
Confidence            6653

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

Probab=97.87  E-value=8.2e-05  Score=63.81  Aligned_cols=79  Identities=25%  Similarity=0.368  Sum_probs=71.1

Q ss_pred             CCCCeEEEcCCC-CCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           28 NSGCNVYIGNLD-EKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp-~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      .+++.+.|-+|. ..++-+.|.++|..||.|.+|++++.+.     |-|.|++.+..+.++|+..||+. .+-|.+|.|+
T Consensus       285 ~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~-----gtamVemgd~~aver~v~hLnn~-~lfG~kl~v~  358 (494)
T KOG1456|consen  285 APGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKP-----GTAMVEMGDAYAVERAVTHLNNI-PLFGGKLNVC  358 (494)
T ss_pred             CCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeeccc-----ceeEEEcCcHHHHHHHHHHhccC-ccccceEEEe
Confidence            568999999999 5688899999999999999999998765     88999999999999999999997 8899999999


Q ss_pred             ecCCCc
Q 038096          107 LSGQDK  112 (211)
Q Consensus       107 ~a~~~~  112 (211)
                      .++...
T Consensus       359 ~SkQ~~  364 (494)
T KOG1456|consen  359 VSKQNF  364 (494)
T ss_pred             eccccc
Confidence            986554

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

Probab=97.73  E-value=0.0002  Score=64.33  Aligned_cols=78  Identities=29%  Similarity=0.442  Sum_probs=62.9

Q ss_pred             CCCCeEEEcCCCCCCc------HHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCC-
Q 038096           28 NSGCNVYIGNLDEKVN------ERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYN-  100 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~------e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~g-  100 (211)
                      .-...|+|.|+|.--.      ..-|..+|+++|+|+.+.++-+.++| .+||.|++|.+..+|+.|++.|||+ .|+. 
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~-~ldkn  133 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGK-RLDKN  133 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccc-eeccc
Confidence            3367899999994322      23456789999999999999888755 9999999999999999999999999 6765 


Q ss_pred             eEEEEEe
Q 038096          101 RTLRFAL  107 (211)
Q Consensus       101 r~l~v~~  107 (211)
                      .+..|..
T Consensus       134 Htf~v~~  140 (698)
T KOG2314|consen  134 HTFFVRL  140 (698)
T ss_pred             ceEEeeh
Confidence            4666653

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

Probab=97.70  E-value=0.00014  Score=45.76  Aligned_cols=52  Identities=17%  Similarity=0.480  Sum_probs=41.6

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHH
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI   89 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai   89 (211)
                      +.|-|.|.+.+..+. +..+|..||+|..+.+.      ....+.+|.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~------~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVP------ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcC------CCCcEEEEEECCHHHHHhhC
Confidence            456788888776644 55589999999999885      33479999999999999985

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.62  E-value=0.00017  Score=66.21  Aligned_cols=76  Identities=20%  Similarity=0.258  Sum_probs=66.1

Q ss_pred             CC-eEEEcCCCCCCcHHHHHHHHhcCCCeEE-EEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           30 GC-NVYIGNLDEKVNERVLYDILIQAGRVVD-LYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        30 ~~-~lfVgnLp~~~~e~~L~~~F~~~G~i~~-v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ++ .|-+.|+|++++-+|+.+||..|-.+-. |.|.++ +.|...|-|-|.|++.++|.+|...|+++ .|..++|.+.+
T Consensus       866 Gp~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~-~i~nr~V~l~i  943 (944)
T KOG4307|consen  866 GPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQ-KIRNRVVSLRI  943 (944)
T ss_pred             CCeEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccC-cccceeEEEEe
Confidence            55 6789999999999999999999987754 445444 45999999999999999999999999999 99999988764

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

Probab=97.61  E-value=3.8e-05  Score=62.70  Aligned_cols=72  Identities=19%  Similarity=0.323  Sum_probs=60.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCC--------CCCc----cEEEEEeCCHHHHHHHHHHcCCCee
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKET--------DKPK----GFAFVEYESEEIGHYAIKLFSGIVT   97 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~t--------g~~r----g~aFV~f~~~~~A~~Ai~~lng~~~   97 (211)
                      .-.||+++||+.++..-|+++|+.||.|-.|.+-....+        |...    --|.|+|.+...|..+...||+. .
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~-~  152 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNT-P  152 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCC-c
Confidence            456999999999999999999999999999988776544        2222    23689999999999999999999 8


Q ss_pred             eCCeE
Q 038096           98 LYNRT  102 (211)
Q Consensus        98 i~gr~  102 (211)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99873

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

Probab=97.60  E-value=0.00021  Score=63.56  Aligned_cols=64  Identities=23%  Similarity=0.284  Sum_probs=59.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHh-cCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHH
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILI-QAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL   91 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~-~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~   91 (211)
                      ++.++||||+||.-++.++|-.+|. -||.|..+-|-+|.+-+-++|-|=|+|.+..+-.+||..
T Consensus       368 DprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  368 DPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            5579999999999999999999998 899999999999987789999999999999999999975

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

Probab=97.60  E-value=0.00027  Score=62.93  Aligned_cols=62  Identities=23%  Similarity=0.378  Sum_probs=49.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCC---CCCCcc---EEEEEeCCHHHHHHHHHHc
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKE---TDKPKG---FAFVEYESEEIGHYAIKLF   92 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~---tg~~rg---~aFV~f~~~~~A~~Ai~~l   92 (211)
                      +++||||+||++++|++|...|..||.+ .+.+....+   ---++|   |+|+.|+++..++.-|...
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             ccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            6899999999999999999999999986 455552111   123567   9999999999888877654

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

Probab=97.56  E-value=0.00027  Score=63.48  Aligned_cols=66  Identities=26%  Similarity=0.314  Sum_probs=53.3

Q ss_pred             HHHHHHhcCCCeEEEEEccC-CC--CCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCCCc
Q 038096           46 VLYDILIQAGRVVDLYIPRD-KE--TDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDK  112 (211)
Q Consensus        46 ~L~~~F~~~G~i~~v~i~~d-~~--tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~~~  112 (211)
                      +++.-+++||.|..|.|.++ .+  -.-.-|--||+|.+.+++++|.+.|+|. .+.|+.|...+-..++
T Consensus       425 dvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~Gr-KF~nRtVvtsYydeDk  493 (500)
T KOG0120|consen  425 DVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGR-KFANRTVVASYYDEDK  493 (500)
T ss_pred             HHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCc-eeCCcEEEEEecCHHH
Confidence            34445678999999999988 22  1234567799999999999999999999 9999999999865543

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

Probab=97.53  E-value=0.00057  Score=58.94  Aligned_cols=78  Identities=14%  Similarity=0.135  Sum_probs=64.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEE---EEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVD---LYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~---v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ...|-+.+||+..+.++|.+||..|-.-..   |.++.+.+ |+..|-|||+|.++++|.+|....+.+ ....|-|.|-
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~q-GrPSGeAFIqm~nae~a~aaaqk~hk~-~mk~RYiEvf  357 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQ-GRPSGEAFIQMRNAERARAAAQKCHKK-LMKSRYIEVF  357 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCC-CCcChhhhhhhhhhHHHHHHHHHHHHh-hcccceEEEe
Confidence            567889999999999999999999875433   56666654 999999999999999999999888876 4567888886


Q ss_pred             ecC
Q 038096          107 LSG  109 (211)
Q Consensus       107 ~a~  109 (211)
                      .+.
T Consensus       358 p~S  360 (508)
T KOG1365|consen  358 PCS  360 (508)
T ss_pred             ecc
Confidence            654

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.52  E-value=0.00018  Score=67.63  Aligned_cols=83  Identities=19%  Similarity=0.206  Sum_probs=71.5

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCC--eEE
Q 038096           26 NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYN--RTL  103 (211)
Q Consensus        26 ~s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~g--r~l  103 (211)
                      ++...+.+|||+|..++....|...|..||.|..|.+-.      ..-||+|.|++...|++|++.|-|. .|+|  +.|
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h------gq~yayi~yes~~~aq~a~~~~rga-p~G~P~~r~  523 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH------GQPYAYIQYESPPAAQAATHDMRGA-PLGGPPRRL  523 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc------CCcceeeecccCccchhhHHHHhcC-cCCCCCccc
Confidence            455688999999999999999999999999999988844      3479999999999999999999997 8887  579


Q ss_pred             EEEecCCCccCC
Q 038096          104 RFALSGQDKNAQ  115 (211)
Q Consensus       104 ~v~~a~~~~~~~  115 (211)
                      +|.++...-...
T Consensus       524 rvdla~~~~~~P  535 (975)
T KOG0112|consen  524 RVDLASPPGATP  535 (975)
T ss_pred             ccccccCCCCCh
Confidence            999987654443

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=97.40  E-value=0.00083  Score=57.17  Aligned_cols=77  Identities=18%  Similarity=0.210  Sum_probs=61.2

Q ss_pred             CCeEEEcCCC----CCCc-------HHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee
Q 038096           30 GCNVYIGNLD----EKVN-------ERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL   98 (211)
Q Consensus        30 ~~~lfVgnLp----~~~~-------e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i   98 (211)
                      .++|.+.||=    +..+       +++|++-..+||.|.+|.|--    ..+.|.+-|.|.+.++|..||+.|+|. .+
T Consensus       265 ~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d----~hPdGvvtV~f~n~eeA~~ciq~m~GR-~f  339 (382)
T KOG1548|consen  265 DRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYD----RHPDGVVTVSFRNNEEADQCIQTMDGR-WF  339 (382)
T ss_pred             CcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEec----cCCCceeEEEeCChHHHHHHHHHhcCe-ee
Confidence            6788888873    2334       345566678999999987642    356799999999999999999999999 99


Q ss_pred             CCeEEEEEecCCC
Q 038096           99 YNRTLRFALSGQD  111 (211)
Q Consensus        99 ~gr~l~v~~a~~~  111 (211)
                      +||.|..+.....
T Consensus       340 dgRql~A~i~DG~  352 (382)
T KOG1548|consen  340 DGRQLTASIWDGK  352 (382)
T ss_pred             cceEEEEEEeCCc
Confidence            9999998775443

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=97.30  E-value=0.00073  Score=58.71  Aligned_cols=78  Identities=21%  Similarity=0.215  Sum_probs=64.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCe-EEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNR-TLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr-~l~v~  106 (211)
                      ++..+|-..|+|.+++|++|+++|..-|...+.....    ++.+-+|++.+++.|+|..|+..++.. .+++. -|+|+
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff----~kd~kmal~q~~sveeA~~ali~~hnh-~lgen~hlRvS  486 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF----QKDRKMALPQLESVEEAIQALIDLHNH-YLGENHHLRVS  486 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeeec----CCCcceeecccCChhHhhhhccccccc-cCCCCceEEEE
Confidence            4577899999999999999999999988776653322    455679999999999999999999876 66665 89999


Q ss_pred             ecCC
Q 038096          107 LSGQ  110 (211)
Q Consensus       107 ~a~~  110 (211)
                      +++.
T Consensus       487 FSks  490 (492)
T KOG1190|consen  487 FSKS  490 (492)
T ss_pred             eecc
Confidence            9753

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.30  E-value=0.00027  Score=61.64  Aligned_cols=68  Identities=24%  Similarity=0.199  Sum_probs=57.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccC---CCC--CC--------CccEEEEEeCCHHHHHHHHHHcCC
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRD---KET--DK--------PKGFAFVEYESEEIGHYAIKLFSG   94 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d---~~t--g~--------~rg~aFV~f~~~~~A~~Ai~~lng   94 (211)
                      .++++|.+-|||.+-.-+.|.++|+.+|.|..|+|..-   ...  +.        .+-+|+|+|...+.|.+|.+.|+.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            46899999999999988999999999999999998765   211  11        256899999999999999999865


Q ss_pred             C
Q 038096           95 I   95 (211)
Q Consensus        95 ~   95 (211)
                      .
T Consensus       309 e  309 (484)
T KOG1855|consen  309 E  309 (484)
T ss_pred             h
Confidence            4

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

Probab=97.26  E-value=0.00026  Score=61.74  Aligned_cols=78  Identities=26%  Similarity=0.291  Sum_probs=61.8

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQ  110 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~  110 (211)
                      .++|+|||.+.++..+|+.+|...-.-..-.++      ...||+||...+...|.+|++.++|++++.|+++.+..+-+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl------~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFL------VKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCccee------eecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            479999999999999999999764111111111      12399999999999999999999999999999999988766


Q ss_pred             CccC
Q 038096          111 DKNA  114 (211)
Q Consensus       111 ~~~~  114 (211)
                      ++.+
T Consensus        76 kkqr   79 (584)
T KOG2193|consen   76 KKQR   79 (584)
T ss_pred             HHHH
Confidence            5543

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

Probab=97.25  E-value=0.0013  Score=51.58  Aligned_cols=59  Identities=27%  Similarity=0.308  Sum_probs=54.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGI   95 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~   95 (211)
                      .-.|.|.+||...+|.||+++..+.|.|....+.+|       |.+.|+|...|+.+-|+..|...
T Consensus       115 e~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~  173 (241)
T KOG0105|consen  115 EYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQ  173 (241)
T ss_pred             ceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhccc
Confidence            678999999999999999999999999999998876       69999999999999999988776

>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=97.20  E-value=0.0028  Score=45.17  Aligned_cols=76  Identities=8%  Similarity=0.145  Sum_probs=51.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEE-EccCCC------CCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCe-
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLY-IPRDKE------TDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNR-  101 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~-i~~d~~------tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr-  101 (211)
                      .+-|.|-+.|.. ..+.+.+.|++||.|.+.. +.++..      ......+-.|+|.++.+|.+||.. ||. .++|. 
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~-i~~g~~   82 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGT-IFSGSL   82 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTE-EETTCE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCe-EEcCcE
Confidence            566788889987 5567788999999998874 211100      023347899999999999999987 898 78886 


Q ss_pred             EEEEEec
Q 038096          102 TLRFALS  108 (211)
Q Consensus       102 ~l~v~~a  108 (211)
                      .+-|.+.
T Consensus        83 mvGV~~~   89 (100)
T PF05172_consen   83 MVGVKPC   89 (100)
T ss_dssp             EEEEEE-
T ss_pred             EEEEEEc
Confidence            4557765

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.

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

Probab=97.10  E-value=0.00022  Score=66.79  Aligned_cols=82  Identities=18%  Similarity=0.191  Sum_probs=71.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      ..++||.|+|+..|.++|+.++..+|.+.++.++..+. |+++|.|||.|.+..+|.+++...... .+.-..+.|+.+.
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~-gkpkg~a~v~y~~ea~~s~~~~s~d~~-~~rE~~~~v~vsn  813 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRA-GKPKGKARVDYNTEADASRKVASVDVA-GKRENNGEVQVSN  813 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhc-cccccceeccCCCcchhhhhcccchhh-hhhhcCccccccC
Confidence            56799999999999999999999999999999888876 999999999999999999999887775 6666677777766


Q ss_pred             CCcc
Q 038096          110 QDKN  113 (211)
Q Consensus       110 ~~~~  113 (211)
                      +...
T Consensus       814 p~~~  817 (881)
T KOG0128|consen  814 PERD  817 (881)
T ss_pred             Cccc
Confidence            5433

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

Probab=97.04  E-value=6.6e-05  Score=70.13  Aligned_cols=66  Identities=21%  Similarity=0.294  Sum_probs=58.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGI   95 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~   95 (211)
                      .+++||.||+..+.+.+|...|..+|.+..+.|.-.+.+++.+|+|+++|...+.+.+||....+.
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~  732 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSC  732 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhh
Confidence            467999999999999999999999999988777655567899999999999999999999877665

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

Probab=97.01  E-value=0.00033  Score=57.29  Aligned_cols=62  Identities=21%  Similarity=0.260  Sum_probs=50.1

Q ss_pred             HHHHHHh-cCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           46 VLYDILI-QAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        46 ~L~~~F~-~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      +|...|+ +||+|+++.|-.+.. -.-+|-.+|.|...++|++|++.||+. .+.|++|.+.+..
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl~-~hl~GNVYV~f~~Ee~ae~a~~~lnnR-w~~G~pi~ae~~p  146 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNLG-DHLVGNVYVKFRSEEDAEAALEDLNNR-WYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhcccc-hhhhhhhhhhcccHHHHHHHHHHHcCc-cccCCcceeeecC
Confidence            4444455 899999986655432 345789999999999999999999999 8999999998853

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.88  E-value=0.0038  Score=52.23  Aligned_cols=65  Identities=18%  Similarity=0.120  Sum_probs=52.0

Q ss_pred             HHHHHHHHhcCCCeEEEEEccCCCCCCCc-cEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           44 ERVLYDILIQAGRVVDLYIPRDKETDKPK-GFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        44 e~~L~~~F~~~G~i~~v~i~~d~~tg~~r-g~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      ++++++-.++||.|..|.|..+..--... ---||+|...++|.+|+-.|||. .|+|+.+...+-.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGR-yFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGR-YFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCc-eecceeeeheecc
Confidence            45677888999999998877765322222 23599999999999999999999 9999999887754

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

Probab=96.84  E-value=0.0067  Score=52.36  Aligned_cols=81  Identities=21%  Similarity=0.249  Sum_probs=63.7

Q ss_pred             CCCeEEEcCCC--CCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCC-eEEEE
Q 038096           29 SGCNVYIGNLD--EKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYN-RTLRF  105 (211)
Q Consensus        29 ~~~~lfVgnLp--~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~g-r~l~v  105 (211)
                      .++.|.+.=|.  .-+|-+.|..+....|.|.+|.|.+-     .---|.|+|++.+.|++|.+.|||.=+..| .+|+|
T Consensus       119 pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk-----ngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKI  193 (494)
T KOG1456|consen  119 PNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK-----NGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKI  193 (494)
T ss_pred             CCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec-----cceeeEEeechhHHHHHHHhhcccccccccceeEEE
Confidence            35555555444  56899999999999999999998763     224689999999999999999999823334 49999


Q ss_pred             EecCCCccC
Q 038096          106 ALSGQDKNA  114 (211)
Q Consensus       106 ~~a~~~~~~  114 (211)
                      ++|++.+-.
T Consensus       194 eyAkP~rln  202 (494)
T KOG1456|consen  194 EYAKPTRLN  202 (494)
T ss_pred             EecCcceee
Confidence            999877543

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

Probab=96.77  E-value=0.0079  Score=38.93  Aligned_cols=55  Identities=15%  Similarity=0.089  Sum_probs=45.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcC---CCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHc
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQA---GRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF   92 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~---G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~l   92 (211)
                      -.+|+|.|++ +++.++++.+|..|   .....|.++-|.       -|-|.|.+.+.|.+||..|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            3579999997 57889999999998   235688888875       5889999999999999764

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

Probab=96.75  E-value=0.0093  Score=45.19  Aligned_cols=77  Identities=21%  Similarity=0.253  Sum_probs=51.8

Q ss_pred             CCCCeEEEcCCC------CCCcH---HHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee
Q 038096           28 NSGCNVYIGNLD------EKVNE---RVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL   98 (211)
Q Consensus        28 ~~~~~lfVgnLp------~~~~e---~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i   98 (211)
                      ++..+|.|.-+.      ....+   .+|.+.|..||.+.-+++.-        +--+|+|.+-+.|.+|+.. +|. ++
T Consensus        25 PpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~--------~~mwVTF~dg~sALaals~-dg~-~v   94 (146)
T PF08952_consen   25 PPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG--------DTMWVTFRDGQSALAALSL-DGI-QV   94 (146)
T ss_dssp             -TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET--------TCEEEEESSCHHHHHHHHG-CCS-EE
T ss_pred             CCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC--------CeEEEEECccHHHHHHHcc-CCc-EE
Confidence            456777776554      12222   26778899999998888765        3579999999999999984 887 99


Q ss_pred             CCeEEEEEecCCCccC
Q 038096           99 YNRTLRFALSGQDKNA  114 (211)
Q Consensus        99 ~gr~l~v~~a~~~~~~  114 (211)
                      +|+.|+|+...++.-.
T Consensus        95 ~g~~l~i~LKtpdW~~  110 (146)
T PF08952_consen   95 NGRTLKIRLKTPDWLK  110 (146)
T ss_dssp             TTEEEEEEE-------
T ss_pred             CCEEEEEEeCCccHHH
Confidence            9999999887665543

; PDB: 1UFW_A 2DNR_A.

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

Probab=96.61  E-value=0.0064  Score=52.66  Aligned_cols=59  Identities=19%  Similarity=0.276  Sum_probs=47.4

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhc----CCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHH
Q 038096           32 NVYIGNLDEKVNERVLYDILIQ----AGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL   91 (211)
Q Consensus        32 ~lfVgnLp~~~~e~~L~~~F~~----~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~   91 (211)
                      .|-..+||+++++.|+.+||..    -|..+.+.+++-.+ |+..|=|||.|..+++|+.||..
T Consensus       163 ivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpd-grpTGdAFvlfa~ee~aq~aL~k  225 (508)
T KOG1365|consen  163 IVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPD-GRPTGDAFVLFACEEDAQFALRK  225 (508)
T ss_pred             EEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCC-CCcccceEEEecCHHHHHHHHHH
Confidence            3556799999999999999973    23445566666544 89999999999999999999965

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.41  E-value=0.0011  Score=62.51  Aligned_cols=78  Identities=24%  Similarity=0.316  Sum_probs=65.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      .+.+||+|||+..+++.+|+..|..+|.|.+|.|-+-+- +.--.||||.|.+.+.+..|+..+.+. .|....+++.+.
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~-~I~~g~~r~glG  448 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGP-LIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCC-ccccCccccccc
Confidence            368899999999999999999999999999998876542 555689999999999999999999887 555545555554

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=96.33  E-value=0.0008  Score=57.11  Aligned_cols=79  Identities=22%  Similarity=0.285  Sum_probs=59.8

Q ss_pred             CCeEEEcCCCCCCcHH-HHH--HHHhcCCCeEEEEEccCCC--CCC-CccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEE
Q 038096           30 GCNVYIGNLDEKVNER-VLY--DILIQAGRVVDLYIPRDKE--TDK-PKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTL  103 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~-~L~--~~F~~~G~i~~v~i~~d~~--tg~-~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l  103 (211)
                      ..-+||-+|+..+..+ .|+  +.|.+||.|..+.+-.+..  .+. .-.-++|+|...++|..||...+|. .++|+.|
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~-~~dg~~l  155 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGF-VDDGRAL  155 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhH-Hhhhhhh
Confidence            3567999999776554 443  6799999999998888662  111 1223799999999999999999997 8899887


Q ss_pred             EEEecC
Q 038096          104 RFALSG  109 (211)
Q Consensus       104 ~v~~a~  109 (211)
                      +..+..
T Consensus       156 ka~~gt  161 (327)
T KOG2068|consen  156 KASLGT  161 (327)
T ss_pred             HHhhCC
Confidence            766643

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

Probab=96.16  E-value=0.0062  Score=50.03  Aligned_cols=63  Identities=17%  Similarity=0.231  Sum_probs=55.1

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSG   94 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng   94 (211)
                      ..|||.||...++-+.|.+.|+.||.|....+..|-. ++..+-++|.|...-.|.+|+..+..
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r-~k~t~eg~v~~~~k~~a~~a~rr~~~   94 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDR-GKPTREGIVEFAKKPNARKAARRCRE   94 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeeccc-ccccccchhhhhcchhHHHHHHHhcc
Confidence            7799999999999999999999999998866655543 88889999999999999999987743

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=96.03  E-value=0.096  Score=47.57  Aligned_cols=73  Identities=15%  Similarity=0.245  Sum_probs=55.9

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhc--CCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCe-eeCCeEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQ--AGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIV-TLYNRTL  103 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~--~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~-~i~gr~l  103 (211)
                      ..+.|.|++.-||..+-.|+++.+|..  +-.+.+|.+..+.       -=||+|++..||+.|.+.|...+ +|-|+.|
T Consensus       172 ~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpI  244 (684)
T KOG2591|consen  172 NHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPI  244 (684)
T ss_pred             CcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcch
Confidence            344688899999999999999999975  6778888776542       24999999999999987764322 5667665


Q ss_pred             EEE
Q 038096          104 RFA  106 (211)
Q Consensus       104 ~v~  106 (211)
                      ...
T Consensus       245 mAR  247 (684)
T KOG2591|consen  245 MAR  247 (684)
T ss_pred             hhh
Confidence            443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.92  E-value=0.079  Score=40.04  Aligned_cols=74  Identities=11%  Similarity=0.091  Sum_probs=57.6

Q ss_pred             CCCCCeEEEcCCCCCCcH-HHHH---HHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeE
Q 038096           27 SNSGCNVYIGNLDEKVNE-RVLY---DILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRT  102 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e-~~L~---~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~  102 (211)
                      .++-.+|.|.=|..++.. +||+   ..++.||+|.++.+       ..+--|.|.|++..+|-+|+.+++.  ...|..
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~-------cGrqsavVvF~d~~SAC~Av~Af~s--~~pgtm  153 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTL-------CGRQSAVVVFKDITSACKAVSAFQS--RAPGTM  153 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeee-------cCCceEEEEehhhHHHHHHHHhhcC--CCCCce
Confidence            355678889877766653 4555   45678999999965       2346799999999999999999876  478889


Q ss_pred             EEEEecC
Q 038096          103 LRFALSG  109 (211)
Q Consensus       103 l~v~~a~  109 (211)
                      +.+.|-.
T Consensus       154 ~qCsWqq  160 (166)
T PF15023_consen  154 FQCSWQQ  160 (166)
T ss_pred             EEeeccc
Confidence            9999853

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=95.89  E-value=0.006  Score=56.42  Aligned_cols=77  Identities=19%  Similarity=0.135  Sum_probs=63.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEE-EEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVD-LYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~-v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+..|||..||..+++.++.++|...-.|++ |.|.+.. +++-++.|||.|..++++..|+..-... .++.+.|+|.-
T Consensus       433 ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~-y~G~r~irv~s  510 (944)
T KOG4307|consen  433 AGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKF-YPGHRIIRVDS  510 (944)
T ss_pred             ccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhccccc-ccCceEEEeec
Confidence            4788999999999999999999988777776 6666655 4888999999999988888887665554 67778888864

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

Probab=95.87  E-value=0.0069  Score=55.07  Aligned_cols=77  Identities=21%  Similarity=0.266  Sum_probs=61.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhc-CCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee---CCeEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQ-AGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL---YNRTL  103 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~-~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i---~gr~l  103 (211)
                      ..++.|+|.||-.-+|.-+|+.+++. .|.|.+.+|      .+.|..|||.|.+.++|.+....|||. .+   +++-|
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm------DkIKShCyV~yss~eEA~atr~AlhnV-~WP~sNPK~L  514 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM------DKIKSHCYVSYSSVEEAAATREALHNV-QWPPSNPKHL  514 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHHHH------HHhhcceeEecccHHHHHHHHHHHhcc-ccCCCCCcee
Confidence            34788999999999999999999995 555566633      345689999999999999999999997 43   44678


Q ss_pred             EEEecCCC
Q 038096          104 RFALSGQD  111 (211)
Q Consensus       104 ~v~~a~~~  111 (211)
                      .+.|...+
T Consensus       515 ~adf~~~d  522 (718)
T KOG2416|consen  515 IADFVRAD  522 (718)
T ss_pred             Eeeecchh
Confidence            88887644

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

Probab=95.82  E-value=0.043  Score=37.58  Aligned_cols=54  Identities=11%  Similarity=0.195  Sum_probs=41.5

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFS   93 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~ln   93 (211)
                      ...+|+ .|..+...||.++|+.||.| .|.++.|       .-|||...+.+.|..|+..+.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~d-------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWIND-------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCE-EEEEECT-------TEEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcC-------CcEEEEeecHHHHHHHHHHhc
Confidence            445565 99999999999999999987 5666665       479999999999999998875

; 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.

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

Probab=95.47  E-value=0.14  Score=44.59  Aligned_cols=76  Identities=11%  Similarity=0.132  Sum_probs=59.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCC---CCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDK---ETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~---~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ...|-|.||.+.++.++++.+|.-.|.|.++.|.-..   ......-.|||.|.+...+..|-.+.|-  .+-++.|.|-
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtnt--vfvdraliv~   84 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNT--VFVDRALIVR   84 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccc--eeeeeeEEEE
Confidence            3489999999999999999999999999999876533   2244567999999999999988776654  3555655554


Q ss_pred             e
Q 038096          107 L  107 (211)
Q Consensus       107 ~  107 (211)
                      .
T Consensus        85 p   85 (479)
T KOG4676|consen   85 P   85 (479)
T ss_pred             e
Confidence            3

>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=95.25  E-value=0.06  Score=42.31  Aligned_cols=81  Identities=12%  Similarity=0.116  Sum_probs=50.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhc-CCCe---EEEE--EccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCe-
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQ-AGRV---VDLY--IPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNR-  101 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~-~G~i---~~v~--i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr-  101 (211)
                      ...+|.|.+||+.++|+++.+.+.. ++..   ..+.  ..........-.-|||.|.+.+++..-+..++|.+-++.+ 
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            3679999999999999999887766 6655   3333  2222211223467899999999999999999997333332 


Q ss_pred             ---EEEEEecC
Q 038096          102 ---TLRFALSG  109 (211)
Q Consensus       102 ---~l~v~~a~  109 (211)
                         ...|.+|-
T Consensus        86 ~~~~~~VE~Ap   96 (176)
T PF03467_consen   86 NEYPAVVEFAP   96 (176)
T ss_dssp             -EEEEEEEE-S
T ss_pred             CCcceeEEEcc
Confidence               45566654

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.

>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=95.08  E-value=0.11  Score=41.18  Aligned_cols=62  Identities=19%  Similarity=0.172  Sum_probs=45.9

Q ss_pred             cHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcC--CCeeeCCeEEEEEecCCC
Q 038096           43 NERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFS--GIVTLYNRTLRFALSGQD  111 (211)
Q Consensus        43 ~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~ln--g~~~i~gr~l~v~~a~~~  111 (211)
                      ..+.|+++|..++.+....+++.      -+-..|.|.+.++|.+|...|+  +. .+.|..|+|-++...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~-~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGT-SFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TS-EETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhccccc-ccCCCceEEEEcccc
Confidence            34789999999999988877653      3668999999999999999999  88 999999999888433

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.

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=94.38  E-value=0.029  Score=49.83  Aligned_cols=74  Identities=15%  Similarity=0.127  Sum_probs=56.9

Q ss_pred             CCeEEEcCCCCCCc-HHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           30 GCNVYIGNLDEKVN-ERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        30 ~~~lfVgnLp~~~~-e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      .+.|-+.-.++.++ -++|...|.+||.|..|.+-..      ---|.|+|.+..+|-.|-.. .+. .|+++-|+|.|-
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~s-~~a-vlnnr~iKl~wh  443 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYAS-HGA-VLNNRFIKLFWH  443 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhcc-ccc-eecCceeEEEEe
Confidence            45555555665554 5899999999999999988544      35789999999999666543 566 899999999997


Q ss_pred             CCC
Q 038096          109 GQD  111 (211)
Q Consensus       109 ~~~  111 (211)
                      ++.
T Consensus       444 nps  446 (526)
T KOG2135|consen  444 NPS  446 (526)
T ss_pred             cCC
Confidence            553

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=93.96  E-value=0.03  Score=47.40  Aligned_cols=78  Identities=19%  Similarity=0.146  Sum_probs=64.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ..+++|+|++.+.+.+.+...++..+|....+..........++|++.+.|...+.+..|+...... .+.+..+....
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~-~~~~~~~~~dl  164 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSK-VLDGNKGEKDL  164 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhcc-ccccccccCcc
Confidence            3688999999999999999999999999988888777777899999999999999999999876544 45555544433

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=93.69  E-value=0.56  Score=39.70  Aligned_cols=67  Identities=13%  Similarity=0.251  Sum_probs=49.1

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeE-EEEEec
Q 038096           33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRT-LRFALS  108 (211)
Q Consensus        33 lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~-l~v~~a  108 (211)
                      |-|-+.+.. .-.-|..+|++||.|++....      ....+-+|.|.++.+|++||.. ||+ +|+|.. |-|...
T Consensus       200 VTVfGFppg-~~s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALsk-ng~-ii~g~vmiGVkpC  267 (350)
T KOG4285|consen  200 VTVFGFPPG-QVSIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALSK-NGT-IIDGDVMIGVKPC  267 (350)
T ss_pred             EEEeccCcc-chhHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhhh-cCe-eeccceEEeeeec
Confidence            334456644 335677899999999887654      3346899999999999999987 788 788764 445553

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

Probab=93.45  E-value=0.52  Score=30.86  Aligned_cols=55  Identities=11%  Similarity=0.198  Sum_probs=41.8

Q ss_pred             CCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEE
Q 038096           41 KVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRF  105 (211)
Q Consensus        41 ~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v  105 (211)
                      .++-++++..|..|+-. +  |..|+.     | =||.|.+..+|+++....+|. .+.+..+.+
T Consensus        11 ~~~v~d~K~~Lr~y~~~-~--I~~d~t-----G-fYIvF~~~~Ea~rC~~~~~~~-~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRWD-R--IRDDRT-----G-FYIVFNDSKEAERCFRAEDGT-LFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCcc-e--EEecCC-----E-EEEEECChHHHHHHHHhcCCC-EEEEEEEEe
Confidence            46678999999999742 3  333432     3 389999999999999999998 777766654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>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=93.36  E-value=0.69  Score=30.76  Aligned_cols=67  Identities=15%  Similarity=0.321  Sum_probs=39.5

Q ss_pred             eEEEc-CCCCCCcHHHHHHHHhcCCCe-----EEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEE
Q 038096           32 NVYIG-NLDEKVNERVLYDILIQAGRV-----VDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRF  105 (211)
Q Consensus        32 ~lfVg-nLp~~~~e~~L~~~F~~~G~i-----~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v  105 (211)
                      ++||. |--..++..+|..++..-+.|     -.+.|..        .|+||+-.. +.|+.++..|++. .+.|++|+|
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~--------~~S~vev~~-~~a~~v~~~l~~~-~~~gk~v~v   71 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFD--------NFSFVEVPE-EVAEKVLEALNGK-KIKGKKVRV   71 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-S--------S-EEEEE-T-T-HHHHHHHHTT---SSS----E
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEee--------eEEEEEECH-HHHHHHHHHhcCC-CCCCeeEEE
Confidence            35553 223567888999999877554     4566643        589998775 4789999999998 999999999


Q ss_pred             Eec
Q 038096          106 ALS  108 (211)
Q Consensus       106 ~~a  108 (211)
                      +.|
T Consensus        72 e~A   74 (74)
T PF03880_consen   72 ERA   74 (74)
T ss_dssp             EE-
T ss_pred             EEC
Confidence            865

; PDB: 2G0C_A 3MOJ_B.

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=92.54  E-value=0.078  Score=48.96  Aligned_cols=71  Identities=20%  Similarity=0.269  Sum_probs=61.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      .++.-++||||+...+.++-++.++..+|.|..+....         |||..|.....+..|+..++.. .++|..+.+.
T Consensus        37 ~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~-~~~~~kl~~~  106 (668)
T KOG2253|consen   37 LPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTEL-NIDDQKLIEN  106 (668)
T ss_pred             CCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhccc-CCCcchhhcc
Confidence            35578999999999999999999999999998876543         9999999999999999998876 8888877655


Q ss_pred             e
Q 038096          107 L  107 (211)
Q Consensus       107 ~  107 (211)
                      .
T Consensus       107 ~  107 (668)
T KOG2253|consen  107 V  107 (668)
T ss_pred             c
Confidence            4

>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=91.93  E-value=1.8  Score=31.36  Aligned_cols=67  Identities=10%  Similarity=0.078  Sum_probs=49.0

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCC-CeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAG-RVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYN  100 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G-~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~g  100 (211)
                      ..+.+...|..++-++|..+.+.+- .|..++|++|.  ...+=.+.+.|.+.++|.+-.+.+||+ .++.
T Consensus        14 ~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk-~Fns   81 (110)
T PF07576_consen   14 TLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGK-PFNS   81 (110)
T ss_pred             eEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCC-ccCC
Confidence            3444555556666677776666554 45678998874  346678899999999999999999998 6654

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=91.45  E-value=0.078  Score=42.86  Aligned_cols=67  Identities=33%  Similarity=0.666  Sum_probs=58.9

Q ss_pred             CCCCeEEEcC----CCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCC
Q 038096           28 NSGCNVYIGN----LDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGI   95 (211)
Q Consensus        28 ~~~~~lfVgn----Lp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~   95 (211)
                      +...+++.|+    |...++++.+.+.|++-|.+..+++.++.+ |+.+.++|+++.-....-.++....+.
T Consensus        78 e~q~~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d-~rnrn~~~~~~qr~~~~P~~~~~y~~l  148 (267)
T KOG4454|consen   78 EEQRTLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDND-GRNRNFGFVTYQRLCAVPFALDLYQGL  148 (267)
T ss_pred             hhhcccccCCCcchhhhhcchhhheeeecccCCCCCcccccccc-CCccCccchhhhhhhcCcHHhhhhccc
Confidence            4467889999    899999999999999999999999999987 899999999998888888888776664

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

Probab=91.21  E-value=0.42  Score=43.43  Aligned_cols=83  Identities=20%  Similarity=0.261  Sum_probs=56.1

Q ss_pred             CeEEEcCCCCCCcHHHHHHHH-hcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCe--eeCC-eEEEEE
Q 038096           31 CNVYIGNLDEKVNERVLYDIL-IQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIV--TLYN-RTLRFA  106 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F-~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~--~i~g-r~l~v~  106 (211)
                      +++-|.|++...|-..|...- ...|....+.++.|-.+....|||||.|.+.+++..+.+++||+.  .|++ +.+.+.
T Consensus       389 tt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~it  468 (549)
T KOG4660|consen  389 TTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASIT  468 (549)
T ss_pred             hhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeee
Confidence            344445555444433333322 235667778888888778899999999999999999999999981  2233 356677


Q ss_pred             ecCCCcc
Q 038096          107 LSGQDKN  113 (211)
Q Consensus       107 ~a~~~~~  113 (211)
                      ||+-+.+
T Consensus       469 YArIQGk  475 (549)
T KOG4660|consen  469 YARIQGK  475 (549)
T ss_pred             hhhhhch
Confidence            8765443

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=91.14  E-value=0.15  Score=48.43  Aligned_cols=75  Identities=19%  Similarity=0.229  Sum_probs=62.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCC-eeeCCeEEEEEec
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGI-VTLYNRTLRFALS  108 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~-~~i~gr~l~v~~a  108 (211)
                      ..+.++.|.+-..+-..|-.+|.+||.|.+.+.++|-      ..|.|+|.+.+.|-.|++.++|+ +..-|-+.+|.+|
T Consensus       298 qp~~~~~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  298 QPKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFA  371 (1007)
T ss_pred             cchhhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEec
Confidence            3455666777778888999999999999999887765      58999999999999999999998 3445668888887


Q ss_pred             CC
Q 038096          109 GQ  110 (211)
Q Consensus       109 ~~  110 (211)
                      +.
T Consensus       372 k~  373 (1007)
T KOG4574|consen  372 KT  373 (1007)
T ss_pred             cc
Confidence            63

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

Probab=86.44  E-value=0.028  Score=49.34  Aligned_cols=74  Identities=26%  Similarity=0.325  Sum_probs=62.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEE-EccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLY-IPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~-i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ++++-+.|+|....++.|..++.+||.+..|. +.+|.+|    ..--|+|...+.+..||..++|. .+....+++.+-
T Consensus        80 srk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~et----avvnvty~~~~~~~~ai~kl~g~-Q~en~~~k~~Yi  154 (584)
T KOG2193|consen   80 SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSET----AVVNVTYSAQQQHRQAIHKLNGP-QLENQHLKVGYI  154 (584)
T ss_pred             hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHH----HHHHHHHHHHHHHHHHHHhhcch-HhhhhhhhcccC
Confidence            57799999999999999999999999999884 4444432    34457899999999999999998 999999998874

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=82.67  E-value=1.7  Score=36.61  Aligned_cols=48  Identities=13%  Similarity=0.203  Sum_probs=38.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCe-EEEEEccCCCCCCCccEEEEEeCCHH
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRV-VDLYIPRDKETDKPKGFAFVEYESEE   83 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i-~~v~i~~d~~tg~~rg~aFV~f~~~~   83 (211)
                      .+-|+++||+.++.-.||+..+.+-|.+ .++.|      .-++|-||+.|.+..
T Consensus       330 ~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~isw------kg~~~k~flh~~~~~  378 (396)
T KOG4410|consen  330 KTDIKLTNLSRDIRVKDLKSELRKRECTPMSISW------KGHFGKCFLHFGNRK  378 (396)
T ss_pred             ccceeeccCccccchHHHHHHHHhcCCCceeEee------ecCCcceeEecCCcc
Confidence            4669999999999999999999988865 45555      345688999997653

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

Probab=81.03  E-value=5.1  Score=35.85  Aligned_cols=68  Identities=12%  Similarity=0.157  Sum_probs=56.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcC-CCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQA-GRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYN  100 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~-G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~g  100 (211)
                      ++.|+|=.+|..++-.||..|...+ -.|..++|++|..  -.+=..+|.|.+.++|..--+.+||+ .|+.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~--pnrymvLIkFr~q~da~~Fy~efNGk-~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGM--PNRYMVLIKFRDQADADTFYEEFNGK-QFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCC--CceEEEEEEeccchhHHHHHHHcCCC-cCCC
Confidence            7889999999999999999998765 4578899999642  23445699999999999999999999 6664

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	211
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		5e-14
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		2e-09
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		2e-09
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		3e-09
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		1e-08
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		1e-08
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		1e-08
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		2e-07
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		3e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		3e-06
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		4e-06
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		5e-06
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		8e-06
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		4e-05
1sxl_A	97	Resonance Assignments And Solution Structure Of The		7e-05
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		1e-04
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		1e-04
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		1e-04
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		1e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		2e-04
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		3e-04
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		4e-04
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		5e-04
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		8e-04

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 74.3 bits (181), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 33/77 (42%), Positives = 54/77 (70%), Gaps = 1/77 (1%)
Query: 28  NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
           N    VY+G LDEKV+E +L+++ +QAG VV+ ++P+D+ T + +G+ FVE+ SEE   Y
Sbjct: 13  NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72
Query: 88  AIKLFSGIVTLYNRTLR 104
           AIK+   ++ LY + +R
Sbjct: 73  AIKIMD-MIKLYGKPIR 88

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 59.3 bits (142), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/85 (38%), Positives = 51/85 (60%), Gaps = 1/85 (1%)
Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           SG + +   +Y+G L E+V+++VL+   I  G + D+ IP D ET+K +GFAFVE+E  E
Sbjct: 6   SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65
Query: 84  IGHYAIKLFSGIVTLYNRTLRFALS 108
               AI   +    L+ RT+R  L+
Sbjct: 66  DAAAAIDNMNE-SELFGRTIRVNLA 89

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 30/72 (41%), Positives = 46/72 (63%), Gaps = 2/72 (2%)
Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
            V++GNL+ +V E +LY++ +QAG +  + I +D+E  KPK F FV ++  E   YAI L
Sbjct: 18  TVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIAL 76
Query: 92  FSGIVTLYNRTL 103
            +GI  LY R +
Sbjct: 77  LNGI-RLYGRPI 87

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 58.2 bits (139), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 31/76 (40%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +Y+G L E+V+++VL+   I  G + D+ IP D ET+K +GFAFVE+E  E    AI   
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 93  SGIVTLYNRTLRFALS 108
           +    L+ RT+R  L+
Sbjct: 126 NE-SELFGRTIRVNLA 140

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 31/76 (40%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +Y+G L E+V+++VL+   I  G + D+ IP D ET+K +GFAFVE+E  E    AI   
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 93  SGIVTLYNRTLRFALS 108
           +    L+ RT+R  L+
Sbjct: 70  NE-SELFGRTIRVNLA 84

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 31/76 (40%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +Y+G L E+V+++VL+   I  G + D+ IP D ET+K +GFAFVE+E  E    AI   
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 93  SGIVTLYNRTLRFALS 108
           +    L+ RT+R  L+
Sbjct: 68  NE-SELFGRTIRVNLA 82

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 56.2 bits (134), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 31/76 (40%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +Y+G L E+V+++VL+   I  G + D+ IP D ET+K +GFAFVE+E  E    AI   
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 93  SGIVTLYNRTLRFALS 108
           +    L+ RT+R  L+
Sbjct: 65  NE-SELFGRTIRVNLA 79

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 45/84 (53%), Gaps = 1/84 (1%)
Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
           +V++GN+  +  E  L DI  + G VV   +  D+ET KPKG+ F EY+ +E    A++ 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 92  FSGIVTLYNRTLRFALSGQDKNAQ 115
            +G      R LR   +  +KN +
Sbjct: 70  LNG-REFSGRALRVDNAASEKNKE 92

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 44/92 (47%), Gaps = 5/92 (5%)
Query: 10  VPNDVVSRNKRQIMS-----GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPR 64
           V N +  RNKR  +S     G S    N+Y+ NL   + +  L  I  + G +V   I R
Sbjct: 75  VLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILR 134
Query: 65  DKETDKPKGFAFVEYESEEIGHYAIKLFSGIV 96
           DK T +P+G AFV Y   E    AI   + ++
Sbjct: 135 DKLTGRPRGVAFVRYNKREEAQEAISALNNVI 166

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 44/92 (47%), Gaps = 5/92 (5%)
Query: 10  VPNDVVSRNKRQIMS-----GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPR 64
           V N +  RNKR  +S     G S    N+Y+ NL   + +  L  I  + G +V   I R
Sbjct: 64  VLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILR 123
Query: 65  DKETDKPKGFAFVEYESEEIGHYAIKLFSGIV 96
           DK T +P+G AFV Y   E    AI   + ++
Sbjct: 124 DKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 22/60 (36%), Positives = 34/60 (56%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
          N+Y+GNL        + ++  Q G+V ++ +  D+ET KPKGF FVE + E +     KL
Sbjct: 3  NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKL 62

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 31/96 (32%), Positives = 51/96 (53%), Gaps = 4/96 (4%)
Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDL-YIPRDKETDKPKGFAFVEYESEEI 84
            S+    ++IGNLD +++E++LYD     G ++    I RD +T   KG+AF+ + S + 
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 85  GHYAIKLFSGIVTLYNR--TLRFALSGQDKNAQNSS 118
              AI+  +G   L NR  T+ +A     K +  SS
Sbjct: 61  SDAAIEAMNG-QYLCNRPITVSYAFKKDSKGSGPSS 95

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 47.0 bits (110), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
            ++ + NL  + +   L  +  + GRV D+YIPRD+ T + +GFAFV +  +     A+ 
Sbjct: 48  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 91  LFSGIVTLYNRTLRFALS 108
              G V L  R LR  ++
Sbjct: 108 AMDGAV-LDGRELRVQMA 124

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
            ++ + NL  + +   L  +  + GRV D+YIPRD+ T + +GFAFV +  +     A+ 
Sbjct: 71  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 91  LFSGIVTLYNRTLRFALS 108
              G V L  R LR  ++
Sbjct: 131 AMDGAV-LDGRELRVQMA 147

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 35/73 (47%)
Query: 24 SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           G S    N+Y+ NL   + +  L  I  + G +V   I RDK T +P+G AFV Y   E
Sbjct: 7  GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE 66
Query: 84 IGHYAIKLFSGIV 96
              AI   + ++
Sbjct: 67 EAQEAISALNNVI 79

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/65 (29%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
          N++I NLD+ ++ + LYD     G ++   +  D+  +  KG+ FV +E++E    AI+ 
Sbjct: 7  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 64
Query: 92 FSGIV 96
           +G++
Sbjct: 65 MNGML 69

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/65 (29%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
           N++I NLD+ ++ + LYD     G ++   +  D+  +  KG+ FV +E++E    AI+ 
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 157
Query: 92  FSGIV 96
            +G++
Sbjct: 158 MNGML 162

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/65 (29%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
           N++I NLD+ ++ + LYD     G ++   +  D+  +  KG+ FV +E++E    AI+ 
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 162
Query: 92  FSGIV 96
            +G++
Sbjct: 163 MNGML 167

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/65 (29%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
          N++I NLD+ ++ + LYD     G ++   +  D+  +  KG+ FV +E++E    AI+ 
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 70
Query: 92 FSGIV 96
           +G++
Sbjct: 71 MNGML 75

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE 80
          +++G LD    +  L     Q G VVD  I +DK T++ +GF FV+++
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 31/65 (47%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
            + + NL E   E  L ++    G +  +Y+ +DK T + KGFAF+ +   E    AI 
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75
Query: 91 LFSGI 95
            SG 
Sbjct: 76 GVSGF 80

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 1/78 (1%)
Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
             + + NL  + +   L  +  + GRV D+YIPR+  T  P+GFAFV +        A  
Sbjct: 14  ITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEA 73
Query: 91  LFSGIVTLYNRTLRFALS 108
              G   L  R LR  ++
Sbjct: 74  AMDG-AELDGRELRVQVA 90

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 17/53 (32%), Positives = 28/53 (52%)
Query: 27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEY 79
           +SGC ++IG L  +  +  L +   Q G V +  + RD  T + +GF FV +
Sbjct: 22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 40.4 bits (93), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 19/78 (24%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +++G L    NE+ L  +  + G++ ++ + +D+ET + +GF FV +E+ +    A+   
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 93  SGIVTLYNRTLRFALSGQ 110
           +G  ++  R +R   +G+
Sbjct: 75  NG-KSVDGRQIRVDQAGK 91

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	211
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	5e-25
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-23
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-22
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-22
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-14
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-22
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-21
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-20
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-12
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-19
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-15
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-18
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-15
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-18
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-18
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	7e-18
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-18
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-14
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-17
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-17
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-17
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-17
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-17
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	7e-17
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	7e-17
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-12
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-16
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-16
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-15
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-16
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-16
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-16
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-12
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-16
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	5e-16
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-16
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-10
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-16
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	6e-16
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	6e-16
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	8e-16
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-15
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-15
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-15
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-13
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-15
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-15
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-15
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-13
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-15
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-13
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	5e-15
2div_A	99	TRNA selenocysteine associated protein; structural	5e-15
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-15
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	4e-11
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	7e-15
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-14
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-14
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-14
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-14
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-14
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-14
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-14
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	6e-14
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	6e-14
1x5o_A	114	RNA binding motif, single-stranded interacting pro	9e-14
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-13
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-13
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-13
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-13
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-13
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-13
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-13
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-13
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-09
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-13
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-13
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-05
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-13
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	6e-13
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-13
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	8e-13
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	8e-13
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	8e-13
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-12
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-12
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-12
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-12
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	3e-12
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-12
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-12
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	4e-12
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-12
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	6e-12
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	6e-12
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	6e-12
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	7e-12
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	8e-12
1x5p_A	97	Negative elongation factor E; structure genomics,	8e-12
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	9e-12
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-11
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-11
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-11
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-11
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-11
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-11
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	3e-11
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-11
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-11
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	4e-11
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	5e-11
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	9e-11
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-06
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-10
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	3e-10
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-07
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-10
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	6e-10
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	6e-10
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	6e-10
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	7e-10
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-08
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-09
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	3e-09
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	3e-09
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-09
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	3e-09
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-09
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-09
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-09
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	8e-09
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	9e-09
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-08
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-08
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-08
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-08
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-08
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	7e-08
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-07
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	3e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	4e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	5e-07
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	5e-07
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	5e-07
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	6e-07
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	7e-07
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	7e-07
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	8e-07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-06
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-06
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-06
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-06
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-06
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	4e-06
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-06
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	6e-06
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-05
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	4e-05
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	8e-05
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-04
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	2e-04
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	3e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	3e-04
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	8e-04

>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 = 93.1 bits (232), Expect = 5e-25
 Identities = 34/95 (35%), Positives = 55/95 (57%), Gaps = 1/95 (1%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
               N    VY+G LDEKV+E +L+++ +QAG VV+ ++P+D+ T + +G+ FVE+ SEE
Sbjct: 9   ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 68

Query: 84  IGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSS 118
              YAIK+   I  LY + +R   +       +  
Sbjct: 69  DADYAIKIMDMI-KLYGKPIRVNKASAHNKNLSGP 102

>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 = 87.7 bits (218), Expect = 4e-23
 Identities = 32/89 (35%), Positives = 49/89 (55%), Gaps = 4/89 (4%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
                 +   V++GNL+ +V E +LY++ +QAG +  + I +D+E  KPK F FV ++  
Sbjct: 9   FPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFVCFKHP 67

Query: 83  EIGHYAIKLFSGIVTLYNRTLR--FALSG 109
           E   YAI L +GI  LY R +      SG
Sbjct: 68  ESVSYAIALLNGI-RLYGRPINVSGPSSG 95

>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 = 86.0 bits (214), Expect = 2e-22
 Identities = 30/78 (38%), Positives = 47/78 (60%), Gaps = 1/78 (1%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
           + +   +Y+G L E+V+++VL+   I  G + D+ IP D ET+K +GFAFVE+E  E   
Sbjct: 4   ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63

Query: 87  YAIKLFSGIVTLYNRTLR 104
            AI   +    L+ RT+R
Sbjct: 64  AAIDNMNES-ELFGRTIR 80

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 89.3 bits (222), Expect = 3e-22
 Identities = 26/116 (22%), Positives = 44/116 (37%), Gaps = 1/116 (0%)

Query: 15  VSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGF 74
           + R       G       VY+G++  ++ E  +       G +  + +  D  T K KGF
Sbjct: 13  MGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGF 72

Query: 75  AFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSR 130
           AFVEYE  E    A++  + +  L  R ++         AQ         +   +R
Sbjct: 73  AFVEYEVPEAAQLALEQMNSV-MLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNR 127

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 67.3 bits (165), Expect = 5e-14
 Identities = 17/94 (18%), Positives = 42/94 (44%), Gaps = 5/94 (5%)

Query: 15  VSRNKRQ----IMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDK 70
            +  + Q     ++  + +   +Y+ ++ + +++  +  +    G++    + RD  T K
Sbjct: 106 SNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGK 165

Query: 71  PKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR 104
            KG+ F+EYE  +    A+   +    L  + LR
Sbjct: 166 HKGYGFIEYEKAQSSQDAVSSMNL-FDLGGQYLR 198

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

 Score = 86.8 bits (215), Expect = 4e-22
 Identities = 31/90 (34%), Positives = 49/90 (54%), Gaps = 1/90 (1%)

Query: 15  VSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGF 74
                     G++ +   +Y+G L E+V+++VL+   I  G + D+ IP D ET+K +GF
Sbjct: 48  GGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGF 107

Query: 75  AFVEYESEEIGHYAIKLFSGIVTLYNRTLR 104
           AFVE+E  E    AI   +    L+ RT+R
Sbjct: 108 AFVEFELAEDAAAAIDNMNES-ELFGRTIR 136

>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 = 83.4 bits (207), Expect = 3e-21
 Identities = 36/97 (37%), Positives = 55/97 (56%), Gaps = 3/97 (3%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           SG + +   +Y+G L E+V+++VL+   I  G + D+ IP D ET+K +GFAFVE+E  E
Sbjct: 6   SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65

Query: 84  IGHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSS 118
               AI   +    L+ RT+R   A   + K +  SS
Sbjct: 66  DAAAAIDNMNE-SELFGRTIRVNLAKPMRIKESGPSS 101

>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 = 83.5 bits (207), Expect = 4e-20
 Identities = 23/98 (23%), Positives = 47/98 (47%), Gaps = 1/98 (1%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           S  S    ++Y+G+L   V E +LY+    AG ++ + + RD  T +  G+A+V ++   
Sbjct: 9   SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 68

Query: 84  IGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTT 121
               A+   +  V +  + +R   S +D + + S +  
Sbjct: 69  DAERALDTMNFDV-IKGKPVRIMWSQRDPSLRKSGVGN 105

>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 = 62.3 bits (152), Expect = 3e-12
 Identities = 24/100 (24%), Positives = 49/100 (49%), Gaps = 5/100 (5%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           S   +   N++I NLD+ ++ + LYD     G ++   +  D   +  KG+ FV +E++E
Sbjct: 97  SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQE 154

Query: 84  IGHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSSMTT 121
               AI+  +G + L +R +      S +++ A+  +   
Sbjct: 155 AAERAIEKMNG-MLLNDRKVFVGRFKSRKEREAELGARAK 193

>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 = 80.3 bits (199), Expect = 2e-19
 Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 29  SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
           S  N+ +  L + + +R LY +    G +    I RD +T    G+AFV++ SE     A
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 89  IKLFSGIVTLYNRTLR 104
           IK+ +GI T+ N+ L+
Sbjct: 62  IKVLNGI-TVRNKRLK 76

>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 = 69.5 bits (171), Expect = 3e-15
 Identities = 24/71 (33%), Positives = 33/71 (46%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
            G S    N+Y+ NL   + +  L  I  + G +V   I RDK T +P+G AFV Y   E
Sbjct: 83  GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE 142

Query: 84  IGHYAIKLFSG 94
               AI   + 
Sbjct: 143 EAQEAISALNN 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 = 78.0 bits (193), Expect = 2e-18
 Identities = 17/76 (22%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 29  SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
           S  N+ +  L + + +     +    G +    + RDK T +  G+ FV Y   +    A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 89  IKLFSGIVTLYNRTLR 104
           I   +G+  L  +T++
Sbjct: 61  INTLNGL-RLQTKTIK 75

>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 = 69.1 bits (170), Expect = 4e-15
 Identities = 18/71 (25%), Positives = 33/71 (46%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           S  S    N+Y+  L + + ++ L  +  Q GR++   I  D+ T   +G  F+ ++   
Sbjct: 82  SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI 141

Query: 84  IGHYAIKLFSG 94
               AIK  +G
Sbjct: 142 EAEEAIKGLNG 152

>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 = 75.7 bits (187), Expect = 2e-18
 Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
            +  ++    + + NL E   E  L ++    G +  +Y+ +DK T + KGFAF+ +   
Sbjct: 8   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67

Query: 83  EIGHYAIKLFSGIVTLYNRTLR 104
           E    AI   SG     +  L 
Sbjct: 68  EDAARAIAGVSG-FGYDHLILN 88

>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 = 75.0 bits (185), Expect = 5e-18
 Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 1/80 (1%)

Query: 25  GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
           G + S   VY+ NL   +    LY I  + G+VV + I +DK+T K KG AF+ +  ++ 
Sbjct: 11  GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDS 70

Query: 85  GHYAIKLFSGIVTLYNRTLR 104
                +  +    L+ R ++
Sbjct: 71  AQNCTRAINNK-QLFGRVIK 89

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

 Score = 74.6 bits (184), Expect = 7e-18
 Identities = 17/78 (21%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
           S  G  +++  + E+  E  ++D   + G + ++++  D+ T   KG+  VEYE+ +   
Sbjct: 20  SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 79

Query: 87  YAIKLFSGIVTLYNRTLR 104
            A++  +G   L  + + 
Sbjct: 80  AAMEGLNGQ-DLMGQPIS 96

>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 = 76.0 bits (188), Expect = 8e-18
 Identities = 21/86 (24%), Positives = 42/86 (48%), Gaps = 2/86 (2%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +Y+GNLD+ + E +L       G + ++ I  DK  +K   +AFVEY      + A++  
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61

Query: 93  SGIVTLYNRTLRFALSGQDKNAQNSS 118
           +G   + N  ++   + Q + + +  
Sbjct: 62  NGKQ-IENNIVKINWAFQSQQSSSDD 86

>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 = 66.4 bits (163), Expect = 4e-14
 Identities = 18/81 (22%), Positives = 38/81 (46%), Gaps = 1/81 (1%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
             +S+   N+++G+L+  V++  L +        +  ++  D +T   +G+ FV + S++
Sbjct: 81  QSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQD 140

Query: 84  IGHYAIKLFSGIVTLYNRTLR 104
               A+    G   L  R LR
Sbjct: 141 DAQNAMDSMQG-QDLNGRPLR 160

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 74.4 bits (183), Expect = 1e-17
 Identities = 22/118 (18%), Positives = 36/118 (30%), Gaps = 10/118 (8%)

Query: 25  GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
           G       V    L++ V E  L D+  + G V ++ I     T K  G A V + S   
Sbjct: 1   GGQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRG 60

Query: 85  GHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSSMTTTPLSSRKSRSDPVPMPVNG 140
               +K       +    +     + GQ +      +             P  +P  G
Sbjct: 61  AKETVKNLHLTS-VMGNIIHAQLDIKGQQRMKYYELIV-------NGSYTPQTVPTGG 110

>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 = 73.9 bits (182), Expect = 2e-17
 Identities = 17/78 (21%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
           S  G  +++ ++ E+  E  + +     G + ++++  D+ T   KG+A VEYE+ +   
Sbjct: 23  SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 82

Query: 87  YAIKLFSGIVTLYNRTLR 104
            A +  +G   +  +T++
Sbjct: 83  AAKEALNG-AEIMGQTIQ 99

>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 = 73.4 bits (181), Expect = 2e-17
 Identities = 28/97 (28%), Positives = 42/97 (43%), Gaps = 3/97 (3%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
             + +    + + NL  + +   L  +  + GRV D+YIPR+  T  P+GFAFV +    
Sbjct: 7   GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRR 66

Query: 84  IGHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSS 118
               A     G   L  R LR   A  G+   +  SS
Sbjct: 67  DAQDAEAAMDG-AELDGRELRVQVARYGRRDLSGPSS 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 = 73.5 bits (181), Expect = 2e-17
 Identities = 19/96 (19%), Positives = 40/96 (41%), Gaps = 3/96 (3%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKE-TDKPKGFAFVEYESEEI 84
              +   + + N+  + N+R + ++    G +  + +P+    T   +GF FV++ +++ 
Sbjct: 11  KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70

Query: 85  GHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSS 118
              A         LY R L   +A S     +  SS
Sbjct: 71  AKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106

>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 = 73.2 bits (180), Expect = 4e-17
 Identities = 19/94 (20%), Positives = 44/94 (46%), Gaps = 1/94 (1%)

Query: 11  PNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDK 70
             D V ++  +     S  G  +++  + E+  E  ++D   + G + ++++  D+ T  
Sbjct: 3   DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 62

Query: 71  PKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR 104
            KG+  VEYE+ +    A++  +G   L  + + 
Sbjct: 63  LKGYTLVEYETYKEAQAAMEGLNG-QDLMGQPIS 95

>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 = 71.9 bits (177), Expect = 7e-17
 Identities = 18/98 (18%), Positives = 40/98 (40%), Gaps = 5/98 (5%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
           M  +      +Y+GNL   V E ++  +  Q G      +  +  ++ P  + FVE+   
Sbjct: 8   MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEH 65

Query: 83  EIGHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSS 118
                A+   +G   +  + ++  +A +   + +  SS
Sbjct: 66  RDAAAALAAMNGRK-ILGKEVKVNWATTPSSQKSGPSS 102

>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 = 73.7 bits (181), Expect = 7e-17
 Identities = 17/78 (21%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
           S  G  +++ ++ E+  E  + +     G + ++++  D+ T   KG+A VEYE+ +   
Sbjct: 69  SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 128

Query: 87  YAIKLFSGIVTLYNRTLR 104
            A +  +G   +  +T++
Sbjct: 129 AAKEALNGA-EIMGQTIQ 145

>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 = 75.4 bits (186), Expect = 1e-16
 Identities = 18/105 (17%), Positives = 48/105 (45%), Gaps = 4/105 (3%)

Query: 18  NKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRV-VDLYIPRDKETDKPKGFAF 76
            + +I+     + C +++ N      +R + D+L     V + + +P  +  +  + FA+
Sbjct: 106 GQNEIIVS-HLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAY 163

Query: 77  VEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTT 121
           ++  S+E   Y ++  +G+  +   TL   +S   + ++ +   T
Sbjct: 164 IDVTSKEDARYCVEKLNGL-KIEGYTLVTKVSNPLEKSKRTDSAT 207

>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 = 71.2 bits (175), Expect = 3e-15
 Identities = 13/67 (19%), Positives = 25/67 (37%), Gaps = 2/67 (2%)

Query: 30  GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
              V + NL +  N+  +Y      G ++ + +       K   FA +E+   +    AI
Sbjct: 41  LTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAI 98

Query: 90  KLFSGIV 96
                +V
Sbjct: 99  TKTHKVV 105

>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 = 62.7 bits (153), Expect = 4e-12
 Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 4/92 (4%)

Query: 19  KRQIMSGNSNSGCNVYIGNLDEKV-NERVLYDILIQAGRVVDLYIPRD-KETDKPKGFAF 76
           K +     +  G  + I NL  ++ +E +L +     G +  + IP   KE       AF
Sbjct: 199 KSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAF 258

Query: 77  VEYESEEIGHYAIKLFSGIVTLYNRTLRFALS 108
           + +E+++    A+++      L NR +  +L+
Sbjct: 259 MVFENKDSAERALQMNR--SLLGNREISVSLA 288

>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 = 71.5 bits (176), Expect = 1e-16
 Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
             S  +V++GN+  +  E  L DI  + G VV   +  D+ET KPKG+ F EY+ +E   
Sbjct: 5   DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64

Query: 87  YAIKLFSGIVTLYNRTLR 104
            A++  +G      R LR
Sbjct: 65  SAMRNLNGR-EFSGRALR 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 = 74.7 bits (184), Expect = 1e-16
 Identities = 20/88 (22%), Positives = 35/88 (39%), Gaps = 7/88 (7%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
                C +++GNL   + E     +  + G   +++I RD      +GF F+  ES  + 
Sbjct: 18  TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLA 71

Query: 86  HYAIKLFSGIVTLYNRTLRFALSGQDKN 113
             A     G + L +R LR   +     
Sbjct: 72  EIAKAELDGTI-LKSRPLRIRFATHGAA 98

>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 = 70.9 bits (174), Expect = 4e-15
 Identities = 24/137 (17%), Positives = 43/137 (31%), Gaps = 6/137 (4%)

Query: 18  NKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFV 77
             R +    +  G  + + NL   V+  +L     Q G V    +  D +  +  G  FV
Sbjct: 84  KSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFV 142

Query: 78  EYESEEIGHYAIKLFSGIVTLYNRTLR-----FALSGQDKNAQNSSMTTTPLSSRKSRSD 132
           E+ ++     A++       L   T R           D++     +        K R  
Sbjct: 143 EFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQ 202

Query: 133 PVPMPVNGMEISHHSMR 149
           P      G     ++ R
Sbjct: 203 PPRFAQPGTFEFEYASR 219

>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 = 71.2 bits (175), Expect = 2e-16
 Identities = 23/95 (24%), Positives = 42/95 (44%), Gaps = 3/95 (3%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
                  +Y+ NL  +V ER L  +  +        I     T + +G AF+ + ++EI 
Sbjct: 21  PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIA 80

Query: 86  HYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSS 118
             A+ L +G   LY + L   F  + + +++  SS
Sbjct: 81  WQALHLVNGYK-LYGKILVIEFGKNKKQRSSGPSS 114

>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 = 70.0 bits (172), Expect = 3e-16
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
             VY+G++     E  + D+    G V++L +  D +T + KG+AF+E+   E    A++
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 91  LFSGIVTLYNRTLR 104
             +G   L +R L+
Sbjct: 63  NLNGY-QLGSRFLK 75

>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 = 71.9 bits (177), Expect = 4e-16
 Identities = 20/98 (20%), Positives = 43/98 (43%), Gaps = 3/98 (3%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
              S +  N++IGNL+   +   L   + +     DL +  D  T   + F +V++ES E
Sbjct: 7   GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAE 65

Query: 84  IGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTT 121
               A++L +G+  ++   ++        + +  +  T
Sbjct: 66  DLEKALEL-TGL-KVFGNEIKLEKPKGRDSKKVRAART 101

>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 = 61.5 bits (150), Expect = 3e-12
 Identities = 15/87 (17%), Positives = 33/87 (37%), Gaps = 7/87 (8%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
              +   +   NL   + E  L ++   A  +         +  K KG A++E++SE   
Sbjct: 95  KVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADA 149

Query: 86  HYAIKLFSGIVTLYNRTLRFALSGQDK 112
              ++   G   +  R++    +  +K
Sbjct: 150 EKNLEEKQG-AEIDGRSVSLYYT-GEK 174

>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 = 71.4 bits (175), Expect = 4e-16
 Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 1/89 (1%)

Query: 16  SRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFA 75
            R   +         C +Y+GNL     E  +Y++  ++G +  + +  DK      GF 
Sbjct: 25  FRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFC 84

Query: 76  FVEYESEEIGHYAIKLFSGIVTLYNRTLR 104
           FVEY S      A++  +G   L +R +R
Sbjct: 85  FVEYYSRADAENAMRYINGT-RLDDRIIR 112

>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 = 70.0 bits (172), Expect = 5e-16
 Identities = 20/76 (26%), Positives = 32/76 (42%)

Query: 16 SRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFA 75
           R     +S        V+   L  ++  R L D     G+V D+ I  D+ + + KG A
Sbjct: 11 VREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIA 70

Query: 76 FVEYESEEIGHYAIKL 91
          +VE+   +    AI L
Sbjct: 71 YVEFCEIQSVPLAIGL 86

>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 = 73.5 bits (181), Expect = 5e-16
 Identities = 20/103 (19%), Positives = 42/103 (40%), Gaps = 3/103 (2%)

Query: 18  NKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFV 77
            +R++      +   + + NL   + ++   +++   G +   ++   + T + KG+ F 
Sbjct: 83  RERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFA 142

Query: 78  EYESEEIGHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSS 118
           EY  ++    A     G   L  RTL   +  +GQ   A   S
Sbjct: 143 EYMKKDSAARAKSDLLG-KPLGPRTLYVHWTDAGQLTPALLHS 184

>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 = 59.2 bits (144), Expect = 6e-11
 Identities = 22/97 (22%), Positives = 32/97 (32%), Gaps = 8/97 (8%)

Query: 17  RNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAF 76
           R + +       +   + I  L   V  + ++D+L            +    DK KG AF
Sbjct: 9   RKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAF 61

Query: 77  VEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDKN 113
           V   + E    AI  F     L  R L   L   D  
Sbjct: 62  VTLLNGEQAEAAINAFHQSR-LRERELSVQLQPTDAL 97

>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 = 56.5 bits (137), Expect = 6e-10
 Identities = 20/108 (18%), Positives = 38/108 (35%), Gaps = 5/108 (4%)

Query: 15  VSRNKRQIMSGNSNSGCNVYIGNLDEKVNER-VLYDILIQAGRVVDLYIPRDKETDKPKG 73
           V       ++        + +  L    N+   L   L          +    +  + KG
Sbjct: 169 VHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLKG 227

Query: 74  FAFVEYESEEIGHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSSM 119
           FA +EYE+ E+   A +   G ++L    LR  F   G    +  +++
Sbjct: 228 FAVLEYETAEMAEEAQQQADG-LSLGGSHLRVSFCAPGPPGRSMLAAL 274

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

 Score = 69.1 bits (170), Expect = 6e-16
 Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 3/81 (3%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           S  S+  C +++ NL      ++L D   + G V+   I  +    K KG   V++ES E
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPE 59

Query: 84  IGHYAIKLFSGIVTLYNRTLR 104
           +   A ++ +G + L  R + 
Sbjct: 60  VAERACRMMNG-MKLSGREID 79

>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 = 71.0 bits (174), Expect = 6e-16
 Identities = 28/110 (25%), Positives = 48/110 (43%), Gaps = 4/110 (3%)

Query: 11  PNDVVSRNKRQIMS-GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETD 69
               V+          +     ++ + NL  + +   L  +  + GRV D+YIPRD+ T 
Sbjct: 50  KTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTK 109

Query: 70  KPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNS 117
           + +GFAFV +  +     A+    G   L  R LR   A  G+  ++ +S
Sbjct: 110 ESRGFAFVRFHDKRDAEDAMDAMDG-AVLDGRELRVQMARYGRPPDSHHS 158

>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 = 69.2 bits (170), Expect = 6e-16
 Identities = 23/86 (26%), Positives = 43/86 (50%), Gaps = 3/86 (3%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
           N +  C + +  L     ER L ++  + G + D+ I  D+++ + +GFAFV +E+ +  
Sbjct: 11  NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70

Query: 86  HYAIKLFSGIVTLYNRTLR--FALSG 109
             A +  +G + L  R +R     SG
Sbjct: 71  KEAKERANG-MELDGRRIRVSGPSSG 95

>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 = 69.1 bits (170), Expect = 8e-16
 Identities = 32/97 (32%), Positives = 52/97 (53%), Gaps = 5/97 (5%)

Query: 25  GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLY-IPRDKETDKPKGFAFVEYESEE 83
           G+S S   ++IGNLD +++E++LYD     G ++    I RD +T   KG+AF+ + S +
Sbjct: 1   GSSGSS-GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFD 59

Query: 84  IGHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSS 118
               AI+  +G   L NR +   +A     K +  SS
Sbjct: 60  ASDAAIEAMNG-QYLCNRPITVSYAFKKDSKGSGPSS 95

>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 = 68.4 bits (168), Expect = 1e-15
 Identities = 27/98 (27%), Positives = 46/98 (46%), Gaps = 10/98 (10%)

Query: 25  GNSNS-GCN-VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
           G+S S G N +YIGNL   V    L  +           +P   +     G+AFV+Y  +
Sbjct: 1   GSSGSSGMNKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQ 54

Query: 83  EIGHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSS 118
                AI+  SG V L+ + +   +++S + +++  SS
Sbjct: 55  NWAIRAIETLSGKVELHGKIMEVDYSVSKKLRSSGPSS 92

>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 = 68.5 bits (168), Expect = 2e-15
 Identities = 23/103 (22%), Positives = 44/103 (42%), Gaps = 7/103 (6%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
           +  +   G  V+I NL     E  L ++L Q G +  + +    +T+  KG AF ++ ++
Sbjct: 8   LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 67

Query: 83  EIGHYAIKLFSGI-----VTLYNRTLR--FALSGQDKNAQNSS 118
           E     +   S       + L  R L+   A++  +  +  SS
Sbjct: 68  EAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSS 110

>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 = 69.9 bits (172), Expect = 2e-15
 Identities = 18/91 (19%), Positives = 42/91 (46%), Gaps = 5/91 (5%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKP--KGFAFVEYESEEI 84
           S++   +++G +    +E+ L ++  Q G V ++ + RD+  + P  KG  FV + + + 
Sbjct: 1   SDAI-KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 59

Query: 85  GHYAIKLFSGIVTL--YNRTLRFALSGQDKN 113
              A      +  L   +  ++   +  +KN
Sbjct: 60  ALEAQNALHNMKVLPGMHHPIQMKPADSEKN 90

>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 = 63.8 bits (156), Expect = 4e-13
 Identities = 16/85 (18%), Positives = 32/85 (37%), Gaps = 1/85 (1%)

Query: 14  VVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKG 73
            +          N+     ++IG + +K  E  +  +    G++ +  I R       +G
Sbjct: 79  PIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRG 137

Query: 74  FAFVEYESEEIGHYAIKLFSGIVTL 98
            AFV + +  +   AIK      T+
Sbjct: 138 CAFVTFTTRAMAQTAIKAMHQAQTM 162

>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 = 68.1 bits (167), Expect = 3e-15
 Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 2/81 (2%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
              G  V++ NLD KV  + L ++   AG VV   I  DK+  K +G   V +E      
Sbjct: 12  GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAV 70

Query: 87  YAIKLFSGIVTLYNRTLRFAL 107
            AI +F+G   L++R +   +
Sbjct: 71  QAISMFNG-QLLFDRPMHVKM 90

>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 = 67.6 bits (166), Expect = 3e-15
 Identities = 19/78 (24%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
           S+    +Y+G+L   + E +L  I    G++ ++ + +D +T + KG+ F+ +   E   
Sbjct: 2   SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61

Query: 87  YAIKLFSGIVTLYNRTLR 104
            A++  +G   L  R +R
Sbjct: 62  RALEQLNG-FELAGRPMR 78

>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 = 70.1 bits (172), Expect = 3e-15
 Identities = 22/102 (21%), Positives = 44/102 (43%), Gaps = 3/102 (2%)

Query: 16  SRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFA 75
                 + +   +S   ++IG L   +N+  + ++L   G +    + +D  T   KG+A
Sbjct: 100 VYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYA 159

Query: 76  FVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNS 117
           F EY    +   AI   +G+  L ++ L    +     A+N+
Sbjct: 160 FCEYVDINVTDQAIAGLNGMQ-LGDKKLLVQRA--SVGAKNA 198

>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 = 64.7 bits (158), Expect = 3e-13
 Identities = 21/114 (18%), Positives = 39/114 (34%), Gaps = 8/114 (7%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPR-----DKETDKPKGFAFVEYESEEIG 85
             +Y+GN+   + E  + D      R+  L           + ++ K FAF+E+ S +  
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 86  HYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSRSDPVPMPVN 139
             A+    GI     ++L+      D            +      S  VP   +
Sbjct: 65  TQAMAF-DGI-IFQGQSLKIRRP-HDYQPLPGMSENPSVYVPGVVSTVVPDSAH 115

>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 = 69.2 bits (170), Expect = 3e-15
 Identities = 20/86 (23%), Positives = 37/86 (43%), Gaps = 1/86 (1%)

Query: 19  KRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVE 78
           +R            ++IG L   +N+  + ++L   G +    + +D  T   KG+AF E
Sbjct: 83  RRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE 142

Query: 79  YESEEIGHYAIKLFSGIVTLYNRTLR 104
           Y    +   AI   +G+  L ++ L 
Sbjct: 143 YVDINVTDQAIAGLNGM-QLGDKKLL 167

>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 = 63.4 bits (155), Expect = 5e-13
 Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPR-----DKETDKPKGFAFVEYESEEIGHY 87
           +Y+GN+   + E  + D      R+  L           + ++ K FAF+E+ S +    
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 88  AIKLFSGIVTLYNRTLR 104
           A+  F GI+    ++L+
Sbjct: 67  AMA-FDGII-FQGQSLK 81

>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 = 67.3 bits (165), Expect = 5e-15
 Identities = 24/97 (24%), Positives = 44/97 (45%), Gaps = 3/97 (3%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
                 G N++I +L ++  ++ L  + +  G VV   +  DK+T+  K F FV Y++  
Sbjct: 19  QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 78

Query: 84  IGHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSS 118
               AI+  +G   +  + L+     S  D  +  SS
Sbjct: 79  SAQAAIQSMNG-FQIGMKRLKVQLKRSKNDSKSGPSS 114

>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 = 67.0 bits (164), Expect = 5e-15
 Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 24 SGNSNSGCNVYIGNLDEKVNERVLYDILIQAG-RVVDLYIPRDKETDKPKGFAFVEYESE 82
          SG+S    ++++G+L+  ++E  +       G  V+ + I R++ T  P G+ FVE+   
Sbjct: 3  SGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADL 62

Query: 83 EIGHYAIKLFSG 94
                +   +G
Sbjct: 63 ATAEKCLHKING 74

>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 = 68.3 bits (168), Expect = 7e-15
 Identities = 17/65 (26%), Positives = 32/65 (49%)

Query: 19  KRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVE 78
           KR I     +    +++G +   V  +   +   Q G ++D  +  DK+T + +GF FV 
Sbjct: 76  KRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVT 135

Query: 79  YESEE 83
           Y+S +
Sbjct: 136 YDSAD 140

>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 = 57.9 bits (141), Expect = 4e-11
 Identities = 18/60 (30%), Positives = 29/60 (48%)

Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
          C ++IG L+    E  L +   + G V DL I +D  T + +GF F+ +E        +K
Sbjct: 4  CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63

>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 = 66.0 bits (162), Expect = 7e-15
 Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 10/84 (11%)

Query: 25  GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
           G      ++Y+GN+D       L       G V  + I  DK +  PKGFA++E+  +E 
Sbjct: 1   GMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES 60

Query: 85  GHYAIKL----FSGIVTLYNRTLR 104
              ++ L    F G      R ++
Sbjct: 61  VRTSLALDESLFRG------RQIK 78

>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 = 67.1 bits (164), Expect = 1e-14
 Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 1/89 (1%)

Query: 16  SRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFA 75
             ++      N +  C + +  L     ER L ++  + G + D+ I  D+++ + +GFA
Sbjct: 32  RGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 91

Query: 76  FVEYESEEIGHYAIKLFSGIVTLYNRTLR 104
           FV +E+ +    A +  +G + L  R +R
Sbjct: 92  FVYFENVDDAKEAKERANG-MELDGRRIR 119

>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 = 66.2 bits (162), Expect = 1e-14
 Identities = 17/70 (24%), Positives = 32/70 (45%)

Query: 29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
              ++IG +   ++E+ L  +  + G++ +L + +D+ T   KG AF+ Y   E    A
Sbjct: 12 DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71

Query: 89 IKLFSGIVTL 98
                  TL
Sbjct: 72 QSALHEQKTL 81

>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 = 65.3 bits (160), Expect = 2e-14
 Identities = 20/81 (24%), Positives = 45/81 (55%), Gaps = 1/81 (1%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           SG ++    +++G L    NE+ L  +  + G++ ++ + +D+ET + +GF FV +E+ +
Sbjct: 6   SGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENID 65

Query: 84  IGHYAIKLFSGIVTLYNRTLR 104
               A+   +G  ++  R +R
Sbjct: 66  DAKDAMMAMNG-KSVDGRQIR 85

>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 = 68.2 bits (166), Expect = 2e-14
 Identities = 24/164 (14%), Positives = 49/164 (29%), Gaps = 3/164 (1%)

Query: 3   PSPKHSFVPNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAG--RVVDL 60
                  V +DV       ++   +     +YIGNL     +  L + +   G   ++++
Sbjct: 41  MDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEI 100

Query: 61  YIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMT 120
               ++   + KGFA V   SE      + L      L+ +        +   +Q    +
Sbjct: 101 KFFENRANGQSKGFALVGVGSEASSKKLMDLLPKR-ELHGQNPVVTPVNKQFLSQFEMQS 159

Query: 121 TTPLSSRKSRSDPVPMPVNGMEISHHSMRISVPRHYSSEEPPPP 164
                S +   +    P  G   +           +    P   
Sbjct: 160 RKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGD 203

>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 = 65.5 bits (160), Expect = 2e-14
 Identities = 21/90 (23%), Positives = 35/90 (38%), Gaps = 4/90 (4%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
                  +YI NL  K+    +YDI  + G +  + +       + +G A+V YE     
Sbjct: 4   PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDA 60

Query: 86  HYAIKLFSGIVTLYNRTLRFALSGQDKNAQ 115
             A+   SG   + NR L       ++  Q
Sbjct: 61  KNAVDHLSG-FNVSNRYLVVLYYNANRAFQ 89

>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 = 66.3 bits (162), Expect = 3e-14
 Identities = 19/101 (18%), Positives = 43/101 (42%), Gaps = 1/101 (0%)

Query: 4   SPKHSFVPNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIP 63
           + +   +            M+   +   N+ +  +   V+E  L  +  + G +  + I 
Sbjct: 16  TAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIV 75

Query: 64  RDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR 104
            D+ET + +G+ FV+++S      AI   +G   + N+ L+
Sbjct: 76  CDRETRQSRGYGFVKFQSGSSAQQAIAGLNG-FNILNKRLK 115

>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 = 64.1 bits (157), Expect = 4e-14
 Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDK-ETDKPKGFAFVEYESEEIG 85
          S     V+IG L   V +  + +I    G++  + +P ++      KG+A+VE+E+ +  
Sbjct: 1  SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60

Query: 86 HYAIK 90
            A+K
Sbjct: 61 EKALK 65

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

 Score = 64.4 bits (157), Expect = 6e-14
 Identities = 22/61 (36%), Positives = 31/61 (50%)

Query: 34 YIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFS 93
           I +    V ++ L  +  +AG+VV++  P D+ T K KGF FVE  S       IK F 
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 94 G 94
          G
Sbjct: 76 G 76

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

 Score = 64.2 bits (157), Expect = 6e-14
 Identities = 25/93 (26%), Positives = 41/93 (44%), Gaps = 2/93 (2%)

Query: 16  SRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFA 75
           S +        S     ++I  L     +  L +I    G V DL +  ++   KPKG A
Sbjct: 3   SGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLA 61

Query: 76  FVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS 108
           +VEYE+E     A+    G +T+    ++ A+S
Sbjct: 62  YVEYENESQASQAVMKMDG-MTIKENIIKVAIS 93

>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 = 64.2 bits (157), Expect = 9e-14
 Identities = 26/102 (25%), Positives = 42/102 (41%), Gaps = 4/102 (3%)

Query: 19  KRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVE 78
           + Q+         N+YI NL   ++E+ L ++L   G+V+   I RD  +   +G  F  
Sbjct: 14  QAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFAR 72

Query: 79  YESEEIGHYAIKLFSGIVTLYNRTLRFALSG--QDKNAQNSS 118
            ES E     I  F+G   +       A +     K +  SS
Sbjct: 73  MESTEKCEAVIGHFNG-KFIKTPPGVSAPTEPLLCKFSGPSS 113

>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 = 63.9 bits (156), Expect = 1e-13
 Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 1/79 (1%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
            S     +Y+G+L   + E +L  I    GR+  + +  D ET + KG+ F+ +   E  
Sbjct: 22  GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECA 81

Query: 86  HYAIKLFSGIVTLYNRTLR 104
             A++  +G   L  R ++
Sbjct: 82  KKALEQLNG-FELAGRPMK 99

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 63.5 bits (155), Expect = 1e-13
 Identities = 13/83 (15%), Positives = 33/83 (39%), Gaps = 5/83 (6%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGR--VVDLYIPRDKETDKPKGFAFVEYESEEI 84
            +    + + N+        +   L       V ++ + +DK+T + +GFAFV+  S   
Sbjct: 6   HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMD 65

Query: 85  GHYAIKLFSG---IVTLYNRTLR 104
               +++       + +  +T+ 
Sbjct: 66  ASQLLQILQSLHPPLKIDGKTIG 88

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 64.4 bits (157), Expect = 1e-13
 Identities = 27/95 (28%), Positives = 46/95 (48%), Gaps = 3/95 (3%)

Query: 25  GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
            +     ++ + NL  + +   L  +  + GRV D+YIPRD+ T + +GFAFV +  +  
Sbjct: 42  PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101

Query: 85  GHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNS 117
              A+    G   L  R LR   A  G+  ++ +S
Sbjct: 102 AEDAMDAMDG-AVLDGRELRVQMARYGRPPDSHHS 135

>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 = 62.9 bits (154), Expect = 1e-13
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 1/80 (1%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
           S+    +YI  L     ++ L  +    G++V      DK T+K KG+ FV+++S     
Sbjct: 2   SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61

Query: 87  YAIKLFSGIVTLYNRTLRFA 106
            A+        +  +  + +
Sbjct: 62  KAVTALKA-SGVQAQMAKQS 80

>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 = 63.1 bits (154), Expect = 2e-13
 Identities = 17/100 (17%), Positives = 45/100 (45%), Gaps = 9/100 (9%)

Query: 21  QIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE 80
            +++ +S   C VY G +   + ++++       G+++++ +  +      KG++FV + 
Sbjct: 16  DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFS 69

Query: 81  SEEIGHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSS 118
           + E   +AI   +G   +    ++  +     D  +  SS
Sbjct: 70  THESAAHAIVSVNGTT-IEGHVVKCYWGKESPDMTSGPSS 108

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 62.7 bits (153), Expect = 2e-13
 Identities = 20/95 (21%), Positives = 33/95 (34%), Gaps = 7/95 (7%)

Query: 10  VPNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETD 69
           +P  V  +    I+          YIGN+     E  L  +    G ++D     +    
Sbjct: 7   LPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE---- 62

Query: 70  KPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR 104
             KG  F++Y++ E     I   +       R LR
Sbjct: 63  --KGCCFIKYDTHEQAAVCIVALAN-FPFQGRNLR 94

>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 = 63.6 bits (155), Expect = 2e-13
 Identities = 16/60 (26%), Positives = 29/60 (48%)

Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
          +VY+GN+D     + L       G +  + I  DK +  PKG+A++E+        A+ +
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAM 97

>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 = 2e-13
 Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 1/80 (1%)

Query: 25  GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
           G   S  +V++G+L  ++    +       GR+ D  + +D  T K KG+ FV + ++  
Sbjct: 1   GPLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 60

Query: 85  GHYAIKLFSGIVTLYNRTLR 104
              AI+   G   L  R +R
Sbjct: 61  AENAIQQMGG-QWLGGRQIR 79

>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 = 62.7 bits (153), Expect = 2e-13
 Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 4/79 (5%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
            S     +++  L E   E  L +        V   I  D+ET   KGF FV++ SEE  
Sbjct: 11  RSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEEDA 67

Query: 86  HYAIKLFSGIVTLYNRTLR 104
             A +       +    + 
Sbjct: 68  KAAKEAMED-GEIDGNKVT 85

>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 = 64.6 bits (158), Expect = 3e-13
 Identities = 28/110 (25%), Positives = 47/110 (42%), Gaps = 5/110 (4%)

Query: 11  PNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDK 70
           P   VSR   Q   G   +   +++G + E   E  L D   Q G++  + I  D+ + K
Sbjct: 86  PKRAVSREDSQ-RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK 144

Query: 71  PKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSS 118
            +GFAFV ++  +     +       T+         ALS Q+  + +SS
Sbjct: 145 KRGFAFVTFDDHDSVDKIVI--QKYHTVNGHNCEVRKALSKQEMASASSS 192

>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 = 53.8 bits (130), Expect = 2e-09
 Identities = 16/64 (25%), Positives = 26/64 (40%)

Query: 20 RQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEY 79
          +            ++IG L  +  +  L     Q G + D  + RD  T + +GF FV Y
Sbjct: 3  KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62

Query: 80 ESEE 83
           + E
Sbjct: 63 ATVE 66

>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 = 61.8 bits (151), Expect = 3e-13
 Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
           N+Y+GNL        + ++  Q G+V ++ +  D+ET KPKGF FVE + E     AI  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAK 61

Query: 92  FSGIVTLYNRTLR 104
                    RT+R
Sbjct: 62  LDN-TDFMGRTIR 73

>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 = 66.1 bits (160), Expect = 3e-13
 Identities = 30/140 (21%), Positives = 52/140 (37%), Gaps = 10/140 (7%)

Query: 31  CNVYIGNLDEKVNERVL----YDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
             +YI NL+EK+ +  L    Y I  Q G+++D+ + R     K +G AFV ++      
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL---KMRGQAFVIFKEVSSAT 66

Query: 87  YAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSSMTTTPLSSRKSRSDPVPMPVNGMEIS 144
            A++   G    Y++ +R  +A +  D  A+           R+ R           +  
Sbjct: 67  NALRSMQGFP-FYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAV 125

Query: 145 HHSMRISVPRHYSSEEPPPP 164
                  V        P  P
Sbjct: 126 QGGGATPVVGAVQGPVPGMP 145

>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 = 43.7 bits (102), Expect = 1e-05
 Identities = 16/106 (15%), Positives = 36/106 (33%), Gaps = 5/106 (4%)

Query: 3   PSPKHSFVPNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYI 62
             P        +  +         +     +++ NL E+ NE +L  +  Q     ++ +
Sbjct: 180 IPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRL 239

Query: 63  PRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS 108
              +        AFVE+++E     A     G     N  ++ + +
Sbjct: 240 VPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFA 280

>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 = 61.4 bits (150), Expect = 5e-13
 Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
           N+++G+L+  V++  L +        +  ++  D +T   +G+ FV + S++    A+  
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 92  FSGIVTLYNRTLR 104
             G   L  R LR
Sbjct: 63  MQG-QDLNGRPLR 74

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 62.0 bits (151), Expect = 6e-13
 Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
               GCN++I +L ++  +  L    +  G V+   +  DK+T   K F FV +++ +  
Sbjct: 36  EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95

Query: 86  HYAIKLFSGIVTLYNRTLRFAL 107
             AIK  +G   +  + L+  L
Sbjct: 96  QVAIKAMNG-FQVGTKRLKVQL 116

>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 = 61.5 bits (150), Expect = 7e-13
 Identities = 24/81 (29%), Positives = 34/81 (41%), Gaps = 1/81 (1%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           S  S+    +++ NL    +E  L  +    G + +L+ P D  T KPKGFAFV +   E
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

Query: 84  IGHYAIKLFSGIVTLYNRTLR 104
               A     G      R L 
Sbjct: 62  HAVKAYAEVDG-QVFQGRMLH 81

>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 = 61.7 bits (150), Expect = 8e-13
 Identities = 24/76 (31%), Positives = 33/76 (43%), Gaps = 8/76 (10%)

Query: 27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRV--------VDLYIPRDKETDKPKGFAFVE 78
           +    +Y+  L++ V    L D   Q G V          ++I  DKET KPKG A V 
Sbjct: 12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 71

Query: 79 YESEEIGHYAIKLFSG 94
          YE       A++ F G
Sbjct: 72 YEDPPTAKAAVEWFDG 87

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 61.1 bits (149), Expect = 8e-13
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
            Y+GNL     +  +  I      +  + + RDK+TDK KGF +VE++  +    A+   
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY- 75

Query: 93  SGIVTLYNRTLR 104
            G   L +R+LR
Sbjct: 76  DG-ALLGDRSLR 86

>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 = 61.5 bits (150), Expect = 8e-13
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 29  SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
              N++I NLD+ ++ + LYD     G ++   +  D   +  KG+ FV +E++E    A
Sbjct: 4   GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERA 61

Query: 89  IKLFSGIVTLYNRTLR 104
           I+  +G + L +R + 
Sbjct: 62  IEKMNG-MLLNDRKVF 76

>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 = 60.4 bits (147), Expect = 1e-12
 Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 9/81 (11%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVD--------LYIPRDKETDKPKGFAFVEYESEE 83
            +++  L E V    + D   Q G +          + +  D+ET K KG A V ++   
Sbjct: 15  TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74

Query: 84  IGHYAIKLFSGIVTLYNRTLR 104
               AI  F G        ++
Sbjct: 75  SAKAAIDWFDG-KEFSGNPIK 94

>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 = 60.4 bits (147), Expect = 3e-12
 Identities = 24/101 (23%), Positives = 54/101 (53%), Gaps = 3/101 (2%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
           ++    ++IG L+ + NE++L  +  + G + ++ + +D+ T K +GFAF+ +E+     
Sbjct: 4   ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAK 62

Query: 87  YAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSR 127
            A K  +G  +L+ + ++   + +  + Q+      P SSR
Sbjct: 63  NAAKDMNG-KSLHGKAIKVEQA-KKPSFQSGGRRRPPASSR 101

>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 = 60.0 bits (146), Expect = 3e-12
 Identities = 19/78 (24%), Positives = 39/78 (50%), Gaps = 3/78 (3%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
           S +  N++IGNL+   +   L   + +     DL +  D  T   + F +V++ES E   
Sbjct: 14  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAEDLE 72

Query: 87  YAIKLFSGIVTLYNRTLR 104
            A++L +G + ++   ++
Sbjct: 73  KALEL-TG-LKVFGNEIK 88

>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 = 59.6 bits (145), Expect = 3e-12
 Identities = 20/95 (21%), Positives = 38/95 (40%), Gaps = 9/95 (9%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
                  +++GNL   + E  +  +  + G+  +++I +D      KGF F+  E+  + 
Sbjct: 11  TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLA 64

Query: 86  HYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSS 118
             A      +  L  + LR  FA       +  SS
Sbjct: 65  EIAKVELDNMP-LRGKQLRVRFACHSASLTSGPSS 98

>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 = 59.6 bits (145), Expect = 3e-12
 Identities = 20/89 (22%), Positives = 35/89 (39%), Gaps = 6/89 (6%)

Query: 16  SRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFA 75
           S       S  S     + + NL     E  L ++  +A  +    +P   +  K KG+A
Sbjct: 2   SSGSSG-NSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIK---VP-QNQNGKSKGYA 56

Query: 76  FVEYESEEIGHYAIKLFSGIVTLYNRTLR 104
           F+E+ S E    A+   +    +  R +R
Sbjct: 57  FIEFASFEDAKEALNSCNK-REIEGRAIR 84

>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 = 59.1 bits (144), Expect = 3e-12
 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 3/75 (4%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAG--RVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
            +YIGNL     +  L + +   G   ++++    ++   + KGFA V   SE      +
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 90  KLFSGIVTLYNRTLR 104
            L      L+ +   
Sbjct: 63  DLLPK-RELHGQNPV 76

>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 = 59.6 bits (145), Expect = 3e-12
 Identities = 20/91 (21%), Positives = 38/91 (41%), Gaps = 3/91 (3%)

Query: 30  GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
              +++G L+++ +E  +  +    G + +  + R       KG AFV++ S      AI
Sbjct: 15  DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAI 73

Query: 90  KLFSGIVTLYN--RTLRFALSGQDKNAQNSS 118
               G  T+     +L    +  DK +  SS
Sbjct: 74  HALHGSQTMPGASSSLVVKFADTDKESGPSS 104

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 60.7 bits (147), Expect = 4e-12
 Identities = 27/135 (20%), Positives = 48/135 (35%), Gaps = 9/135 (6%)

Query: 3   PSPKHSFVPNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAG--RVVDL 60
           P  +      +  +       SG  N    VY+G+      ++ L  ++   G   VV+L
Sbjct: 28  PVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVEL 87

Query: 61  YIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMT 120
               ++   + KG+A V   SE   H  ++L  G   L    +          A   +++
Sbjct: 88  KFAENRANGQSKGYAEVVVASENSVHKLLELLPG-KVLNGEKVDVRP------ATRQNLS 140

Query: 121 TTPLSSRKSRSDPVP 135
                +RK     VP
Sbjct: 141 QFEAQARKRECVRVP 155

>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 = 59.4 bits (144), Expect = 4e-12
 Identities = 23/102 (22%), Positives = 43/102 (42%), Gaps = 5/102 (4%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVV-DLYIPRD-KETDKPKGFAFVEYESEEI 84
           S+  C ++IG + +      + + + +    V D+ +     +  K +GFAFVEYES   
Sbjct: 5   SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRA 64

Query: 85  GHYAIK-LFSGIVTLYNRTLR--FALSGQDKNAQNSSMTTTP 123
              A + L  G + L+   +   +A    D +       + P
Sbjct: 65  AAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGP 106

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 59.3 bits (144), Expect = 6e-12
 Identities = 22/98 (22%), Positives = 35/98 (35%), Gaps = 11/98 (11%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRV--------VDLYIPRDKETDKPKGFAFVEYESEE 83
            +++  L E V    + D   Q G +          + +  D+ET K KG A V ++   
Sbjct: 9   TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68

Query: 84  IGHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSSM 119
               AI  F G        ++  FA    D N    + 
Sbjct: 69  SAKAAIDWFDG-KEFSGNPIKVSFATRRADFNRGGGNG 105

>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 = 58.8 bits (143), Expect = 6e-12
 Identities = 18/86 (20%), Positives = 37/86 (43%), Gaps = 2/86 (2%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
                +G  + + NLD  V++  + ++  + G +    +  D  + +  G A V +E + 
Sbjct: 23  GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKA 81

Query: 84  IGHYAIKLFSGIVTLYNRTLRFALSG 109
               A+K ++G V L  R +   L  
Sbjct: 82  DALKAMKQYNG-VPLDGRPMNIQLVT 106

>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 = 58.8 bits (143), Expect = 6e-12
 Identities = 23/96 (23%), Positives = 47/96 (48%), Gaps = 10/96 (10%)

Query: 26  NSNSGCNVYIGNLDEKVNE----RVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYES 81
            +     +YI NL+EK+ +    + L+ I  + G+++D+ + R     K +G AFV ++ 
Sbjct: 4   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKE 60

Query: 82  EEIGHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQ 115
                 A++   G    Y++ +R  +A +  D  A+
Sbjct: 61  VSSATNALRSMQGFP-FYDKPMRIQYAKTDSDIIAK 95

>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 = 58.8 bits (143), Expect = 7e-12
 Identities = 20/95 (21%), Positives = 39/95 (41%), Gaps = 5/95 (5%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
                 N+Y+ NLD+ +++  L       G +    +  +    + KGF FV + S E  
Sbjct: 11  TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEA 68

Query: 86  HYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSS 118
             A+   +G   +  + L    A   +++ +  SS
Sbjct: 69  TKAVTEMNG-RIVATKPLYVALAQRKEERQSGPSS 102

>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 = 58.8 bits (143), Expect = 8e-12
 Identities = 17/82 (20%), Positives = 38/82 (46%), Gaps = 3/82 (3%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
            S + ++   +++ N+  +  +  L  +  Q G+++D+ I  ++     KGF FV +E+ 
Sbjct: 8   NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENS 65

Query: 83  EIGHYAIKLFSGIVTLYNRTLR 104
                A +   G V +  R + 
Sbjct: 66  ADADRAREKLHGTV-VEGRKIE 86

>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 = 58.5 bits (142), Expect = 8e-12
 Identities = 17/96 (17%), Positives = 34/96 (35%), Gaps = 10/96 (10%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
                  G  +Y+   D  +   +L       G ++DL +   +        AFV YE  
Sbjct: 8   ERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKM 59

Query: 83  EIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSS 118
           E    A+   +G   + +  L+  +  + +   +S 
Sbjct: 60  ESADQAVAELNG-TQVESVQLKVNI-ARKQPMLDSG 93

>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 = 9e-12
 Identities = 16/71 (22%), Positives = 33/71 (46%), Gaps = 8/71 (11%)

Query: 30 GCNVYIGNL----DEKVN--ERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
             + + N+     +++   + V++ I  + G++ + + P   E  K KG+ F+EY S  
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPA 72

Query: 84 IGHYAIKLFSG 94
              A+K   G
Sbjct: 73 HAVDAVKNADG 83

>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 = 58.9 bits (143), Expect = 1e-11
 Identities = 19/94 (20%), Positives = 37/94 (39%), Gaps = 4/94 (4%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
              +G  + + NLD  V++  + ++  + G +    +  D  + +  G A V +E     
Sbjct: 31  GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADA 89

Query: 86  HYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNS 117
             A+K + G V L  R +      S  D    + 
Sbjct: 90  LKAMKQYKG-VPLDGRPMDIQLVASQIDLEHHHH 122

>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 = 58.1 bits (141), Expect = 1e-11
 Identities = 21/93 (22%), Positives = 44/93 (47%), Gaps = 1/93 (1%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
           ++++  +V++G+L  ++    +       GR+ D  + +D  T K KG+ FV + ++   
Sbjct: 11  DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 70

Query: 86  HYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSS 118
             AI+   G   L  R +R   + +   A  S+
Sbjct: 71  ENAIQQMGG-QWLGGRQIRTNWATRKPPAPKST 102

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 58.1 bits (141), Expect = 1e-11
 Identities = 14/75 (18%), Positives = 33/75 (44%), Gaps = 2/75 (2%)

Query: 16 SRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFA 75
                + + N +    +++ N+  +  +  L  +  Q G+++D+ I  ++     KGF 
Sbjct: 15 VPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFG 72

Query: 76 FVEYESEEIGHYAIK 90
          FV +E+      A +
Sbjct: 73 FVTFENSADADRARE 87

>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 = 57.7 bits (140), Expect = 2e-11
 Identities = 25/104 (24%), Positives = 41/104 (39%), Gaps = 6/104 (5%)

Query: 17  RNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAF 76
                I     N+ C +Y+GNL   +  + + D+  + G + D+ +   +       FAF
Sbjct: 9   SGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAF 65

Query: 77  VEYESEEIGHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSS 118
           VE+E       A+    G        LR  F  SG+   +  SS
Sbjct: 66  VEFEDPRDAEDAVYGRDG-YDYDGYRLRVEFPRSGRGTGSGPSS 108

>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 = 57.7 bits (140), Expect = 2e-11
 Identities = 24/97 (24%), Positives = 37/97 (38%), Gaps = 6/97 (6%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKET---DKPKGFAFVEYESEE 83
           S+    ++I NL+    E  L  +  + G +    I + K         GF FVEY+  E
Sbjct: 2   SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61

Query: 84  IGHYAIKLFSGIVTLYNRTLRFALS--GQDKNAQNSS 118
               A+K   G  T+    L   +S       +  SS
Sbjct: 62  QAQKALKQLQG-HTVDGHKLEVRISERATKPASGPSS 97

>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 = 57.7 bits (140), Expect = 2e-11
 Identities = 23/89 (25%), Positives = 43/89 (48%), Gaps = 6/89 (6%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDK-ETDKPKGFAFVEYESEEIGHYAIKL 91
            ++GNL   V E  + +       +  + +PR+    ++ KGF + E+E  +    A+ L
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 76

Query: 92  FSGIVTLYNRTLR--FALSGQDKNAQNSS 118
            +   +L N+ +R   A   QDK++  SS
Sbjct: 77  -NE-ESLGNKRIRVDVADQAQDKDSGPSS 103

>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 = 56.9 bits (138), Expect = 3e-11
 Identities = 19/82 (23%), Positives = 40/82 (48%), Gaps = 4/82 (4%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKET-DKPKGFAFVEYESEEIGHYAIKL 91
            ++GNL   V E  + +       +  + +PR+    ++ KGF + E+E  +    A+ L
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 80

Query: 92  FSGIVTLYNRTLRFALSGQDKN 113
            +   +L NR +R  ++ Q ++
Sbjct: 81  -NE-ESLGNRRIRVDVADQAQD 100

>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 = 58.0 bits (140), Expect = 3e-11
 Identities = 24/100 (24%), Positives = 40/100 (40%), Gaps = 6/100 (6%)

Query: 5   PKHSFVPNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPR 64
              +F   +    +   +   +    C VY+GNL    N+  L       G +  +++ R
Sbjct: 48  ATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVAR 107

Query: 65  DKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR 104
           +     P GFAFVE+E       A++   G  TL    +R
Sbjct: 108 N-----PPGFAFVEFEDPRDAADAVRELDG-RTLCGCRVR 141

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 58.3 bits (141), Expect = 4e-11
 Identities = 18/91 (19%), Positives = 38/91 (41%), Gaps = 2/91 (2%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
              +G  + + NLD  V++  + ++  + G +    +  D  + +  G A V +E     
Sbjct: 84  GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADA 142

Query: 86  HYAIKLFSGIVTLYNRTLRFALSGQDKNAQN 116
             A+K + G V L  R +   L     + ++
Sbjct: 143 LKAMKQYKG-VPLDGRPMDIQLVASQIDLEH 172

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 57.2 bits (138), Expect = 4e-11
 Identities = 22/117 (18%), Positives = 48/117 (41%), Gaps = 18/117 (15%)

Query: 16  SRNKRQIMSGNSNSG--------CNVYIGNLDEKVNE----RVLYDILIQAGRVVDLYIP 63
           ++ +RQ M                 V I N++ +V +     +LY +    G ++D+ + 
Sbjct: 7   AKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD 66

Query: 64  RDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSS 118
               +D   G A++ + ++E     ++ F G        L   F+ + Q + A++ S
Sbjct: 67  L---SDDNSGKAYIVFATQESAQAFVEAFQGYP-FQGNPLVITFSETPQSQVAEDGS 119

>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 = 56.5 bits (137), Expect = 5e-11
 Identities = 17/90 (18%), Positives = 41/90 (45%), Gaps = 6/90 (6%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
            V++G +D +++E  +     + G V ++ I  D+ T   KG+ FV + ++       K+
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVD---VQKI 66

Query: 92  FSGIVTLYNRTLR--FALSGQDKNAQNSSM 119
               +  + + L+   A+  Q+ +  +   
Sbjct: 67  VESQINFHGKKLKLGPAIRKQNLSTYHVQP 96

>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 = 55.7 bits (135), Expect = 9e-11
 Identities = 13/51 (25%), Positives = 27/51 (52%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          +++G +     E  L +   + G V ++ +  D E  +P+GF F+ +E E+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQ 63

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 55.2 bits (133), Expect = 1e-10
 Identities = 23/88 (26%), Positives = 34/88 (38%), Gaps = 6/88 (6%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
            +    +VY+GNL        L   L + G V     P       P+  AF+ Y      
Sbjct: 15  GAPLAADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSAAA 69

Query: 86  HYAIKLFSGIVTLYNRTLRFALSGQDKN 113
             A+    G + L   TLR AL+ Q ++
Sbjct: 70  QQAVSCLQG-LRLGTDTLRVALARQQRD 96

>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 = 57.3 bits (138), Expect = 2e-10
 Identities = 30/157 (19%), Positives = 52/157 (33%), Gaps = 13/157 (8%)

Query: 3   PSPKHSFVPNDVVSRNKRQIMSGNSNSG-CNVYIGNLD-EKVNERVLYDILIQAGRVVDL 60
               HS       S   R  + G + +G   + + NL+ E+V  + L+ +    G V  +
Sbjct: 6   HHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV 65

Query: 61  YIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQD-----KNAQ 115
            I  +K     K  A V+         A+   +G   L+ + +R  LS        +  Q
Sbjct: 66  KILFNK-----KENALVQMADGNQAQLAMSHLNG-HKLHGKPIRITLSKHQNVQLPREGQ 119

Query: 116 NSSMTTTPLSSRKSRSDPVPMPVNGMEISHHSMRISV 152
                T    +        P   N   I   S  + +
Sbjct: 120 EDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHL 156

>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 = 46.9 bits (111), Expect = 1e-06
 Identities = 21/106 (19%), Positives = 34/106 (32%), Gaps = 10/106 (9%)

Query: 3   PSPKHSFVPNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYI 62
            SP H F      +       S        +++ N+   V+E  L  +    G VV  + 
Sbjct: 130 NSPLHRFKKPGSKNFQNIFPPS------ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFK 183

Query: 63  PRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS 108
                  K +  A ++  S E    A+          N  LR + S
Sbjct: 184 ----FFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 225

>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 = 54.6 bits (132), Expect = 2e-10
 Identities = 14/79 (17%), Positives = 30/79 (37%), Gaps = 6/79 (7%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
              +   +   NL   + E  L ++   A  +         +  K KG A++E++SE   
Sbjct: 12  KVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADA 66

Query: 86  HYAIKLFSGIVTLYNRTLR 104
              ++   G   +  R++ 
Sbjct: 67  EKNLEEKQG-AEIDGRSVS 84

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 54.6 bits (132), Expect = 3e-10
 Identities = 26/108 (24%), Positives = 53/108 (49%), Gaps = 13/108 (12%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDI------LIQAGRVVDLYIPRDKETDKPKGFAFV 77
           SG+S    ++++G+L   V++ +LY+         + G+VV      D+ T   KG+ FV
Sbjct: 3   SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVV-----LDQ-TGVSKGYGFV 56

Query: 78  EYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLS 125
           ++  E     A+    G V L ++ +R +++   K ++   + + P S
Sbjct: 57  KFTDELEQKRALTECQGAVGLGSKPVRLSVA-IPKASRVKPVESGPSS 103

>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 = 53.8 bits (130), Expect = 3e-10
 Identities = 14/81 (17%), Positives = 33/81 (40%), Gaps = 6/81 (7%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           SG   +   +Y+G L + + E  L +   Q G +  + + +       +  AF+++ + +
Sbjct: 6   SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQ 59

Query: 84  IGHYAIKLFSGIVTLYNRTLR 104
               A +     + +  R L 
Sbjct: 60  AAEVAAEKSFNKLIVNGRRLN 80

>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 = 56.4 bits (136), Expect = 3e-10
 Identities = 24/126 (19%), Positives = 42/126 (33%), Gaps = 12/126 (9%)

Query: 31  CNVYIGNLD-EKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
             + + NL+ E+V  + L+ +    G V  + I  +K     K  A V+         A+
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAM 58

Query: 90  KLFSGIVTLYNRTLRFALSGQD-----KNAQNSSMTTTPLSSRKSRSDPVPMPVNGMEIS 144
              +G   L+ + +R  LS        +  Q     T    +        P   N   I 
Sbjct: 59  SHLNG-HKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117

Query: 145 HHSMRI 150
             S  +
Sbjct: 118 PPSATL 123

>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 = 48.7 bits (116), Expect = 2e-07
 Identities = 17/93 (18%), Positives = 30/93 (32%), Gaps = 4/93 (4%)

Query: 16  SRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFA 75
            +   +           +++ N+   V+E  L  +    G VV       K   K +  A
Sbjct: 106 KKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVK----GFKFFQKDRKMA 161

Query: 76  FVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS 108
            ++  S E    A+          N  LR + S
Sbjct: 162 LIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 194

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 54.0 bits (130), Expect = 4e-10
 Identities = 22/89 (24%), Positives = 33/89 (37%), Gaps = 4/89 (4%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
                 + I N+   +   VL  +L+Q G V          TD       V Y S++   
Sbjct: 12  RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESC---EQVNTDSETAVVNVTYSSKDQAR 68

Query: 87  YAIKLFSGIVTLYNRTLRFALSGQDKNAQ 115
            A+   +G   L N TL+ A    +  AQ
Sbjct: 69  QALDKLNG-FQLENFTLKVAYIPDEMAAQ 96

>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 = 53.5 bits (129), Expect = 6e-10
 Identities = 13/85 (15%), Positives = 29/85 (34%), Gaps = 1/85 (1%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           S        + + N+   V+   + D       +      +  E   P G A V +ES +
Sbjct: 9   SSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD 68

Query: 84  IGHYAIKLFSGIVTLYNRTLRFALS 108
               A+   +    + +R ++ +  
Sbjct: 69  EATAAVIDLND-RPIGSRKVKLSGP 92

>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 = 52.9 bits (128), Expect = 6e-10
 Identities = 14/51 (27%), Positives = 27/51 (52%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          +++G L     E  + +     G V  + +P D +T+K +GF F+ ++ EE
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 52

>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 = 54.4 bits (131), Expect = 6e-10
 Identities = 23/93 (24%), Positives = 39/93 (41%), Gaps = 8/93 (8%)

Query: 30  GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIP-----RDKETDKPKGFAFVEYESEEI 84
            C +Y+ NL + V E+ L  I  +               R  +  + KG AF+   +E+ 
Sbjct: 45  NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104

Query: 85  GHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQ 115
              A+K  +G V L+ + +   FA S + K   
Sbjct: 105 AAKALKEANGYV-LFGKPMVVQFARSARPKQDP 136

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

 Score = 53.5 bits (129), Expect = 7e-10
 Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 6/73 (8%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
            VY+GNL     +  L       G +  ++I R+     P GFAFVE+E       A++ 
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56

Query: 92  FSGIVTLYNRTLR 104
             G   +    +R
Sbjct: 57  LDG-KVICGSRVR 68

>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 = 54.3 bits (130), Expect = 2e-09
 Identities = 24/142 (16%), Positives = 40/142 (28%), Gaps = 7/142 (4%)

Query: 30  GCNVYIGNLD-EKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
              + +  LD  K+N   ++++    G V  +   + K      G A VE         A
Sbjct: 4   SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRA 58

Query: 89  IKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSRSDPVPMPVNGMEISHHSM 148
           I   +    ++ + +   +S Q       S      S                       
Sbjct: 59  ITHLNN-NFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKN 117

Query: 149 RISVPRHYSSEEPPPPGVTLET 170
           RI  P +       P  VT E 
Sbjct: 118 RIQHPSNVLHFFNAPLEVTEEN 139

>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 = 51.6 bits (123), Expect = 2e-08
 Identities = 9/73 (12%), Positives = 26/73 (35%)

Query: 11  PNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDK 70
            N+  S  ++   +   +    ++  N   +V E   ++I  + G      +       +
Sbjct: 104 RNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSE 163

Query: 71  PKGFAFVEYESEE 83
                 +E++S+ 
Sbjct: 164 RSSSGLLEWDSKS 176

>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 = 51.7 bits (124), Expect = 2e-09
 Identities = 17/77 (22%), Positives = 34/77 (44%), Gaps = 7/77 (9%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPR-----DKETDKPKGFAFVEYESEEIGHY 87
           +Y+GN+   + E  + D      R+  L           + ++ K FAF+E+ S +    
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 88  AIKLFSGIVTLYNRTLR 104
           A+    GI+    ++L+
Sbjct: 69  AMAF-DGII-FQGQSLK 83

>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 = 51.9 bits (125), Expect = 2e-09
 Identities = 14/85 (16%), Positives = 29/85 (34%), Gaps = 1/85 (1%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           S        + + N+   V+   + D       +      +  E   P G A V +ES +
Sbjct: 9   SSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD 68

Query: 84  IGHYAIKLFSGIVTLYNRTLRFALS 108
               A+   +    + +R ++  L 
Sbjct: 69  EATAAVIDLND-RPIGSRKVKLVLG 92

>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 = 52.2 bits (125), Expect = 3e-09
 Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 7/78 (8%)

Query: 33  VYIGNLDEKVNERVL---YDILIQAGRVVDLYIPRDKETDK---PKGFAFVEYESEEIGH 86
           V++  L +++ +  +    +   + G++  + I           P   A+V Y   E   
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 87  YAIKLFSGIVTLYNRTLR 104
            AI+  + +  +  RTL+
Sbjct: 78  RAIQCVNNV-VVDGRTLK 94

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 51.2 bits (123), Expect = 3e-09
 Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 8/78 (10%)

Query: 33  VYIGNL----DEKVN--ERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
           + + N+     +++   + V++ I  + G++ + + P  +E  K KG+ F+EY S     
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAV 61

Query: 87  YAIKLFSGIVTLYNRTLR 104
            A+K   G       T R
Sbjct: 62  DAVKNADGYKLDKQHTFR 79

>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 = 51.0 bits (123), Expect = 3e-09
 Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 8/67 (11%)

Query: 24 SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          S  S+    ++IGNL  +  E+ +  +  Q G+V+        E D  K + FV  E + 
Sbjct: 2  SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVL--------ECDIIKNYGFVHIEDKT 53

Query: 84 IGHYAIK 90
              AI+
Sbjct: 54 AAEDAIR 60

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 51.8 bits (124), Expect = 3e-09
 Identities = 15/81 (18%), Positives = 27/81 (33%), Gaps = 4/81 (4%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           S        + + NL E  + + L D+  +              T    G   +E+ SEE
Sbjct: 22  SKLPAKRYRITMKNLPEGCSWQDLKDLARENSLET---TFSSVNTRDFDGTGALEFPSEE 78

Query: 84  IGHYAIKLFSGIVTLYNRTLR 104
           I   A++  + I       + 
Sbjct: 79  ILVEALERLNNI-EFRGSVIT 98

>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 = 51.5 bits (124), Expect = 3e-09
 Identities = 13/68 (19%), Positives = 28/68 (41%), Gaps = 6/68 (8%)

Query: 16 SRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFA 75
          S +  +I  G +N    +++G L    +   L     + G +  +   +         FA
Sbjct: 3  SGSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFA 56

Query: 76 FVEYESEE 83
          +++YES +
Sbjct: 57 YIQYESLD 64

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

 Score = 51.3 bits (123), Expect = 4e-09
 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          +VYI           + + L   G+V+++ + R       KG  FV ++S E
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIE 63

>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 = 50.9 bits (122), Expect = 4e-09
 Identities = 20/88 (22%), Positives = 35/88 (39%), Gaps = 9/88 (10%)

Query: 25  GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
           G+S S   + + NL +  N + ++D+L            +    D+ K  AFV   + E 
Sbjct: 1   GSSGS-SGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQ 52

Query: 85  GHYAIKLFSGIVTLYNRTLRFALSGQDK 112
              AI++F    +   + L   L   D 
Sbjct: 53  AQNAIQMFHQ-YSFRGKDLIVQLQPTDA 79

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 49.8 bits (120), Expect = 8e-09
 Identities = 16/51 (31%), Positives = 27/51 (52%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          +++G L        +     Q G+V D  +  DK T++ +GF FV +ESE+
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52

>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 = 49.9 bits (120), Expect = 9e-09
 Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 8/67 (11%)

Query: 24 SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          SG+S +   +++GN+      + L  +  + GRV++         D  K +AFV  E E 
Sbjct: 3  SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIEC--------DVVKDYAFVHMEKEA 54

Query: 84 IGHYAIK 90
              AI 
Sbjct: 55 DAKAAIA 61

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

 Score = 50.4 bits (121), Expect = 1e-08
 Identities = 18/79 (22%), Positives = 28/79 (35%), Gaps = 9/79 (11%)

Query: 6  KHSFVPNDVVSRNKRQIMSG-NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPR 64
           H    + +V R            S   +++      V E  L +I    G + ++ I  
Sbjct: 6  HHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI-- 63

Query: 65 DKETDKPKGFAFVEYESEE 83
                  GFAFVE+E  E
Sbjct: 64 ------LNGFAFVEFEEAE 76

>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 = 49.5 bits (119), Expect = 2e-08
 Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 8/68 (11%)

Query: 23 MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
             +  +   +++GN+      + L     + G V++         D  K +AFV  E  
Sbjct: 3  SGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIEC--------DIVKDYAFVHMERA 54

Query: 83 EIGHYAIK 90
          E    AI+
Sbjct: 55 EDAVEAIR 62

>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 = 49.6 bits (119), Expect = 2e-08
 Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 7/79 (8%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
             +S   +Y+ NL    +E ++                  +   K + +AFV + + E  
Sbjct: 11  TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPG------AVERVKKIRDYAFVHFSNREDA 64

Query: 86  HYAIKLFSGIVTLYNRTLR 104
             A+K  +G V L    + 
Sbjct: 65  VEAMKALNGKV-LDGSPIE 82

>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 = 49.4 bits (118), Expect = 2e-08
 Identities = 16/79 (20%), Positives = 28/79 (35%), Gaps = 8/79 (10%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
           +  S   V +  L    + + L D + +AG V    + RD       G   VE+  +E  
Sbjct: 11  SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDM 63

Query: 86  HYAIKLFSGIVTLYNRTLR 104
            YA++         +    
Sbjct: 64  TYAVRKLDNT-KFRSHEGE 81

>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 = 48.5 bits (116), Expect = 3e-08
 Identities = 16/84 (19%), Positives = 37/84 (44%), Gaps = 10/84 (11%)

Query: 22  IMSGNSNSGCNVYIGNLD-EKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE 80
           ++   S+    ++IGNL  + V++  L+ I    G ++ + I           F F++++
Sbjct: 14  LVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFD 65

Query: 81  SEEIGHYAIKLFSGIVTLYNRTLR 104
           + +    AI+  S     + + L 
Sbjct: 66  NPQSVRDAIEXESQE-MNFGKKLI 88

>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 = 48.1 bits (115), Expect = 7e-08
 Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 10/88 (11%)

Query: 30  GCNVYIGNLD-EKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
              V+IGNL+   V +  +  I  + GRV    +         KG+AFV+Y +E     A
Sbjct: 27  NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAA 78

Query: 89  IKLFSGIVTLYNRTLRFALSGQDKNAQN 116
           +   +G   L  +TL   ++G+ K  ++
Sbjct: 79  VLGENG-RVLAGQTLDINMAGEPKPDRS 105

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 46.3 bits (111), Expect = 1e-07
 Identities = 15/53 (28%), Positives = 26/53 (49%)

Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          C ++IG L  +  +  L +   Q G V +  + RD  T + +GF FV +  + 
Sbjct: 1  CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQA 53

>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 = 1e-07
 Identities = 13/67 (19%), Positives = 25/67 (37%)

Query: 24 SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          S    +   +++G L     +  L       G + +  +  D++T K +G+ FV      
Sbjct: 11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRA 70

Query: 84 IGHYAIK 90
              A K
Sbjct: 71 AAERACK 77

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 46.0 bits (109), Expect = 3e-07
 Identities = 18/105 (17%), Positives = 41/105 (39%), Gaps = 7/105 (6%)

Query: 15  VSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGF 74
           +  +      G+      ++I  L   V E  +  + +  G+V +L + +       K  
Sbjct: 1   MRGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQ 54

Query: 75  AFVEYESEEIGHYAIKLFSGI-VTLYNRTLRFALSGQDKNAQNSS 118
           AF+E  +EE  +  +  ++ +   L  + +    S   +   +SS
Sbjct: 55  AFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSS 99

>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 = 48.7 bits (115), Expect = 4e-07
 Identities = 22/184 (11%), Positives = 48/184 (26%), Gaps = 3/184 (1%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
             +++  ++    E  L       G +  +++   K + KP+G+AF+EYE E   H A K
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162

Query: 91  LFSGIV---TLYNRTLRFALSGQDKNAQNSSMTTTPLSSRKSRSDPVPMPVNGMEISHHS 147
              G           +    + +    +             +  +      +        
Sbjct: 163 HADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDER 222

Query: 148 MRISVPRHYSSEEPPPPGVTLETNGYETHLNVTNYDYSRRVFGATLDSISRSRSGHYNSS 207
              S   H   +          +   +            R   +        R     S 
Sbjct: 223 PGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSK 282

Query: 208 NRHY 211
           ++  
Sbjct: 283 DKDR 286

>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 = 46.0 bits (109), Expect = 4e-07
 Identities = 16/82 (19%), Positives = 28/82 (34%), Gaps = 8/82 (9%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
              +  S   V +  L    + + L D + +AG V    + RD       G   VE+  +
Sbjct: 9   GPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRK 61

Query: 83  EIGHYAIKLFSGIVTLYNRTLR 104
           E   YA++         +    
Sbjct: 62  EDMTYAVRKLDN-TKFRSHEGE 82

>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 = 45.3 bits (108), Expect = 5e-07
 Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 8/65 (12%)

Query: 23 MSGNSNS---GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEY 79
          M G+ +    G  V++G   E +    L     Q G VVD++IP+       + FAFV +
Sbjct: 1  MRGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTF 55

Query: 80 ESEEI 84
            +++
Sbjct: 56 ADDKV 60

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

 Score = 45.3 bits (108), Expect = 5e-07
 Identities = 16/80 (20%), Positives = 34/80 (42%), Gaps = 10/80 (12%)

Query: 26  NSNSGCNVYIGNLD-EKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
           N      ++IGNL  + V++  L+ I    G ++ + I           F F+++++ + 
Sbjct: 6   NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQS 57

Query: 85  GHYAIKLFSGIVTLYNRTLR 104
              AI+  S     + + L 
Sbjct: 58  VRDAIECESQ-EMNFGKKLI 76

>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 = 45.7 bits (109), Expect = 5e-07
 Identities = 14/51 (27%), Positives = 24/51 (47%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          + +  L  K  E+ L +     G V+ + + +D +T   KGF FV +   E
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 45.5 bits (108), Expect = 5e-07
 Identities = 16/106 (15%), Positives = 32/106 (30%), Gaps = 14/106 (13%)

Query: 4   SPKHSFVPNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIP 63
              H     +    +        + +   V+I  L + V E  L + L + G +  + + 
Sbjct: 2   GHHHHHHMENYDDPH-------KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM 54

Query: 64  RDKETDKPKGFAFVEYESEEIGHYAIKLFSGI-VTLYNRTLRFALS 108
                   K  A VE+E       A+   +   + +         S
Sbjct: 55  PK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYS 94

>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 = 47.1 bits (111), Expect = 6e-07
 Identities = 13/63 (20%), Positives = 25/63 (39%), Gaps = 1/63 (1%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
            +VYI           + + L   G+V+++ + R       KG  FV ++S E     ++
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHK-AFKGSIFVVFDSIESAKKFVE 168

Query: 91  LFS 93
              
Sbjct: 169 TPG 171

>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 = 45.0 bits (107), Expect = 7e-07
 Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 8/59 (13%)

Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
           +++ NL   V E +L     Q G++            K K +AF+ ++  +    A++
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLE--------RVKKLKDYAFIHFDERDGAVKAME 63

>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 = 45.2 bits (107), Expect = 7e-07
 Identities = 16/88 (18%), Positives = 34/88 (38%), Gaps = 7/88 (7%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
            V++  L E V E  L + L + G +  + +         K  A VE+E+ +     +  
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTF 70

Query: 92  FSGI-VTLYNRTLRFALSGQDKNAQNSS 118
            + + V +  +   F  S   +  +  +
Sbjct: 71  AADVPVYIAGQQAFFNYSTSKRITRPGN 98

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

 Score = 45.0 bits (107), Expect = 8e-07
 Identities = 11/52 (21%), Positives = 20/52 (38%), Gaps = 5/52 (9%)

Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          +V++      V+   L +  +  G V  + + +DK       FA VE     
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIVEMGDVG 56

>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 = 44.1 bits (105), Expect = 1e-06
 Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 6/60 (10%)

Query: 25 GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
          G+S S   V++G     + E  L +   Q G V+D++IP+       + FAFV +  ++I
Sbjct: 1  GSSGSS-GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQI 54

>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 = 44.4 bits (105), Expect = 1e-06
 Identities = 16/107 (14%), Positives = 32/107 (29%), Gaps = 9/107 (8%)

Query: 29  SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
           S   +   NL        + +   + G +  + +P           A VE+        A
Sbjct: 9   SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG------GITAIVEFLEPLEARKA 62

Query: 89  IKLFSGIVTLYNRTLR--FALSGQDKNAQNSSMTTTPLSSRKSRSDP 133
            +  +     ++  L   +A  G    A     +     + K+ S P
Sbjct: 63  FRHLAYS-KFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGP 108

>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 = 43.7 bits (104), Expect = 2e-06
 Identities = 16/60 (26%), Positives = 28/60 (46%)

Query: 24 SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          S N      +++G L    +++ L D   + G VVD  I  D  T + +GF F+ ++   
Sbjct: 5  SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAA 64

>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 = 43.8 bits (104), Expect = 2e-06
 Identities = 18/68 (26%), Positives = 33/68 (48%)

Query: 16 SRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFA 75
          S     + +  ++    +++G LD    +  L     Q G VVD  I +DK T++ +GF 
Sbjct: 2  SSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFG 61

Query: 76 FVEYESEE 83
          FV+++   
Sbjct: 62 FVKFKDPN 69

>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 = 43.8 bits (104), Expect = 3e-06
 Identities = 18/60 (30%), Positives = 30/60 (50%)

Query: 24 SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          S   +SGC ++IG L  +  +  L +   Q G V +  + RD  T + +GF FV +  + 
Sbjct: 19 SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQA 78

>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 = 43.4 bits (103), Expect = 4e-06
 Identities = 15/65 (23%), Positives = 27/65 (41%)

Query: 19 KRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVE 78
            +           ++IG L  +  E  L +   Q G++ D  + RD  + + +GF FV 
Sbjct: 16 PLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVT 75

Query: 79 YESEE 83
          + S  
Sbjct: 76 FSSMA 80

>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 = 43.4 bits (102), Expect = 5e-06
 Identities = 21/118 (17%), Positives = 43/118 (36%), Gaps = 8/118 (6%)

Query: 3   PSPKHSFVPNDVVSRNKR-QIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLY 61
            S  H    + +V R                ++I  L   V E  +  + +  G+V +L 
Sbjct: 3   SSHHHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLL 62

Query: 62  IPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGI-VTLYNRTLRFALSGQDKNAQNSS 118
           + +       K  AF+E  +EE  +  +  ++ +   L  + +    S   +   +SS
Sbjct: 63  MLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSS 114

>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 = 42.5 bits (100), Expect = 6e-06
 Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 7/77 (9%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           ++I  L  +V E  +  + +  G+V ++ + +       K  AF+E  +EE     +  +
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYY 71

Query: 93  SGI-VTLYNRTLRFALS 108
           S +   L N+ +    S
Sbjct: 72  SAVTPHLRNQPIYIQYS 88

>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 = 41.6 bits (98), Expect = 1e-05
 Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 3/77 (3%)

Query: 16 SRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVD-LYIPRDKETDKPKGF 74
          S         NS   C  +I N+   + +  +   L       + +++  D    +  G 
Sbjct: 2  SSGSSGEGDVNSAKVC-AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNG-QGLGQ 59

Query: 75 AFVEYESEEIGHYAIKL 91
          A V++++E+    + +L
Sbjct: 60 ALVQFKNEDDARKSERL 76

>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 = 14/76 (18%), Positives = 26/76 (34%)

Query: 16  SRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFA 75
            +  R   S +S +   V +  L     +  +         V +          K  G A
Sbjct: 28  QQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEA 87

Query: 76  FVEYESEEIGHYAIKL 91
           FV++ S+E+   A+  
Sbjct: 88  FVQFASQELAEKALGK 103

>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 = 42.1 bits (99), Expect = 2e-05
 Identities = 15/76 (19%), Positives = 29/76 (38%), Gaps = 2/76 (2%)

Query: 16  SRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFA 75
             +     +  S +G  V++  L  K  E  +Y+        V ++I    +  +  G A
Sbjct: 32  RGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEA 89

Query: 76  FVEYESEEIGHYAIKL 91
            VE+ + E    A+  
Sbjct: 90  DVEFATHEEAVAAMSK 105

>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 = 41.1 bits (97), Expect = 2e-05
 Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 3/69 (4%)

Query: 24 SGNSNSGCN-VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
          SG+S + C+ V +      V E+ + + L    + V + I R+       G+ FV++ +E
Sbjct: 3  SGSSGTTCHTVKLRGAPFNVTEKNVMEFL-APLKPVAIRIVRNAHG-NKTGYIFVDFSNE 60

Query: 83 EIGHYAIKL 91
          E    A+K 
Sbjct: 61 EEVKQALKC 69

>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 = 41.1 bits (96), Expect = 3e-05
 Identities = 17/75 (22%), Positives = 29/75 (38%), Gaps = 6/75 (8%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           V  G L   V+   L  +L + G V  L +P +K       ++F  Y + E    A    
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTL 83

Query: 93  SGIVTLYNRTLRFAL 107
           +G   + +   +  L
Sbjct: 84  NGKEVVDDLGQKITL 98

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 40.7 bits (95), Expect = 4e-05
 Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 2/62 (3%)

Query: 24 SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETD--KPKGFAFVEYES 81
          S  S+    V++G L   ++E  +     + G +V  +  + +      PKG+AF+ ++ 
Sbjct: 2  SSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQE 61

Query: 82 EE 83
          E 
Sbjct: 62 ES 63

>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 = 39.7 bits (93), Expect = 8e-05
 Identities = 14/68 (20%), Positives = 28/68 (41%), Gaps = 2/68 (2%)

Query: 24 SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
          S  S +G  V++  L  +  E  +Y+        + ++I    +  +  G A VE+ + E
Sbjct: 9  SFQSTTGHCVHMRGLPYRATENDIYNFF-SPLNPMRVHIEIGPDG-RVTGEADVEFATHE 66

Query: 84 IGHYAIKL 91
              A+  
Sbjct: 67 DAVAAMAK 74

>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 = 39.0 bits (91), Expect = 1e-04
 Identities = 15/76 (19%), Positives = 26/76 (34%), Gaps = 1/76 (1%)

Query: 16 SRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFA 75
          S          +N G  V +  L    ++  +         V +          +  G A
Sbjct: 2  SSGSSGNSPDTANDGF-VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60

Query: 76 FVEYESEEIGHYAIKL 91
          FV++ S+EI   A+K 
Sbjct: 61 FVQFASQEIAEKALKK 76

>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 = 39.0 bits (91), Expect = 1e-04
 Identities = 13/76 (17%), Positives = 29/76 (38%), Gaps = 3/76 (3%)

Query: 16 SRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFA 75
          S +  + +  N +    V +  +     E  + D      RV  +++ +D    +  G  
Sbjct: 3  SGSSGKPLPINPDDLY-VSVHGMPFSAMENDVRDFF-HGLRVDAVHLLKDHVG-RNNGNG 59

Query: 76 FVEYESEEIGHYAIKL 91
           V++ S +    A+K 
Sbjct: 60 LVKFLSPQDTFEALKR 75

>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 = 38.4 bits (89), Expect = 2e-04
 Identities = 14/70 (20%), Positives = 35/70 (50%), Gaps = 7/70 (10%)

Query: 24 SGNSNSGCNVYIGNLDEKVNE----RVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEY 79
          SG+S +G +V + N+D +++     ++L +   + G+V  + +    +    +  A V+ 
Sbjct: 3  SGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQM 59

Query: 80 ESEEIGHYAI 89
          E+ +    A+
Sbjct: 60 ENLQDAIGAV 69

>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 = 38.7 bits (90), Expect = 3e-04
 Identities = 17/76 (22%), Positives = 26/76 (34%)

Query: 16 SRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFA 75
          S  KR        +G  VY+  L  +   + + D   +   V D          K  G  
Sbjct: 11 SGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEG 70

Query: 76 FVEYESEEIGHYAIKL 91
          FVE+ +E     A+  
Sbjct: 71 FVEFRNEADYKAALCR 86

>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 = 38.4 bits (89), Expect = 3e-04
 Identities = 18/96 (18%), Positives = 34/96 (35%), Gaps = 6/96 (6%)

Query: 16  SRNKRQIMSGNSNSGCNVYIGNLDEKVNE---RVLYDILIQAGRVVDLYIPRDKETDKPK 72
           S +   ++      G  V +  L    +    +           V  ++    +E  +  
Sbjct: 3   SGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREG-RQS 61

Query: 73  GFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS 108
           G AFVE ESE+    A+K      ++ +R +    S
Sbjct: 62  GEAFVELESEDDVKLALKKDRE--SMGHRYIEVFKS 95

>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 = 37.8 bits (87), Expect = 8e-04
 Identities = 29/137 (21%), Positives = 53/137 (38%), Gaps = 19/137 (13%)

Query: 12  NDVVSRNKRQIMSGNSNSGCN----VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKE 67
           N  ++ +   + +G + +G +    + + NL   V   VL+ I  + G V+     +   
Sbjct: 24  NLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVL-----KIIT 78

Query: 68  TDKPKGF-AFVEYESEEIGHYAIKLFSGIVTLYNR--TLR--FA----LSGQDKNAQNSS 118
             K   F A ++Y       +A     G   +YN   TLR  F+    L+ +  N ++  
Sbjct: 79  FTKNNQFQALLQYADPVSAQHAKLSLDGQ-NIYNACCTLRIDFSKLTSLNVKYNNDKSRD 137

Query: 119 MTTTPLSSRKSRSDPVP 135
            T   L S  S+     
Sbjct: 138 YTRPDLPSGDSQPSLDQ 154

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	211
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.91
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.89
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.89
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.87
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.87
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.87
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.87
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.87
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.87
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.87
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.87
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.87
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.87
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.87
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.87
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.86
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.86
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.86
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.86
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.86
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.86
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.86
2div_A	99	TRNA selenocysteine associated protein; structural	99.86
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.86
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.86
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.86
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.86
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.86
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.86
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.86
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.86
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.86
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.86
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.85
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.85
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.85
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.85
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.85
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.85
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.85
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.85
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.85
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.85
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.85
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.85
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.85
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.85
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.85
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.85
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.84
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.84
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.84
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.84
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.84
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.84
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.84
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.84
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.84
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.84
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.84
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.84
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.84
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.84
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.84
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.83
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.83
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.83
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.83
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.83
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.83
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.83
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.83
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.83
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.83
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.83
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.83
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.83
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.83
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.83
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.83
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.82
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.82
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.82
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.82
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.82
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.82
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.82
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.82
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.82
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.82
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.81
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.81
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.81
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.81
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.81
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.81
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.81
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.81
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.81
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.81
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.81
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.81
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.81
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.81
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.8
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.8
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.8
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.8
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.8
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.8
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.8
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.8
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.8
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.8
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.8
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.8
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.79
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.79
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.79
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.79
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.66
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.79
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.79
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.79
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.79
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.79
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.79
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.79
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.78
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.78
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.78
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.78
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.78
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.78
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.78
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.78
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.77
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.77
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.77
1x5p_A	97	Negative elongation factor E; structure genomics,	99.77
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.76
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.76
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.76
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.76
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.76
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.76
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.76
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.76
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.76
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.76
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.76
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.76
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.76
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.75
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.75
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.75
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.75
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.74
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.74
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.74
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.74
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.74
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.73
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.73
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.73
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.73
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.73
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.73
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.72
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.72
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.72
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.72
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.72
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.71
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.71
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.7
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.7
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.7
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.69
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.68
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.67
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.67
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.67
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.66
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.66
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.65
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.64
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.64
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.62
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.62
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.61
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.61
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.6
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.6
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.6
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.59
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.59
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.59
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.59
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.56
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.53
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.5
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.4
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.33
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.28
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.12
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.12
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.6
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.7
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.63
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.5
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.29
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.22
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.01
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.61
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.43
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.39
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.24
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.66
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	90.55

>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=99.91  E-value=2.4e-24  Score=153.18  Aligned_cols=82  Identities=22%  Similarity=0.405  Sum_probs=79.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .++++|||+|||+++++++|+++|++||.|.+|.|++|+.||+++|||||+|.+.++|++||+.|||. .|+|+.|+|+|
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~-~~~gr~l~V~~   95 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGL-RLQSKTIKVSY   95 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEE
Confidence            56899999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cCC
Q 038096          108 SGQ  110 (211)
Q Consensus       108 a~~  110 (211)
                      |++
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            864

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

Probab=99.89  E-value=6.2e-23  Score=148.59  Aligned_cols=86  Identities=20%  Similarity=0.180  Sum_probs=81.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ++.++|||+||++++++++|+++|++||.|.+|.|++|+.|++++|||||+|.+.++|++||+.|||. .|+|+.|+|.+
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~-~~~gr~i~V~~   82 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLT-SVMGNIIHAQL   82 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEE
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCC-EECCeEEEEEE
Confidence            45789999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cCCCccC
Q 038096          108 SGQDKNA  114 (211)
Q Consensus       108 a~~~~~~  114 (211)
                      |......
T Consensus        83 a~~~~~~   89 (110)
T 3s8s_A           83 DIKGQQR   89 (110)
T ss_dssp             CSTTHHH
T ss_pred             CCCCcHH
Confidence            9766543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.89  E-value=3e-23  Score=145.20  Aligned_cols=84  Identities=17%  Similarity=0.257  Sum_probs=77.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCC-CeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAG-RVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G-~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +++|||+|||++++|++|+++|++|| .|.+|+|++|+.||.++|||||+|.+.++|++||+.+++...++|++|+|++|
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            47899999999999999999999999 89999999999999999999999999999999999875544899999999999


Q ss_pred             CCCcc
Q 038096          109 GQDKN  113 (211)
Q Consensus       109 ~~~~~  113 (211)
                      .++..
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            76543

>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=99.87  E-value=6.3e-22  Score=135.32  Aligned_cols=82  Identities=21%  Similarity=0.395  Sum_probs=78.0

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      +.+|||+|||.++++++|+++|++||.|.++.|+.++.+|.++|||||+|.+.++|++|++.|||. .++|+.|+|.+++
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~-~~~g~~l~v~~a~   79 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQ-DLNGRPLRINWAA   79 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTC-EETTEECEEEECC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCC-eeCCcEEEEEecC
Confidence            368999999999999999999999999999999999999999999999999999999999999998 9999999999997


Q ss_pred             CCc
Q 038096          110 QDK  112 (211)
Q Consensus       110 ~~~  112 (211)
                      ++.
T Consensus        80 ~~~   82 (83)
T 3md1_A           80 KLE   82 (83)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            653

>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=99.87  E-value=1.3e-21  Score=138.35  Aligned_cols=86  Identities=29%  Similarity=0.360  Sum_probs=81.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.|||. .|+|+.|+|.+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~V~~   84 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQ-VFQGRMLHVLP   84 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTE-ESSSCEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCC-EECCcEEEEEE
Confidence            45799999999999999999999999999999999999989999999999999999999999999998 99999999999


Q ss_pred             cCCCccC
Q 038096          108 SGQDKNA  114 (211)
Q Consensus       108 a~~~~~~  114 (211)
                      +.+....
T Consensus        85 a~~~~~~   91 (99)
T 1whw_A           85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             cCCCccc
Confidence            9876553

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.87  E-value=1.3e-22  Score=143.25  Aligned_cols=82  Identities=16%  Similarity=0.287  Sum_probs=76.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCC--eEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCC---eeeCCeEE
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGR--VVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGI---VTLYNRTL  103 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~--i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~---~~i~gr~l  103 (211)
                      .-.+|||+|||+++|+++|+++|++||.  |.+|+|++|+.||++||||||+|.+.++|++||+.|||.   +.|+|++|
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i   87 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI   87 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEE
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEE
Confidence            3678999999999999999999999995  678999999999999999999999999999999999986   35999999


Q ss_pred             EEEecCC
Q 038096          104 RFALSGQ  110 (211)
Q Consensus       104 ~v~~a~~  110 (211)
                      .|+||+.
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999864

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

Probab=99.87  E-value=2.2e-21  Score=140.78  Aligned_cols=87  Identities=23%  Similarity=0.371  Sum_probs=81.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.|||. .|+|+.|+|.|
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~V~~   91 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQ-WLGGRQIRTNW   91 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTC-EETTEECEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEE
Confidence            45799999999999999999999999999999999999989999999999999999999999999998 99999999999


Q ss_pred             cCCCccCC
Q 038096          108 SGQDKNAQ  115 (211)
Q Consensus       108 a~~~~~~~  115 (211)
                      +.......
T Consensus        92 a~~~~~~~   99 (115)
T 2dgo_A           92 ATRKPPAP   99 (115)
T ss_dssp             SSCCCCCS
T ss_pred             ccCCCCCC
Confidence            98765543

>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=99.87  E-value=5.4e-22  Score=136.81  Aligned_cols=83  Identities=24%  Similarity=0.397  Sum_probs=77.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||.++++++|+++|++||.|.++.|+.++.++.++|||||+|.+.++|++|++.|||. .++|+.|+|.|
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v~~   82 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQ-WLGGRQIRTNW   82 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCC-EECCeEEEEEe
Confidence            45789999999999999999999999999999999999989999999999999999999999999998 99999999999


Q ss_pred             cCCC
Q 038096          108 SGQD  111 (211)
Q Consensus       108 a~~~  111 (211)
                      ++++
T Consensus        83 a~~k   86 (87)
T 3bs9_A           83 ATRK   86 (87)
T ss_dssp             EC--
T ss_pred             cCCC
Confidence            8653

>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=99.87  E-value=1e-21  Score=138.17  Aligned_cols=83  Identities=27%  Similarity=0.444  Sum_probs=79.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      +++|||+|||.++++++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|++|++.|||. .++|+.|+|.+|.
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~~l~V~~a~   80 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGY-QLGSRFLKCGYSS   80 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEECS
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCC-eECCeEEEEEEcC
Confidence            689999999999999999999999999999999999999999999999999999999999999998 9999999999997


Q ss_pred             CCcc
Q 038096          110 QDKN  113 (211)
Q Consensus       110 ~~~~  113 (211)
                      +...
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            7654

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

Probab=99.87  E-value=1.1e-21  Score=137.57  Aligned_cols=86  Identities=21%  Similarity=0.491  Sum_probs=81.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||.++++++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|++||+.|||. .|+|+.|+|.+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~V~~   81 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGF-ELAGRPMRVGH   81 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTC-CSSSSCCEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCC-eeCCcEEEEEE
Confidence            45799999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cCCCccC
Q 038096          108 SGQDKNA  114 (211)
Q Consensus       108 a~~~~~~  114 (211)
                      +.+....
T Consensus        82 a~~~~~~   88 (95)
T 2dnz_A           82 VTERLDG   88 (95)
T ss_dssp             SSCCCCC
T ss_pred             cccccCC
Confidence            9776543

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

Probab=99.87  E-value=1.1e-21  Score=139.50  Aligned_cols=88  Identities=35%  Similarity=0.564  Sum_probs=82.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.|||. .|+|+.|+|.
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~V~   87 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES-ELFGRTIRVN   87 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTE-EETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCC-EECCcEEEEE
Confidence            345899999999999999999999999999999999999999999999999999999999999999998 9999999999


Q ss_pred             ecCCCccCC
Q 038096          107 LSGQDKNAQ  115 (211)
Q Consensus       107 ~a~~~~~~~  115 (211)
                      ++.+.....
T Consensus        88 ~a~~~~~~~   96 (102)
T 2cqb_A           88 LAKPMRIKE   96 (102)
T ss_dssp             ECCCCCCCC
T ss_pred             eCCCCCCCC
Confidence            997765543

>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=99.87  E-value=9.2e-22  Score=135.09  Aligned_cols=81  Identities=38%  Similarity=0.616  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..+.|+.++.++.++|||||+|.+.++|++|++.|||. .++|+.|+|+|
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~   83 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES-ELFGRTIRVNL   83 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCC-EECCcEEEEEE
Confidence            45899999999999999999999999999999999999989999999999999999999999999998 99999999999


Q ss_pred             cC
Q 038096          108 SG  109 (211)
Q Consensus       108 a~  109 (211)
                      |+
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            84

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

Probab=99.87  E-value=1.1e-21  Score=137.89  Aligned_cols=86  Identities=29%  Similarity=0.558  Sum_probs=80.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEE-EEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDL-YIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v-~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      .+.++|||+|||+++++++|+++|++||.|..+ .|++++.++.++|||||+|.+.++|++||+.|||. .|+|+.|+|.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v~   81 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQ-YLCNRPITVS   81 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTC-EETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCC-EECCEEEEEE
Confidence            457999999999999999999999999999999 99999999999999999999999999999999998 9999999999


Q ss_pred             ecCCCccC
Q 038096          107 LSGQDKNA  114 (211)
Q Consensus       107 ~a~~~~~~  114 (211)
                      ++.+....
T Consensus        82 ~a~~~~~~   89 (96)
T 1x5t_A           82 YAFKKDSK   89 (96)
T ss_dssp             ESCCCCCC
T ss_pred             EecccCCC
Confidence            99766543

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

Probab=99.87  E-value=2e-21  Score=137.42  Aligned_cols=85  Identities=16%  Similarity=0.383  Sum_probs=79.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+ |++. .|+|+.|+|.+
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~-~~~g~~l~V~~   85 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFH-DIMGKKVEVKR   85 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCC-BSSSCBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCC-EECCeEEEEEE
Confidence            457999999999999999999999999999999999999999999999999999999999999 8998 99999999999


Q ss_pred             cCCCccC
Q 038096          108 SGQDKNA  114 (211)
Q Consensus       108 a~~~~~~  114 (211)
                      +.++...
T Consensus        86 a~~~~~~   92 (99)
T 2dgs_A           86 AEPRDSK   92 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCCccc
Confidence            9766543

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

Probab=99.87  E-value=1.3e-21  Score=139.35  Aligned_cols=87  Identities=25%  Similarity=0.428  Sum_probs=81.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.|||. .|+|+.|+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v~   90 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGF-GYDHLILNVE   90 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTC-EETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCC-eeCCcEEEEE
Confidence            345899999999999999999999999999999999999999999999999999999999999999998 9999999999


Q ss_pred             ecCCCccC
Q 038096          107 LSGQDKNA  114 (211)
Q Consensus       107 ~a~~~~~~  114 (211)
                      ++.+....
T Consensus        91 ~a~~~~~~   98 (103)
T 2cq0_A           91 WAKPSTNS   98 (103)
T ss_dssp             ESSCCCCS
T ss_pred             ECCCCCCC
Confidence            99776543

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

Probab=99.86  E-value=2.1e-21  Score=137.53  Aligned_cols=85  Identities=28%  Similarity=0.452  Sum_probs=79.6

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+.++ +|+++|||||+|.+.++|++||+.|||. .|+|+.|+|.
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~   91 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGM-TIKENIIKVA   91 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTE-ESSSCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEE
Confidence            3457999999999999999999999999999999999998 8999999999999999999999999997 9999999999


Q ss_pred             ecCCCcc
Q 038096          107 LSGQDKN  113 (211)
Q Consensus       107 ~a~~~~~  113 (211)
                      ++++...
T Consensus        92 ~a~~~~~   98 (100)
T 2do4_A           92 ISNSGPS   98 (100)
T ss_dssp             ECCCCSC
T ss_pred             ECCCCCC
Confidence            9976543

>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=99.86  E-value=1.9e-21  Score=138.84  Aligned_cols=86  Identities=40%  Similarity=0.734  Sum_probs=81.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+. .|+|+.|+|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~   91 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMI-KLYGKPIRVNK   91 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSC-BCSSCBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCC-eECCeEEEEEE
Confidence            45899999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cCCCccC
Q 038096          108 SGQDKNA  114 (211)
Q Consensus       108 a~~~~~~  114 (211)
                      +.++...
T Consensus        92 a~~~~~~   98 (105)
T 1x5u_A           92 ASAHNKN   98 (105)
T ss_dssp             TTTTSCC
T ss_pred             CCCCCcC
Confidence            9876554

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

Probab=99.86  E-value=1.3e-21  Score=139.43  Aligned_cols=87  Identities=28%  Similarity=0.463  Sum_probs=81.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+.++.|+.++|||||+|.+.++|++||+.|||. .|+|+.|+|.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~V~   88 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGA-ELDGRELRVQ   88 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSC-CBTTBCCEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCC-EECCcEEEEE
Confidence            345799999999999999999999999999999999999999999999999999999999999999998 9999999999


Q ss_pred             ecCCCccC
Q 038096          107 LSGQDKNA  114 (211)
Q Consensus       107 ~a~~~~~~  114 (211)
                      +++.....
T Consensus        89 ~a~~~~~~   96 (103)
T 2dnm_A           89 VARYGRRD   96 (103)
T ss_dssp             ECSSCCSC
T ss_pred             ECCcCCCC
Confidence            99766543

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

Probab=99.86  E-value=2.4e-21  Score=135.57  Aligned_cols=82  Identities=27%  Similarity=0.476  Sum_probs=78.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      .++.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|++.|||. .|+|+.|+|+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v~   91 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNK-QLFGRVIKAS   91 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTE-EETTEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCC-eeCCcEEEEE
Confidence            355799999999999999999999999999999999999999999999999999999999999999998 9999999999


Q ss_pred             ecC
Q 038096          107 LSG  109 (211)
Q Consensus       107 ~a~  109 (211)
                      ||+
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            984

>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=99.86  E-value=2.9e-21  Score=139.12  Aligned_cols=86  Identities=27%  Similarity=0.401  Sum_probs=80.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcC------CCeeeCCe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFS------GIVTLYNR  101 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~ln------g~~~i~gr  101 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|++|+.++.++|||||+|.+.++|++||+.||      +. .|+|+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~-~~~g~   91 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGL-KLDGR   91 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCE-ESSSC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCc-EEcCE
Confidence            458999999999999999999999999999999999999999999999999999999999999999      87 99999


Q ss_pred             EEEEEecCCCccC
Q 038096          102 TLRFALSGQDKNA  114 (211)
Q Consensus       102 ~l~v~~a~~~~~~  114 (211)
                      .|+|.|+.+....
T Consensus        92 ~l~v~~a~~~~~~  104 (111)
T 1x4h_A           92 QLKVDLAVTRDEA  104 (111)
T ss_dssp             EEEEECCCCCCCC
T ss_pred             EEEEEECCCCccC
Confidence            9999999766543

>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=99.86  E-value=1.7e-21  Score=141.56  Aligned_cols=86  Identities=24%  Similarity=0.434  Sum_probs=80.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|++||+.||+. .|+|+.|+|.|
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~V~~  101 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGF-QIGMKRLKVQL  101 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTC-EETTEECEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCC-EECCEEEEEEE
Confidence            45789999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cCCCccC
Q 038096          108 SGQDKNA  114 (211)
Q Consensus       108 a~~~~~~  114 (211)
                      ++++...
T Consensus       102 a~~~~~~  108 (115)
T 2cpz_A          102 KRSKNDS  108 (115)
T ss_dssp             CCCSCCC
T ss_pred             cCCCCcC
Confidence            9766543

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

Probab=99.86  E-value=1.5e-21  Score=137.75  Aligned_cols=86  Identities=24%  Similarity=0.401  Sum_probs=79.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCC---CCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKE---TDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR  104 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~---tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~  104 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++.   |+.++|||||+|.+.++|++||+.|||. .|+|+.|.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~   81 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGH-TVDGHKLE   81 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTC-EETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCC-eeCCeEEE
Confidence            4589999999999999999999999999999999999876   6799999999999999999999999998 99999999


Q ss_pred             EEecCCCccC
Q 038096          105 FALSGQDKNA  114 (211)
Q Consensus       105 v~~a~~~~~~  114 (211)
                      |.++......
T Consensus        82 V~~a~~~~~~   91 (98)
T 2cpf_A           82 VRISERATKP   91 (98)
T ss_dssp             EECSSCSSCC
T ss_pred             EEEccCCCCC
Confidence            9999766543

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

Probab=99.86  E-value=1.3e-21  Score=138.32  Aligned_cols=85  Identities=20%  Similarity=0.400  Sum_probs=80.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeE-EEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeE---
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVV-DLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRT---  102 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~-~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~---  102 (211)
                      +.+.++|||+|||+++++++|+++|++||.|. .|.|++++.++.++|||||+|.+.++|++|++.|||. .++|+.   
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~~~~   84 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGK-PLPGATPAK   84 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTS-EESSCSSCE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCC-ccCCCCcce
Confidence            45689999999999999999999999999999 9999999999999999999999999999999999998 999998   


Q ss_pred             -EEEEecCCCc
Q 038096          103 -LRFALSGQDK  112 (211)
Q Consensus       103 -l~v~~a~~~~  112 (211)
                       |+|.||+...
T Consensus        85 ~l~v~~a~~~~   95 (99)
T 2div_A           85 RFKLNYATYSG   95 (99)
T ss_dssp             ECCEEETTCCS
T ss_pred             eEEEeecCCCC
Confidence             9999997654

>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=99.86  E-value=1.5e-21  Score=134.69  Aligned_cols=84  Identities=20%  Similarity=0.330  Sum_probs=78.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCC-CccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDK-PKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~-~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      .+.++|||+|||.++++++|+++|++||.|..+.|+.+..++. ++|||||+|.+.++|++|++.|||. .++|+.|+|+
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~   80 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGG-QIDGQEITAT   80 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCC-eECCeEEEEE
Confidence            3478999999999999999999999999999999999987766 9999999999999999999999998 9999999999


Q ss_pred             ecCCCc
Q 038096          107 LSGQDK  112 (211)
Q Consensus       107 ~a~~~~  112 (211)
                      ++.+.+
T Consensus        81 ~a~~~~   86 (88)
T 4a8x_A           81 AVLAPW   86 (88)
T ss_dssp             EECCCC
T ss_pred             ECCCCC
Confidence            987654

>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=99.86  E-value=1.6e-21  Score=142.00  Aligned_cols=81  Identities=27%  Similarity=0.525  Sum_probs=75.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||||||+++++++|+++|++||.|.+|+|++|+  +.++|||||+|.+.++|++||+.|+|. .|+|+.|+|.++.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~-~~~g~~i~V~~a~   81 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGM-LLNDRKVFVGRFK   81 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTC-EETTEECEEEESS
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCC-EECCEEEEEEECC
Confidence            5789999999999999999999999999999999986  458999999999999999999999998 9999999999987


Q ss_pred             CCcc
Q 038096          110 QDKN  113 (211)
Q Consensus       110 ~~~~  113 (211)
                      ....
T Consensus        82 ~~~~   85 (115)
T 4f25_A           82 SRKE   85 (115)
T ss_dssp             CCCC
T ss_pred             Cccc
Confidence            6543

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

Probab=99.86  E-value=3.4e-21  Score=137.90  Aligned_cols=87  Identities=17%  Similarity=0.399  Sum_probs=81.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccC-CCCCCCccEEEEEeCCHHHHHHHHHHc-CCCeeeCCeEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRD-KETDKPKGFAFVEYESEEIGHYAIKLF-SGIVTLYNRTLR  104 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d-~~tg~~rg~aFV~f~~~~~A~~Ai~~l-ng~~~i~gr~l~  104 (211)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+.+ +.++.++|||||+|.+.++|++||+.| |+. .|+|+.|+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~-~~~g~~l~   90 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHST-HLYGRRLV   90 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCC-BSSSCBCE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCC-eECCCEEE
Confidence            345899999999999999999999999999999999999 788999999999999999999999999 898 99999999


Q ss_pred             EEecCCCccC
Q 038096          105 FALSGQDKNA  114 (211)
Q Consensus       105 v~~a~~~~~~  114 (211)
                      |.|+..+...
T Consensus        91 v~~a~~~~~~  100 (107)
T 2cph_A           91 LEWADSEVTV  100 (107)
T ss_dssp             EEECCCCCCC
T ss_pred             EEeCCCCCCC
Confidence            9999876543

>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=99.86  E-value=2.1e-21  Score=139.84  Aligned_cols=85  Identities=20%  Similarity=0.355  Sum_probs=80.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      +.+.++|||+|||+++++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|++||+.|||. .|+|+.|+|.
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~~l~V~  101 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGA-EIMGQTIQVD  101 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCC-EECCcEEEEE
Confidence            355789999999999999999999999999999999999999999999999999999999999999998 9999999999


Q ss_pred             ecCCCc
Q 038096          107 LSGQDK  112 (211)
Q Consensus       107 ~a~~~~  112 (211)
                      |+..+.
T Consensus       102 ~a~~~~  107 (110)
T 1oo0_B          102 WCFVKG  107 (110)
T ss_dssp             ESEESS
T ss_pred             EcccCC
Confidence            987654

>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=99.86  E-value=1.9e-22  Score=140.49  Aligned_cols=81  Identities=21%  Similarity=0.293  Sum_probs=72.7

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCC--CeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAG--RVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G--~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      .+|||||||+++++++|+++|++||  .|.++.|+.|+.+|+++|||||+|.+.++|++||+.|||. .++|+.|+|.++
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~-~~~gr~i~V~~~   80 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKR-ELHGQNPVVTPS   80 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGS-CSSSCCCEECCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCC-eeCCEEEEEEEC
Confidence            4799999999999999999999999  9999999999999999999999999999999999999998 999999999998


Q ss_pred             CCCc
Q 038096          109 GQDK  112 (211)
Q Consensus       109 ~~~~  112 (211)
                      .+..
T Consensus        81 ~~~~   84 (90)
T 3p5t_L           81 NKLE   84 (90)
T ss_dssp             ----
T ss_pred             CCCc
Confidence            6543

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

Probab=99.86  E-value=2.9e-21  Score=135.29  Aligned_cols=82  Identities=24%  Similarity=0.398  Sum_probs=78.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|++.|||. .|+|+.|+|++
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v~~   91 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGM-ELDGRRIRVSG   91 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTE-EETTEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEe
Confidence            45789999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cCC
Q 038096          108 SGQ  110 (211)
Q Consensus       108 a~~  110 (211)
                      |+.
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            864

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

Probab=99.86  E-value=1.6e-21  Score=138.48  Aligned_cols=87  Identities=22%  Similarity=0.499  Sum_probs=81.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+. .|+|+.|+|.
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v~   87 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGK-SVDGRQIRVD   87 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTC-CTTSCCCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCC-EECCeEEEEE
Confidence            356899999999999999999999999999999999999999999999999999999999999999998 8999999999


Q ss_pred             ecCCCccC
Q 038096          107 LSGQDKNA  114 (211)
Q Consensus       107 ~a~~~~~~  114 (211)
                      +++.....
T Consensus        88 ~a~~~~~~   95 (102)
T 1x5s_A           88 QAGKSSDN   95 (102)
T ss_dssp             EEECCCCC
T ss_pred             ECCCCCCC
Confidence            99766543

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

Probab=99.86  E-value=1.3e-21  Score=140.00  Aligned_cols=85  Identities=20%  Similarity=0.328  Sum_probs=79.9

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..++++|||+|||+++++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|++|++.|||. .|+|+.|+|.
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~V~   98 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQ-DLMGQPISVD   98 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTC-BSSSSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCC-EECCcEEEEE
Confidence            345789999999999999999999999999999999999999999999999999999999999999998 9999999999


Q ss_pred             ecCCCc
Q 038096          107 LSGQDK  112 (211)
Q Consensus       107 ~a~~~~  112 (211)
                      ||.++.
T Consensus        99 ~a~~~~  104 (106)
T 1p27_B           99 WCFVRG  104 (106)
T ss_dssp             ESEESS
T ss_pred             eecCCC
Confidence            986543

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

Probab=99.86  E-value=1e-20  Score=136.96  Aligned_cols=85  Identities=29%  Similarity=0.447  Sum_probs=79.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|.+|.|+.++ +++++|||||+|.+.++|++||+.||+. .|+|+.|+|.+
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~   90 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQ-LLFDRPMHVKM   90 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCC-EeCCCEEEEEE
Confidence            457999999999999999999999999999999999998 4999999999999999999999999998 99999999999


Q ss_pred             cCCCccC
Q 038096          108 SGQDKNA  114 (211)
Q Consensus       108 a~~~~~~  114 (211)
                      ++.....
T Consensus        91 a~~~~~~   97 (114)
T 2do0_A           91 DERALPK   97 (114)
T ss_dssp             CSCCCCC
T ss_pred             cccCCCC
Confidence            8765443

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

Probab=99.86  E-value=5e-21  Score=143.40  Aligned_cols=88  Identities=23%  Similarity=0.408  Sum_probs=82.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|.|++++.+++++|||||+|.+.++|++||+.|||. .|+|+.|+|.
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~  117 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGF-NILNKRLKVA  117 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTE-ECSSCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCC-EECCeEEEEE
Confidence            355799999999999999999999999999999999999999999999999999999999999999998 9999999999


Q ss_pred             ecCCCccCC
Q 038096          107 LSGQDKNAQ  115 (211)
Q Consensus       107 ~a~~~~~~~  115 (211)
                      +++......
T Consensus       118 ~a~~~~~~~  126 (139)
T 1u6f_A          118 LAASGHQRP  126 (139)
T ss_dssp             ESSCCCCCC
T ss_pred             ECCCCCCCC
Confidence            998765543

>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=99.85  E-value=5.2e-21  Score=139.58  Aligned_cols=84  Identities=23%  Similarity=0.473  Sum_probs=79.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++ +|.++|||||+|.+.++|++||+.|||. .|+|+.|+|.+
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~-~~~g~~l~V~~   82 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGK-SLHGKAIKVEQ   82 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSC-BCSSSBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEE
Confidence            457999999999999999999999999999999999998 8999999999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      ++....
T Consensus        83 a~~~~~   88 (116)
T 2fy1_A           83 AKKPSF   88 (116)
T ss_dssp             CCCSSC
T ss_pred             CCCCCC
Confidence            976544

>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=99.85  E-value=2.6e-21  Score=138.41  Aligned_cols=86  Identities=20%  Similarity=0.361  Sum_probs=80.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee---CCeEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL---YNRTLR  104 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i---~gr~l~  104 (211)
                      .+.++|||+|||.++++++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|++||+.||+. .+   .|+.|+
T Consensus        11 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~-~~~~~~g~~l~   89 (106)
T 2dgp_A           11 HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQ-KTLPGMNRPIQ   89 (106)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTT-CCCTTCSSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCC-cccCCCCceEE
Confidence            45799999999999999999999999999999999999999999999999999999999999999998 66   889999


Q ss_pred             EEecCCCccC
Q 038096          105 FALSGQDKNA  114 (211)
Q Consensus       105 v~~a~~~~~~  114 (211)
                      |.++..+...
T Consensus        90 v~~a~~~~~~   99 (106)
T 2dgp_A           90 VKPADSESRG   99 (106)
T ss_dssp             EEECCCCSCC
T ss_pred             EEECCccccc
Confidence            9999876553

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

Probab=99.85  E-value=5.3e-21  Score=138.38  Aligned_cols=87  Identities=30%  Similarity=0.419  Sum_probs=81.2

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeE--------EEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVV--------DLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL   98 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~--------~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i   98 (211)
                      ..+.++|||+|||+++++++|+++|++||.|.        .|.|+.++.+++++|||||+|.+.++|++||+.|||. .|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~~   90 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK-DF   90 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC-EE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCC-cc
Confidence            34589999999999999999999999999999        6999999999999999999999999999999999998 99


Q ss_pred             CCeEEEEEecCCCccC
Q 038096           99 YNRTLRFALSGQDKNA  114 (211)
Q Consensus        99 ~gr~l~v~~a~~~~~~  114 (211)
                      +|+.|+|.+++.....
T Consensus        91 ~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           91 QGSKLKVSLARKKPPM  106 (113)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCCEEEEEECCCCCCC
Confidence            9999999999776543

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

Probab=99.85  E-value=2.1e-21  Score=137.33  Aligned_cols=82  Identities=22%  Similarity=0.360  Sum_probs=78.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEE--------EEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVD--------LYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL   98 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~--------v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i   98 (211)
                      ....++|||+|||+++++++|+++|++||.|..        +.|+.++.+|+++|||||+|.+.++|++|++.|||. .+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~-~~   88 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK-EF   88 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC-BS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC-Ee
Confidence            355899999999999999999999999999999        999999999999999999999999999999999998 99


Q ss_pred             CCeEEEEEecC
Q 038096           99 YNRTLRFALSG  109 (211)
Q Consensus        99 ~gr~l~v~~a~  109 (211)
                      +|+.|+|++|+
T Consensus        89 ~g~~l~V~~A~   99 (99)
T 2la6_A           89 SGNPIKVSFAT   99 (99)
T ss_dssp             SSSBCEEEECC
T ss_pred             CCcEEEEEecC
Confidence            99999999974

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

Probab=99.85  E-value=7.7e-22  Score=140.23  Aligned_cols=80  Identities=29%  Similarity=0.353  Sum_probs=77.3

Q ss_pred             CCeEEEcCCCC------CCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCC-eE
Q 038096           30 GCNVYIGNLDE------KVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYN-RT  102 (211)
Q Consensus        30 ~~~lfVgnLp~------~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~g-r~  102 (211)
                      +++|||+|||.      ++++++|+++|++||.|.+|.|++|+.||+++|||||+|.+.++|++||+.|||. .|+| +.
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~-~~~g~r~   84 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK-RLDLKHR   84 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTC-BSSSSCB
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCc-ccCCCeE
Confidence            68999999999      9999999999999999999999999999999999999999999999999999998 9999 99


Q ss_pred             EEEEecCC
Q 038096          103 LRFALSGQ  110 (211)
Q Consensus       103 l~v~~a~~  110 (211)
                      |+|.+|.+
T Consensus        85 l~V~~a~~   92 (100)
T 3ns6_A           85 LFLYTMKD   92 (100)
T ss_dssp             CEEEESHH
T ss_pred             EEEEECch
Confidence            99999864

>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=99.85  E-value=7.6e-21  Score=133.96  Aligned_cols=81  Identities=15%  Similarity=0.240  Sum_probs=75.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHH----HHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLY----DILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTL  103 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~----~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l  103 (211)
                      .+.++|||+|||+++++++|+    ++|++||.|.+|.|+.|+.+   +|||||+|.+.++|++||+.|||. .|+|+.|
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~-~~~gr~l   82 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRY-KIGSKKI   82 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTE-EETTEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCC-EECCeEE
Confidence            457899999999999999999    99999999999999999875   899999999999999999999998 9999999


Q ss_pred             EEEecCCCc
Q 038096          104 RFALSGQDK  112 (211)
Q Consensus       104 ~v~~a~~~~  112 (211)
                      +|++|++..
T Consensus        83 ~V~~a~~~~   91 (96)
T 2dgx_A           83 LVSLATGAS   91 (96)
T ss_dssp             EEEECCCSS
T ss_pred             EEEEcCCCC
Confidence            999996654

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

Probab=99.85  E-value=3.5e-21  Score=147.66  Aligned_cols=82  Identities=22%  Similarity=0.368  Sum_probs=77.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCC--CeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAG--RVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G--~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      +.++|||||||+++++++|+++|+.||  .|.+|.|+.|+.||+++|||||+|.+.++|++||+.|||. .|+|+.|+|.
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~-~~~Gr~l~V~  132 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGK-VLNGEKVDVR  132 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTC-EETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCC-EECCeEeEEE
Confidence            468999999999999999999999999  9999999999999999999999999999999999999998 9999999999


Q ss_pred             ecCCC
Q 038096          107 LSGQD  111 (211)
Q Consensus       107 ~a~~~  111 (211)
                      +|.+.
T Consensus       133 ~a~~~  137 (156)
T 3n9u_C          133 PATRQ  137 (156)
T ss_dssp             ECCHH
T ss_pred             EcCCC
Confidence            98643

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

Probab=99.85  E-value=6.8e-21  Score=138.82  Aligned_cols=81  Identities=26%  Similarity=0.478  Sum_probs=77.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|.+|.|+.++.+|+++|||||+|.+.++|++||+.|||. .|+|+.|+|+|
T Consensus        38 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~V~~  116 (118)
T 2khc_A           38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGF-QVGTKRLKVQL  116 (118)
T ss_dssp             CCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCC-EETTEECCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCC-EECCEEEEEEe
Confidence            45799999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cC
Q 038096          108 SG  109 (211)
Q Consensus       108 a~  109 (211)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            74

>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=99.85  E-value=1.8e-21  Score=144.69  Aligned_cols=86  Identities=24%  Similarity=0.397  Sum_probs=81.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|++|+.+++++|||||+|.+.++|++||+.|||. .|+|+.|+|.
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~-~i~g~~l~V~  121 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGM-ELDGRRIRVD  121 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTC-CSSSSCCEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEE
Confidence            356899999999999999999999999999999999999999999999999999999999999999998 9999999999


Q ss_pred             ecCCCcc
Q 038096          107 LSGQDKN  113 (211)
Q Consensus       107 ~a~~~~~  113 (211)
                      |+.++++
T Consensus       122 ~a~~~~p  128 (129)
T 2kxn_B          122 FSITKRP  128 (129)
T ss_dssp             CCSSSSC
T ss_pred             EecCCCC
Confidence            9977653

>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=99.85  E-value=5.7e-21  Score=137.25  Aligned_cols=86  Identities=22%  Similarity=0.446  Sum_probs=79.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCC-eEEEEEc-cCCCCCCCccEEEEEeCCHHHHHHHHHHcC--CCeeeCCeE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGR-VVDLYIP-RDKETDKPKGFAFVEYESEEIGHYAIKLFS--GIVTLYNRT  102 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~-i~~v~i~-~d~~tg~~rg~aFV~f~~~~~A~~Ai~~ln--g~~~i~gr~  102 (211)
                      +.+.++|||+|||+++++++|+++|++||. |..|.|+ .++.+|.++|||||+|.+.++|++|++.|+  +. .++|+.
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~-~~~g~~   83 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRI-QLWGHQ   83 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCS-CBTTBC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCc-eecCCe
Confidence            456899999999999999999999999998 9999998 898899999999999999999999999995  46 899999


Q ss_pred             EEEEecCCCcc
Q 038096          103 LRFALSGQDKN  113 (211)
Q Consensus       103 l~v~~a~~~~~  113 (211)
                      |+|.||.++..
T Consensus        84 l~V~~a~~~~~   94 (109)
T 2dis_A           84 IAVDWAEPEID   94 (109)
T ss_dssp             CEEEESCSSCS
T ss_pred             EEEEEcCCCCC
Confidence            99999976654

>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=99.85  E-value=6e-21  Score=132.06  Aligned_cols=81  Identities=22%  Similarity=0.381  Sum_probs=77.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||+++++++|+++|++||.|..+.|+.++.++.++|||||+|.+.++|++|+ .|||. .++|+.|+|.+++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~-~~~g~~l~V~~a~   83 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDES-LFRGRQIKVIPKR   83 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTC-EETTEECEEEETT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCC-EECCcEEEEEEcc
Confidence            689999999999999999999999999999999999999999999999999999999999 99998 9999999999987


Q ss_pred             CCc
Q 038096          110 QDK  112 (211)
Q Consensus       110 ~~~  112 (211)
                      +..
T Consensus        84 ~~~   86 (89)
T 3ucg_A           84 TNR   86 (89)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            643

>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=99.85  E-value=7.6e-21  Score=131.20  Aligned_cols=79  Identities=20%  Similarity=0.341  Sum_probs=74.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++.+|+++|||||+|.+.++|++|++. ++. .|+|+.|.|++
T Consensus         9 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~-~~~g~~i~v~~   86 (87)
T 3s7r_A            9 EDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-KEH-RLDGRVIDPKK   86 (87)
T ss_dssp             SCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-SCE-EETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-CCC-EECCEEEEEEe
Confidence            4589999999999999999999999999999999999999999999999999999999999975 776 89999999998


Q ss_pred             c
Q 038096          108 S  108 (211)
Q Consensus       108 a  108 (211)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            6

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

Probab=99.85  E-value=9.3e-21  Score=134.97  Aligned_cols=84  Identities=27%  Similarity=0.443  Sum_probs=78.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++|| |..|.|++++.|++++|||||+|.+.++|++|| .|||. .|+|+.|+|.+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~-~~~g~~l~V~~   89 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGA-LLGDRSLRVDI   89 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTC-EETTEECEEEE
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCC-eECCeEEEEEE
Confidence            4479999999999999999999999997 999999999999999999999999999999999 89998 99999999999


Q ss_pred             cCCCccC
Q 038096          108 SGQDKNA  114 (211)
Q Consensus       108 a~~~~~~  114 (211)
                      +.+....
T Consensus        90 a~~~~~~   96 (103)
T 2dng_A           90 AEGRKQD   96 (103)
T ss_dssp             CCCCCCC
T ss_pred             ecCCCCC
Confidence            9766543

>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=99.85  E-value=7.5e-21  Score=135.74  Aligned_cols=85  Identities=20%  Similarity=0.346  Sum_probs=79.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCC---eEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYN---RTLR  104 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~g---r~l~  104 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||+.|||. .+.|   +.|+
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~gg~~~~l~   90 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGS-QTMPGASSSLV   90 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSC-CCCTTCSSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCC-ccCCCCCccEE
Confidence            457999999999999999999999999999999999998 6999999999999999999999999998 7887   9999


Q ss_pred             EEecCCCccC
Q 038096          105 FALSGQDKNA  114 (211)
Q Consensus       105 v~~a~~~~~~  114 (211)
                      |.+|..+...
T Consensus        91 V~~a~~~~~~  100 (105)
T 2dnh_A           91 VKFADTDKES  100 (105)
T ss_dssp             EEESCSSCCC
T ss_pred             EEECccCccc
Confidence            9999876554

>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=99.85  E-value=1.1e-20  Score=134.81  Aligned_cols=85  Identities=20%  Similarity=0.407  Sum_probs=79.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCC-CCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKET-DKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~t-g~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      .+.++|||+|||+++++++|+++|+.|| |..|.|+.++.+ ++++|||||+|.+.++|++|| .||+. .|+|+.|+|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~-~~~g~~l~V~   89 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEE-SLGNKRIRVD   89 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTC-EETTEECEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCC-EeCCcEEEEE
Confidence            3479999999999999999999999999 999999999988 999999999999999999999 99998 9999999999


Q ss_pred             ecCCCccCC
Q 038096          107 LSGQDKNAQ  115 (211)
Q Consensus       107 ~a~~~~~~~  115 (211)
                      ++.+.....
T Consensus        90 ~a~~~~~~~   98 (104)
T 1wi8_A           90 VADQAQDKD   98 (104)
T ss_dssp             ECCCCCCCC
T ss_pred             EccCCCCCC
Confidence            998765543

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

Probab=99.85  E-value=6.3e-21  Score=135.75  Aligned_cols=84  Identities=23%  Similarity=0.383  Sum_probs=78.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.+  ++.++|||||+|.+.++|++||+.|||. .|+|+.|+|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~V~~   89 (103)
T 2d9p_A           13 YQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGR-IVATKPLYVAL   89 (103)
T ss_dssp             SSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTC-BSSSSBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCC-EeCCcEEEEEE
Confidence            45899999999999999999999999999999999998  7999999999999999999999999998 89999999999


Q ss_pred             cCCCccC
Q 038096          108 SGQDKNA  114 (211)
Q Consensus       108 a~~~~~~  114 (211)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2d9p_A           90 AQRKEER   96 (103)
T ss_dssp             CSSCCCC
T ss_pred             ecccccC
Confidence            9876554

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

Probab=99.84  E-value=3.9e-20  Score=134.48  Aligned_cols=83  Identities=17%  Similarity=0.253  Sum_probs=78.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|++++.+++++|||||+|.+.++|++||+.+++  .|+|+.|+|.+
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~--~~~g~~l~V~~   92 (116)
T 2cqd_A           15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP--IIDGRKANVNL   92 (116)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC--EETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC--cCCCEEEEEEE
Confidence            4579999999999999999999999999999999999999999999999999999999999999997  69999999999


Q ss_pred             cCCCc
Q 038096          108 SGQDK  112 (211)
Q Consensus       108 a~~~~  112 (211)
                      +....
T Consensus        93 a~~~~   97 (116)
T 2cqd_A           93 AYLGA   97 (116)
T ss_dssp             STTTC
T ss_pred             cccCC
Confidence            97543

>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=99.84  E-value=4.4e-21  Score=138.23  Aligned_cols=83  Identities=23%  Similarity=0.469  Sum_probs=79.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||..+++++|+++|++||.|..|.|++++.+|.++|||||+|.+.++|++|++.|||. .|+|+.|+|.+
T Consensus        24 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~-~i~g~~l~V~~  102 (108)
T 2jrs_A           24 AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGF-ELAGRPMKVGH  102 (108)
T ss_dssp             SSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTC-CSSSSCCEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCC-EECCEEEEEEE
Confidence            45799999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cCCC
Q 038096          108 SGQD  111 (211)
Q Consensus       108 a~~~  111 (211)
                      ++++
T Consensus       103 a~~k  106 (108)
T 2jrs_A          103 VTER  106 (108)
T ss_dssp             SCSS
T ss_pred             cccC
Confidence            8764

>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=99.84  E-value=5.3e-21  Score=140.97  Aligned_cols=86  Identities=20%  Similarity=0.321  Sum_probs=80.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.|||. .|+|+.|.|.
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~   97 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQ-DLMGQPISVD   97 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTC-BSSSSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCC-eeCCeEEEEE
Confidence            455789999999999999999999999999999999999999999999999999999999999999998 9999999999


Q ss_pred             ecCCCcc
Q 038096          107 LSGQDKN  113 (211)
Q Consensus       107 ~a~~~~~  113 (211)
                      ||.....
T Consensus        98 ~a~~~~~  104 (126)
T 3ex7_B           98 WCFVRGP  104 (126)
T ss_dssp             ESEESSS
T ss_pred             EecCCCC
Confidence            9975544

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

Probab=99.84  E-value=7e-21  Score=136.39  Aligned_cols=82  Identities=18%  Similarity=0.291  Sum_probs=73.5

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCC--CeeeCCeEE
Q 038096           26 NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSG--IVTLYNRTL  103 (211)
Q Consensus        26 ~s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng--~~~i~gr~l  103 (211)
                      ...+.++|||+|||++++|++|+++|++||.|.+|.|+++      ||||||+|.+.++|++||+.|++  . .|+|++|
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~-~l~Gr~l   84 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTP-VLRGQPI   84 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCC-EETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCc-eECCEEE
Confidence            3456899999999999999999999999999999999875      59999999999999999998864  5 8999999


Q ss_pred             EEEecCCCccC
Q 038096          104 RFALSGQDKNA  114 (211)
Q Consensus       104 ~v~~a~~~~~~  114 (211)
                      +|.||+.+...
T Consensus        85 ~V~~A~~~~~~   95 (105)
T 1sjq_A           85 YIQFSNHKELK   95 (105)
T ss_dssp             CBCCCSSSSCC
T ss_pred             EEEEcCCCCCC
Confidence            99999765543

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

Probab=99.84  E-value=1.2e-20  Score=136.11  Aligned_cols=84  Identities=23%  Similarity=0.355  Sum_probs=76.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|++||+.++ . .|+|+.|+|.+
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~-~l~g~~l~V~~  100 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-H-ELDSKTIDPKV  100 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSC-E-EETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCC-C-cCCCEEEEEEE
Confidence            457999999999999999999999999999999999999999999999999999999999999874 5 89999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      +.+...
T Consensus       101 a~~~~~  106 (109)
T 2rs2_A          101 AFPRRA  106 (109)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            876543

>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=99.84  E-value=2.7e-20  Score=132.43  Aligned_cols=84  Identities=15%  Similarity=0.320  Sum_probs=77.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++.  .++|||||+|.+.++|++||+.||+. .|+|+.|+|.|
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~V~~   89 (103)
T 2cqi_A           13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGR-KILGKEVKVNW   89 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTE-EETTEEEEEEE
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCC-CcCCCeEEEEE
Confidence            4579999999999999999999999999999999999864  47899999999999999999999998 99999999999


Q ss_pred             cCCCccC
Q 038096          108 SGQDKNA  114 (211)
Q Consensus       108 a~~~~~~  114 (211)
                      +......
T Consensus        90 a~~~~~~   96 (103)
T 2cqi_A           90 ATTPSSQ   96 (103)
T ss_dssp             CCCTTCC
T ss_pred             CCCCccc
Confidence            9875543

>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=99.84  E-value=1.6e-20  Score=143.46  Aligned_cols=85  Identities=27%  Similarity=0.503  Sum_probs=80.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+. .|+|+.|+|.|
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~~l~V~~  115 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGT-RLDDRIIRTDW  115 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTS-EETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCC-EECCeEEEEEE
Confidence            45799999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      |.+...
T Consensus       116 a~~~~~  121 (156)
T 1h2v_Z          116 DAGFKE  121 (156)
T ss_dssp             ESCCCT
T ss_pred             CCCCCC
Confidence            976443

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

Probab=99.84  E-value=7.2e-21  Score=135.91  Aligned_cols=84  Identities=24%  Similarity=0.330  Sum_probs=79.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+. ++. .|+|+.|+|.+
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~-~~~g~~l~V~~   91 (105)
T 2dh8_A           14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPH-TLDGRNIDPKP   91 (105)
T ss_dssp             SSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSE-EETTEEEBCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCC-eECCEEEEEEE
Confidence            5589999999999999999999999999999999999999999999999999999999999999 997 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      +.++..
T Consensus        92 a~~~~~   97 (105)
T 2dh8_A           92 CTPRGM   97 (105)
T ss_dssp             SCCSSC
T ss_pred             ccCCCC
Confidence            876554

>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=99.84  E-value=1.7e-20  Score=134.31  Aligned_cols=81  Identities=21%  Similarity=0.360  Sum_probs=77.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+.++ +|+++|||||+|.+.++|++||+.|||. .|+|+.|+|+
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~V~  103 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGV-PLDGRPMNIQ  103 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCC-EeCCcEEEEE
Confidence            3558999999999999999999999999999999999998 8999999999999999999999999998 9999999999


Q ss_pred             ecC
Q 038096          107 LSG  109 (211)
Q Consensus       107 ~a~  109 (211)
                      +|.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            974

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

Probab=99.84  E-value=6.6e-21  Score=135.81  Aligned_cols=85  Identities=19%  Similarity=0.379  Sum_probs=79.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhc-CCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCee-eCCeEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQ-AGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVT-LYNRTLRF  105 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~-~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~-i~gr~l~v  105 (211)
                      .+.++|||+|||+++++++|+++|++ ||.|..|.|+.++ +|.++|||||+|.+.++|++||+.|||. . |+|+.|+|
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~~g~~l~v   84 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGA-VGLGSKPVRL   84 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTC-CSSSSSCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCC-cccCCEeEEE
Confidence            45799999999999999999999999 9999999999998 8999999999999999999999999998 8 99999999


Q ss_pred             EecCCCccC
Q 038096          106 ALSGQDKNA  114 (211)
Q Consensus       106 ~~a~~~~~~  114 (211)
                      .++.+....
T Consensus        85 ~~a~~~~~~   93 (104)
T 2dhg_A           85 SVAIPKASR   93 (104)
T ss_dssp             CBCCCCCSC
T ss_pred             EEccCCCcC
Confidence            998765543

>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=99.84  E-value=1.2e-20  Score=132.16  Aligned_cols=81  Identities=37%  Similarity=0.719  Sum_probs=76.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++. +.++|||||+|.+.++|++|++.|||. .|+|+.|+|.+
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~V~~   91 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGI-RLYGRPINVSG   91 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTC-EETTEECEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCC-EECCCEEEEEE
Confidence            4579999999999999999999999999999999999986 999999999999999999999999998 99999999999


Q ss_pred             cCC
Q 038096          108 SGQ  110 (211)
Q Consensus       108 a~~  110 (211)
                      ++.
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            854

>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=99.84  E-value=5.2e-20  Score=130.96  Aligned_cols=84  Identities=18%  Similarity=0.271  Sum_probs=77.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+.++.  .++|||||+|.+.++|++||+.|||. .|+|+.|+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~   88 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGT-VVEGRKIEVN   88 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEE
Confidence            34579999999999999999999999999999999999874  48999999999999999999999998 9999999999


Q ss_pred             ecCCCcc
Q 038096          107 LSGQDKN  113 (211)
Q Consensus       107 ~a~~~~~  113 (211)
                      ++.+...
T Consensus        89 ~a~~~~~   95 (103)
T 2cq3_A           89 NATARVM   95 (103)
T ss_dssp             ECCSSCC
T ss_pred             EcccCCC
Confidence            9976544

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

Probab=99.84  E-value=1.7e-20  Score=130.68  Aligned_cols=83  Identities=23%  Similarity=0.442  Sum_probs=77.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..+.|.++  ++.++|||||+|.+.++|++|++.|||. .++|+.|+|.+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~-~~~g~~l~v~~   82 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGM-KLSGREIDVRI   82 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTC-CBTTBCCCCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCC-EECCcEEEEEE
Confidence            45899999999999999999999999999999999884  6899999999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      +++...
T Consensus        83 a~~~~~   88 (92)
T 2dgv_A           83 DRNASG   88 (92)
T ss_dssp             CSCCSS
T ss_pred             cCCCCC
Confidence            976654

>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=99.84  E-value=9.6e-21  Score=137.30  Aligned_cols=83  Identities=27%  Similarity=0.379  Sum_probs=78.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|| .|||. .|+|+.|+|.++
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~-~~~g~~l~V~~a  101 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQ-RLLGVPIIVQAS  101 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTE-EETTEEEEEEEH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCC-EeCCeEEEEEec
Confidence            3689999999999999999999999999999999999999999999999999999999999 99998 999999999998


Q ss_pred             CCCcc
Q 038096          109 GQDKN  113 (211)
Q Consensus       109 ~~~~~  113 (211)
                      .+...
T Consensus       102 ~~~~~  106 (114)
T 2cq4_A          102 QAEKN  106 (114)
T ss_dssp             HHHHH
T ss_pred             CCCcc
Confidence            76543

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

Probab=99.84  E-value=4e-21  Score=128.96  Aligned_cols=75  Identities=24%  Similarity=0.384  Sum_probs=72.2

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        32 ~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++ +++. .++|+.|.|++|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~-~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFH-EINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCC-CSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCC-EECCEEEEEEeC
Confidence            59999999999999999999999999999999999999999999999999999999998 8998 999999999885

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

Probab=99.83  E-value=1.7e-21  Score=133.98  Aligned_cols=81  Identities=20%  Similarity=0.326  Sum_probs=76.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..+.|+.++.++.++|||||+|.+.++|++|++.|||. .++|+.|++++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~~~~~~   81 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKAS-GVQAQMAKQSG   81 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHH-TCCEESCCSSC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCC-eEeeEEEeecC
Confidence            45799999999999999999999999999999999999999999999999999999999999999998 99999998877


Q ss_pred             cC
Q 038096          108 SG  109 (211)
Q Consensus       108 a~  109 (211)
                      ++
T Consensus        82 ~~   83 (85)
T 1x4e_A           82 PS   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.83  E-value=6.7e-21  Score=135.67  Aligned_cols=84  Identities=33%  Similarity=0.559  Sum_probs=79.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||+++++++|+++|++||.|..+.|+.++.+|.++|||||+|.+.++|++|++.|||. .++|+.|+|.++.
T Consensus         8 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~a~   86 (104)
T 1p1t_A            8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGR-EFSGRALRVDNAA   86 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSB-SCSSSCBEEEETT
T ss_pred             ccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCC-eeCCcEEEEEeCC
Confidence            689999999999999999999999999999999999989999999999999999999999999998 9999999999998


Q ss_pred             CCccC
Q 038096          110 QDKNA  114 (211)
Q Consensus       110 ~~~~~  114 (211)
                      .....
T Consensus        87 ~~~~~   91 (104)
T 1p1t_A           87 SEKNK   91 (104)
T ss_dssp             CTTHH
T ss_pred             Cccch
Confidence            76543

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

Probab=99.83  E-value=7.4e-21  Score=136.05  Aligned_cols=79  Identities=19%  Similarity=0.263  Sum_probs=74.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +.++|||||||+++++++|+++|++||.|.+|.|++|+. |.++|||||+|.+.++|++||. +++. .++|+.|.|.|+
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~-~~~gr~l~V~~~   86 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQ-KYKETDLLILFK   86 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCC-CCTTTTCEEEEH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCC-EECCEEEEEEEc
Confidence            368999999999999999999999999999999999987 9999999999999999999999 8997 999999999987


Q ss_pred             CC
Q 038096          109 GQ  110 (211)
Q Consensus       109 ~~  110 (211)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            54

>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=99.83  E-value=2.4e-20  Score=142.55  Aligned_cols=85  Identities=28%  Similarity=0.492  Sum_probs=80.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.|+.+|.++|||||+|.+.++|++||+.|||. .|+|+.|+|.+
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~  146 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGA-VLDGRELRVQM  146 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTE-ESSSSEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCC-EECCeEEEEEE
Confidence            44789999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      +++...
T Consensus       147 a~~~~~  152 (158)
T 2kn4_A          147 ARYGRP  152 (158)
T ss_dssp             ECCSSC
T ss_pred             CCCCCC
Confidence            977654

>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=99.83  E-value=6.2e-20  Score=130.58  Aligned_cols=83  Identities=19%  Similarity=0.255  Sum_probs=77.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.  +. .|+|+.|.|.+
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~-~~~g~~l~v~~   89 (103)
T 2cqg_A           13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RH-MIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CE-EETTEEEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc--CC-eeCCeEEEEEe
Confidence            4578999999999999999999999999999999999999999999999999999999999994  65 89999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      +..+..
T Consensus        90 a~~~~~   95 (103)
T 2cqg_A           90 PNSKQS   95 (103)
T ss_dssp             CCTTCC
T ss_pred             cCCCCc
Confidence            976544

>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=99.83  E-value=5.9e-21  Score=135.51  Aligned_cols=81  Identities=22%  Similarity=0.419  Sum_probs=74.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCC-CCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDK-ETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~-~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ...++|||+|||+++++++|+++|++|| |.+|.|+.++ .+|+++|||||+|.+.++|++|| .|||. .|+|+.|+|.
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~-~~~g~~l~V~   93 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEE-SLGNRRIRVD   93 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTC-CBTTBCCCCE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCC-EECCeEEEEE
Confidence            4579999999999999999999999999 9999999998 68999999999999999999999 89998 9999999999


Q ss_pred             ecCCC
Q 038096          107 LSGQD  111 (211)
Q Consensus       107 ~a~~~  111 (211)
                      ++++.
T Consensus        94 ~a~~~   98 (100)
T 2j76_E           94 VADQA   98 (100)
T ss_dssp             ECCCS
T ss_pred             eccCC
Confidence            98764

>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=99.83  E-value=1.7e-20  Score=135.63  Aligned_cols=84  Identities=18%  Similarity=0.266  Sum_probs=77.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHH---HHHhcCCCeEEEEEccCCCCC---CCccEEEEEeCCHHHHHHHHHHcCCCeeeCCe
Q 038096           28 NSGCNVYIGNLDEKVNERVLY---DILIQAGRVVDLYIPRDKETD---KPKGFAFVEYESEEIGHYAIKLFSGIVTLYNR  101 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~---~~F~~~G~i~~v~i~~d~~tg---~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr  101 (211)
                      .+.++|||+|||+++++++|+   ++|++||.|.+|.|+.++.++   .++|||||+|.+.++|++||+.|||. .|+|+
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~-~~~gr   91 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNV-VVDGR   91 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTE-EETTE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCC-EECCE
Confidence            447899999999999999999   999999999999999998754   55699999999999999999999998 99999


Q ss_pred             EEEEEecCCCc
Q 038096          102 TLRFALSGQDK  112 (211)
Q Consensus       102 ~l~v~~a~~~~  112 (211)
                      .|+|.||.++.
T Consensus        92 ~l~V~~a~~k~  102 (111)
T 2cpi_A           92 TLKASLGTTKY  102 (111)
T ss_dssp             EEEEESCCCCS
T ss_pred             EEEEEeccccc
Confidence            99999997665

>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=99.83  E-value=7.3e-21  Score=134.14  Aligned_cols=83  Identities=16%  Similarity=0.171  Sum_probs=77.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      +..++|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++||+.|||. .|+|+.|+|.+
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~-~~~g~~l~V~~   91 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDR-PIGSRKVKLVL   91 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTC-EETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCC-eeCCeEEEEEE
Confidence            34688999999999999999999999999998888888889999999999999999999999999998 99999999999


Q ss_pred             cCCC
Q 038096          108 SGQD  111 (211)
Q Consensus       108 a~~~  111 (211)
                      +...
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8643

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

Probab=99.83  E-value=6.7e-20  Score=134.82  Aligned_cols=83  Identities=20%  Similarity=0.360  Sum_probs=78.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ..+++|||+|||+++++++|+++|++||.|..|.|+.++ +|+++|||||+|.+.++|++|++.|||. .|+|+.|+|++
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~~l~V~~  110 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGV-PLDGRPMDIQL  110 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTE-ESSSCEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCC-EECCcEEEEEE
Confidence            457899999999999999999999999999999999998 8999999999999999999999999998 99999999999


Q ss_pred             cCCCc
Q 038096          108 SGQDK  112 (211)
Q Consensus       108 a~~~~  112 (211)
                      |....
T Consensus       111 a~~~~  115 (124)
T 2kt5_A          111 VASQI  115 (124)
T ss_dssp             ECCTT
T ss_pred             eCCCC
Confidence            86643

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

Probab=99.83  E-value=3e-20  Score=135.11  Aligned_cols=83  Identities=20%  Similarity=0.289  Sum_probs=78.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+. ++. .|+|+.|+|.++.
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~-~~~g~~l~V~~a~  104 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPH-SIDGRVVEPKRAV  104 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSE-EETTEEEEEECCS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCc-EECCEEEEEEECC
Confidence            68999999999999999999999999999999999999999999999999999999999998 887 9999999999997


Q ss_pred             CCccC
Q 038096          110 QDKNA  114 (211)
Q Consensus       110 ~~~~~  114 (211)
                      +....
T Consensus       105 ~~~~~  109 (116)
T 1x4b_A          105 AREES  109 (116)
T ss_dssp             SCCCC
T ss_pred             CCccC
Confidence            76543

>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=99.83  E-value=7.9e-20  Score=131.41  Aligned_cols=83  Identities=23%  Similarity=0.417  Sum_probs=76.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|..+   +.++|||||+|.+.++|++||+.||+. .|+|+.|+|+|
T Consensus        20 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~V~~   95 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGY-DYDGYRLRVEF   95 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTC-EETTEECEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCC-EECCeEEEEEE
Confidence            45799999999999999999999999999999999764   568999999999999999999999998 99999999999


Q ss_pred             cCCCccC
Q 038096          108 SGQDKNA  114 (211)
Q Consensus       108 a~~~~~~  114 (211)
                      ++.....
T Consensus        96 a~~~~~~  102 (109)
T 1x4a_A           96 PRSGRGT  102 (109)
T ss_dssp             CCCCCCC
T ss_pred             cccCCCC
Confidence            9776543

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

Probab=99.83  E-value=3.3e-20  Score=136.32  Aligned_cols=82  Identities=22%  Similarity=0.354  Sum_probs=77.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||+++++++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|++|| .|||. .|+|+.|+|.+++
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~-~~~g~~l~V~~a~  113 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDET-VFRGRTIKVLPKR  113 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTC-EETTEECEEEESS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCC-eECCeEEEEEECC
Confidence            689999999999999999999999999999999999999999999999999999999999 79998 9999999999997


Q ss_pred             CCcc
Q 038096          110 QDKN  113 (211)
Q Consensus       110 ~~~~  113 (211)
                      ....
T Consensus       114 ~~~~  117 (124)
T 2jwn_A          114 TNMP  117 (124)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            6544

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

Probab=99.83  E-value=6.1e-20  Score=127.76  Aligned_cols=81  Identities=19%  Similarity=0.248  Sum_probs=76.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ...++|||+|||+++++++|+++|+.| .|..|.|+++ .+|+++|||||+|.+.++|++||+ |||. .|+|+.|.|.+
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~-~~~gr~i~v~~   83 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNRE-YMGGRYIEVFR   83 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSE-EETTEEEEEEE
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCc-eeCCcEEEEEE
Confidence            447999999999999999999999999 9999999999 779999999999999999999999 9998 99999999999


Q ss_pred             cCCCc
Q 038096          108 SGQDK  112 (211)
Q Consensus       108 a~~~~  112 (211)
                      +.+..
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            87653

>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=99.83  E-value=7.6e-21  Score=133.22  Aligned_cols=81  Identities=15%  Similarity=0.154  Sum_probs=75.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      +..++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++||+.||+. .|+|+.|+|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~-~~~gr~l~v~~   91 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDR-PIGSRKVKLSG   91 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCC-eECCcEEEEEe
Confidence            34689999999999999999999999999999999999899999999999999999999999999998 99999999998


Q ss_pred             cC
Q 038096          108 SG  109 (211)
Q Consensus       108 a~  109 (211)
                      +.
T Consensus        92 a~   93 (95)
T 2ek1_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            75

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

Probab=99.83  E-value=4.7e-20  Score=137.85  Aligned_cols=81  Identities=38%  Similarity=0.626  Sum_probs=76.8

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||.++++++|+++|++||.|..+.|+.++.+++++|||||+|.+.++|++|++.|||. .|+|+.|+|+
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~  138 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES-ELFGRTIRVN  138 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEE-EETTEEEEEE
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEE
Confidence            345899999999999999999999999999999999999999999999999999999999999999998 9999999999


Q ss_pred             ec
Q 038096          107 LS  108 (211)
Q Consensus       107 ~a  108 (211)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            86

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

Probab=99.83  E-value=6.1e-21  Score=128.53  Aligned_cols=76  Identities=22%  Similarity=0.364  Sum_probs=73.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ++|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++.++ . .++|+.|+|++|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~-~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-H-ELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-C-CCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-C-ccCCEEEEEEec
Confidence            579999999999999999999999999999999999999999999999999999999999999 6 899999999987

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

Probab=99.82  E-value=1.2e-20  Score=140.32  Aligned_cols=85  Identities=16%  Similarity=0.328  Sum_probs=78.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEE--EEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCC---eeeCCeE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVD--LYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGI---VTLYNRT  102 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~--v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~---~~i~gr~  102 (211)
                      ...++|||+|||+++++++|+++|++||.|..  |+|++|+.||+++|||||+|.+. +|++||+.|||.   +.|+|+.
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~   99 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKT   99 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEE
Confidence            45789999999999999999999999999977  99999999999999999999999 999999999994   3699999


Q ss_pred             EEEEecCCCcc
Q 038096          103 LRFALSGQDKN  113 (211)
Q Consensus       103 l~v~~a~~~~~  113 (211)
                      |+|+++++...
T Consensus       100 l~V~~a~~~~~  110 (131)
T 2m2b_A          100 INVEFAKGSKR  110 (131)
T ss_dssp             CCCEECCCSCC
T ss_pred             EEEEECCCCCC
Confidence            99999977544

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

Probab=99.82  E-value=3.8e-20  Score=133.41  Aligned_cols=82  Identities=18%  Similarity=0.285  Sum_probs=76.2

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||.++++++|+++|++||.|..|.|+.++  +.++|||||+|.+.++|++|++.|||. .|+|+.|+|.
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~-~~~g~~l~V~  102 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGT-VVEGRKIEVN  102 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCC-EECCEEEEEE
Confidence            3458999999999999999999999999999999999986  458999999999999999999999998 9999999999


Q ss_pred             ecCCC
Q 038096          107 LSGQD  111 (211)
Q Consensus       107 ~a~~~  111 (211)
                      +++++
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            98654

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

Probab=99.82  E-value=4.1e-20  Score=132.30  Aligned_cols=80  Identities=25%  Similarity=0.370  Sum_probs=74.3

Q ss_pred             CCCeEEEcCCCCCC------cHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCe-
Q 038096           29 SGCNVYIGNLDEKV------NERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNR-  101 (211)
Q Consensus        29 ~~~~lfVgnLp~~~------~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr-  101 (211)
                      ..++|||||||+.+      ++++|+++|++||.|..|.|+  +.+|+++|||||+|.+.++|++||+.|||. .|+|+ 
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~-~~~g~~   90 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGY-KLDKQH   90 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSE-ECSTTC
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCc-ccCCCc
Confidence            37899999999999      789999999999999999998  467999999999999999999999999998 99998 


Q ss_pred             EEEEEecCCC
Q 038096          102 TLRFALSGQD  111 (211)
Q Consensus       102 ~l~v~~a~~~  111 (211)
                      .|+|.++...
T Consensus        91 ~l~V~~a~~~  100 (105)
T 2nlw_A           91 TFRVNLFTDF  100 (105)
T ss_dssp             EEEEECSCCC
T ss_pred             eEEEEEcchH
Confidence            9999998643

>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=99.82  E-value=3.3e-21  Score=133.88  Aligned_cols=80  Identities=33%  Similarity=0.520  Sum_probs=74.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQ  110 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~  110 (211)
                      ++|||+|||.++++++|+++|++||.|.++.|++++.+|.++|||||+|.+.+ |++|+..|||. .++|+.|+|++|..
T Consensus         2 ~~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            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNT-DFMGRTIRVTEANP   79 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSS-CCSSSSCSEEEC--
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCC-EECCeEEEEEEcCC
Confidence            58999999999999999999999999999999999999999999999999999 99999999998 99999999999866


Q ss_pred             Cc
Q 038096          111 DK  112 (211)
Q Consensus       111 ~~  112 (211)
                      ..
T Consensus        80 ~~   81 (90)
T 2ki2_A           80 KK   81 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            54

>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=99.82  E-value=3.7e-20  Score=132.16  Aligned_cols=81  Identities=19%  Similarity=0.233  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCC-CCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCC-eeeCCeEEEE
Q 038096           28 NSGCNVYIGNLDE-KVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGI-VTLYNRTLRF  105 (211)
Q Consensus        28 ~~~~~lfVgnLp~-~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~-~~i~gr~l~v  105 (211)
                      .++++|||+|||+ ++++++|+++|++||.|.+|.|+++      +|||||+|.+.++|++||+.||+. ..|+|++|+|
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   86 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   86 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEE
Confidence            4589999999999 9999999999999999999999875      389999999999999999998864 2699999999


Q ss_pred             EecCCCccC
Q 038096          106 ALSGQDKNA  114 (211)
Q Consensus       106 ~~a~~~~~~  114 (211)
                      .+|+..+..
T Consensus        87 ~~a~~~~~~   95 (102)
T 1x4d_A           87 HLSQKYKRI   95 (102)
T ss_dssp             EEECCCTTS
T ss_pred             EECCCCCCC
Confidence            999765543

>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=99.82  E-value=7.5e-20  Score=132.48  Aligned_cols=82  Identities=29%  Similarity=0.421  Sum_probs=76.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee--------C
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL--------Y   99 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i--------~   99 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||+.|||. .|        .
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~~~~~~~~~  100 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGK-FIKTPPGVSAP  100 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTC-CCCCCTTSCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCC-EEcCCccccCC
Confidence            457999999999999999999999999999999999998 8999999999999999999999999998 78        5


Q ss_pred             CeEEEEEecCCC
Q 038096          100 NRTLRFALSGQD  111 (211)
Q Consensus       100 gr~l~v~~a~~~  111 (211)
                      ++.|.|.||.+.
T Consensus       101 ~~~l~v~~a~p~  112 (114)
T 1x5o_A          101 TEPLLCKFSGPS  112 (114)
T ss_dssp             SSCBEEEECCCS
T ss_pred             CCceeEEccCCC
Confidence            788999998743

>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=99.82  E-value=3.2e-20  Score=134.80  Aligned_cols=82  Identities=13%  Similarity=0.110  Sum_probs=76.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCe-EEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRV-VDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i-~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      .+.++|||+|||+++++++|+++|+.||.| ..|.|++|+ +|+++|||||+|.+.++|++||+. |+. .|+|+.|.|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~-~~~gr~i~v~   89 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRK-KLNGREAFVH   89 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSE-EETTEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCC-ccCCeEEEEE
Confidence            457899999999999999999999999999 889999998 899999999999999999999998 997 9999999999


Q ss_pred             ecCCCc
Q 038096          107 LSGQDK  112 (211)
Q Consensus       107 ~a~~~~  112 (211)
                      ++..+.
T Consensus        90 ~a~~~~   95 (114)
T 2cpy_A           90 VVTLED   95 (114)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            987554

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

Probab=99.82  E-value=1.6e-20  Score=140.55  Aligned_cols=86  Identities=28%  Similarity=0.488  Sum_probs=80.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|++||+.|||. .|+|+.|+|.|
T Consensus        45 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~-~i~g~~l~V~~  123 (135)
T 2lea_A           45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGA-VLDGRELRVQM  123 (135)
T ss_dssp             GGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTC-CSSSSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCC-EECCEEEEEEE
Confidence            34789999999999999999999999999999999999999999999999999999999999999998 89999999999


Q ss_pred             cCCCccC
Q 038096          108 SGQDKNA  114 (211)
Q Consensus       108 a~~~~~~  114 (211)
                      +++....
T Consensus       124 a~~~~~~  130 (135)
T 2lea_A          124 ARYGRPP  130 (135)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9776543

>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=99.82  E-value=7e-20  Score=141.34  Aligned_cols=86  Identities=20%  Similarity=0.347  Sum_probs=79.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..++++|||+|||+.+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|++||+.|||. .|+|+.|.|.
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~~l~V~  147 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGA-EIMGQTIQVD  147 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEE
Confidence            345788999999999999999999999999999999999999999999999999999999999999998 9999999999


Q ss_pred             ecCCCcc
Q 038096          107 LSGQDKN  113 (211)
Q Consensus       107 ~a~~~~~  113 (211)
                      |+.....
T Consensus       148 ~a~~~~~  154 (165)
T 1rk8_A          148 WCFVKGP  154 (165)
T ss_dssp             ESEECC-
T ss_pred             EecCCCC
Confidence            9876544

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

Probab=99.82  E-value=1.5e-19  Score=128.14  Aligned_cols=82  Identities=24%  Similarity=0.415  Sum_probs=74.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||+++++++|+++|++||.|   .++.+ .+++++|||||+|.+.++|++||+.||+. .|+|+.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v~   86 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKR-EIEGRAIRLE   86 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSE-EETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCC-EeCCeEEEEE
Confidence            3458999999999999999999999999977   56666 57999999999999999999999999998 9999999999


Q ss_pred             ecCCCcc
Q 038096          107 LSGQDKN  113 (211)
Q Consensus       107 ~a~~~~~  113 (211)
                      ++++...
T Consensus        87 ~a~~~~~   93 (101)
T 2fc9_A           87 LQGPRGS   93 (101)
T ss_dssp             ECSSCCC
T ss_pred             EcCCCCC
Confidence            9977644

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

Probab=99.81  E-value=1.1e-19  Score=125.41  Aligned_cols=74  Identities=19%  Similarity=0.240  Sum_probs=69.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      -+..||||||++.++|++|+++|.+||+|.++.+..      +||||||+|.+.++|++|++.||+. .++|++|+|++|
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~-~l~gr~I~V~~A   78 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNC-VLANTTIFAESP   78 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTE-EETTEEEEEECC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCC-EECCcEEEEEEC
Confidence            367899999999999999999999999999999864      6799999999999999999999998 999999999998


Q ss_pred             C
Q 038096          109 G  109 (211)
Q Consensus       109 ~  109 (211)
                      .
T Consensus        79 ~   79 (89)
T 2wbr_A           79 S   79 (89)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.81  E-value=2.9e-20  Score=151.04  Aligned_cols=82  Identities=20%  Similarity=0.287  Sum_probs=77.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCC--CeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAG--RVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G--~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..++|||+||++++++++|+++|++||  .|++|.|++|+.|+++||||||+|.+.++|++||+.||+. .|+|+.|+|.
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~-~~~Gr~l~V~  145 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKR-ELHGQNPVVT  145 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTS-CBTTBCCEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCC-eECCEEeEEE
Confidence            468899999999999999999999999  9999999999999999999999999999999999999998 9999999999


Q ss_pred             ecCCC
Q 038096          107 LSGQD  111 (211)
Q Consensus       107 ~a~~~  111 (211)
                      +|...
T Consensus       146 ~a~~~  150 (229)
T 3q2s_C          146 PVNKQ  150 (229)
T ss_dssp             ECCHH
T ss_pred             ECCCC
Confidence            98643

>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=99.81  E-value=2e-19  Score=128.20  Aligned_cols=80  Identities=19%  Similarity=0.267  Sum_probs=71.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHc--CCCeeeCCeEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF--SGIVTLYNRTLRF  105 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~l--ng~~~i~gr~l~v  105 (211)
                      .++++|||+|||+++++++|+++|++||.|.+|.|+++      ||||||+|.+.++|++|++.|  ++. .+.|++|+|
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~-~~~Gr~l~V   85 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTP-HLRNQPIYI   85 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCC-EETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCc-eECCcEEEE
Confidence            45799999999999999999999999999999999875      699999999999999999977  455 899999999


Q ss_pred             EecCCCccC
Q 038096          106 ALSGQDKNA  114 (211)
Q Consensus       106 ~~a~~~~~~  114 (211)
                      .||+.+...
T Consensus        86 ~~a~~~~~~   94 (101)
T 2cq1_A           86 QYSNHKELK   94 (101)
T ss_dssp             EECSCSSCC
T ss_pred             EEcCcccCc
Confidence            999765443

>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=99.81  E-value=1.9e-20  Score=135.77  Aligned_cols=82  Identities=24%  Similarity=0.451  Sum_probs=73.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCe----EEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRV----VDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTL  103 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i----~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l  103 (211)
                      .+.++|||+|||+++++++|+++|++||.|    ..+.+.    +++++|||||+|.+.++|++||+.|||. .|+|+.|
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~----~g~~~g~afV~f~~~~~a~~Ai~~l~g~-~~~g~~l   97 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM----TGRMRGQAFITFPNKEIAWQALHLVNGY-KLYGKIL   97 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE----CSSSCSEEEEECSSHHHHHHHHHHSTTC-BCSSCBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC----CCccceEEEEEECCHHHHHHHHHHhCCC-EeCCcEE
Confidence            457999999999999999999999999998    455544    6899999999999999999999999998 9999999


Q ss_pred             EEEecCCCccC
Q 038096          104 RFALSGQDKNA  114 (211)
Q Consensus       104 ~v~~a~~~~~~  114 (211)
                      +|.|+......
T Consensus        98 ~v~~a~~~~~~  108 (115)
T 2cpx_A           98 VIEFGKNKKQR  108 (115)
T ss_dssp             EEEECCCCSCC
T ss_pred             EEEEccCCCCC
Confidence            99999876554

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

Probab=99.81  E-value=1.4e-19  Score=128.48  Aligned_cols=79  Identities=19%  Similarity=0.118  Sum_probs=71.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCC-eeeCCeEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGI-VTLYNRTLRF  105 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~-~~i~gr~l~v  105 (211)
                      .+++++|||+|||+++++++|+++|++||.|.++.+++      .||||||+|.+.++|.+|++.|++. +.+.|++|+|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            35689999999999999999999999999999999975      3599999999999999999999886 2489999999


Q ss_pred             EecCCC
Q 038096          106 ALSGQD  111 (211)
Q Consensus       106 ~~a~~~  111 (211)
                      ++|+.+
T Consensus        92 ~~S~~k   97 (100)
T 3r27_A           92 NYSTSQ   97 (100)
T ss_dssp             EECSCS
T ss_pred             Eecccc
Confidence            999764

>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=99.81  E-value=1.1e-19  Score=129.90  Aligned_cols=81  Identities=20%  Similarity=0.228  Sum_probs=75.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEE-EEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVD-LYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~-v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ...++|||+|||+++++++|+++|++||.|.. |.|+.+ .+|+++|||||+|.+.++|++||+. ++. .|+|+.|.|.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~-~~~gr~i~v~   89 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKE-RIGHRYIEIF   89 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTC-CSSSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-Ccc-hhCCcEEEEE
Confidence            44799999999999999999999999999988 889998 7899999999999999999999998 898 9999999999


Q ss_pred             ecCCC
Q 038096          107 LSGQD  111 (211)
Q Consensus       107 ~a~~~  111 (211)
                      ++...
T Consensus        90 ~~~~~   94 (104)
T 1wg5_A           90 KSSRA   94 (104)
T ss_dssp             EECTT
T ss_pred             ECCHH
Confidence            98654

>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=99.81  E-value=2.1e-19  Score=126.55  Aligned_cols=81  Identities=20%  Similarity=0.345  Sum_probs=73.8

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeC--CeEE
Q 038096           26 NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLY--NRTL  103 (211)
Q Consensus        26 ~s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~--gr~l  103 (211)
                      ...+.++|||+|||+++++++|+++|++||.|..|.+.++      +|||||+|.+.++|++|++.||+. .|+  |+.|
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~-~~~~~g~~l   85 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGF-PLGGPDRRL   85 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTC-BCSSSSCBC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCC-EeCCCCcEE
Confidence            3456799999999999999999999999999999999764      689999999999999999999998 899  9999


Q ss_pred             EEEecCCCcc
Q 038096          104 RFALSGQDKN  113 (211)
Q Consensus       104 ~v~~a~~~~~  113 (211)
                      +|.|++++..
T Consensus        86 ~V~~a~~~~~   95 (97)
T 1why_A           86 RVDFAKSGPS   95 (97)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEECCCCCC
Confidence            9999977543

>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=99.81  E-value=1.6e-20  Score=138.32  Aligned_cols=82  Identities=20%  Similarity=0.180  Sum_probs=75.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|+.||.|..+.++.+..+|+++|||||+|.+.++|++||+ |||. .|+|+.|.|.+
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~-~~~gr~i~V~~  100 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQ-YMGNRFIQVHP  100 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSB-CSTTSCBEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCC-eECCcEEEEEE
Confidence            457999999999999999999999999999887677777789999999999999999999999 9998 99999999999


Q ss_pred             cCCC
Q 038096          108 SGQD  111 (211)
Q Consensus       108 a~~~  111 (211)
                      +..+
T Consensus       101 a~~~  104 (124)
T 1wel_A          101 ITKK  104 (124)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8654

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

Probab=99.81  E-value=9.9e-20  Score=131.90  Aligned_cols=79  Identities=16%  Similarity=0.146  Sum_probs=71.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCC-CeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAG-RVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G-~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ...++|||+|||+++++++|+++|++|| .|..+.|..    +.++|||||+|.+.++|++||+.|||. .|+|+.|+|.
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~-~l~Gr~i~V~  100 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNI-EFRGSVITVE  100 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTE-EETTEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCC-EECCeEEEEE
Confidence            3478999999999999999999999999 899999864    357899999999999999999999998 9999999999


Q ss_pred             ecCCC
Q 038096          107 LSGQD  111 (211)
Q Consensus       107 ~a~~~  111 (211)
                      ++...
T Consensus       101 ~a~~~  105 (111)
T 2jvr_A          101 RDDNP  105 (111)
T ss_dssp             ESCC-
T ss_pred             ECCCC
Confidence            98643

>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=99.81  E-value=2.8e-19  Score=128.57  Aligned_cols=80  Identities=19%  Similarity=0.450  Sum_probs=74.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ....++|||+|||.++++++|+++|++||.|..|.|+.+      +|||||+|.+.++|++||+.|+|. .|+|+.|+|.
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~   94 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGT-TIEGHVVKCY   94 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCC-EECCcEEEEE
Confidence            355899999999999999999999999999999999876      699999999999999999999998 9999999999


Q ss_pred             ecCCCcc
Q 038096          107 LSGQDKN  113 (211)
Q Consensus       107 ~a~~~~~  113 (211)
                      |+++...
T Consensus        95 ~a~~~~~  101 (109)
T 1x4g_A           95 WGKESPD  101 (109)
T ss_dssp             CCCCCCS
T ss_pred             ecCCCCC
Confidence            9977654

>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=99.81  E-value=8.4e-20  Score=133.70  Aligned_cols=81  Identities=19%  Similarity=0.306  Sum_probs=72.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCC-eeeCCeEEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGI-VTLYNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~-~~i~gr~l~v~  106 (211)
                      .++++|||+|||++++|++|+++|++||.|.+|.|+++      ||||||+|.+.++|++|++.+++. ..|+|++|+|.
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~  102 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ  102 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEE
Confidence            45799999999999999999999999999999999875      699999999999999999988741 27999999999


Q ss_pred             ecCCCccC
Q 038096          107 LSGQDKNA  114 (211)
Q Consensus       107 ~a~~~~~~  114 (211)
                      +|+.+...
T Consensus       103 ~a~~k~~~  110 (119)
T 2ad9_A          103 FSNHKELK  110 (119)
T ss_dssp             ECSSSSCC
T ss_pred             EccCCCCC
Confidence            99765543

>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=99.81  E-value=3.5e-19  Score=128.00  Aligned_cols=78  Identities=23%  Similarity=0.280  Sum_probs=72.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCC-----eEE
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYN-----RTL  103 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~g-----r~l  103 (211)
                      ..++|||+|||+++++++|+++|++||.|..|.|+.+       |||||+|.+.++|++||+.|||. .|+|     +.|
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~-~~~g~~~~~~~i   85 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNT-KFRSHEGETAYI   85 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSE-EEECTTSCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcC-CccCCcCcceEE
Confidence            4789999999999999999999999999999999886       89999999999999999999998 9999     999


Q ss_pred             EEEecCCCccC
Q 038096          104 RFALSGQDKNA  114 (211)
Q Consensus       104 ~v~~a~~~~~~  114 (211)
                      +|.+|.+....
T Consensus        86 ~V~~a~~~~~~   96 (108)
T 1x4c_A           86 RVKVDGPRSPS   96 (108)
T ss_dssp             EEEESSCCSCC
T ss_pred             EEEeCCCCCCC
Confidence            99999875543

>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=99.81  E-value=2.4e-20  Score=125.10  Aligned_cols=75  Identities=19%  Similarity=0.353  Sum_probs=71.4

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        32 ~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++. ++. .++|+.|.|++|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~-~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYH-NVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSC-CBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCC-eECCEEEEEEEC
Confidence            589999999999999999999999999999999999999999999999999999999996 776 899999999875

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

Probab=99.81  E-value=1.1e-19  Score=134.70  Aligned_cols=82  Identities=18%  Similarity=0.352  Sum_probs=74.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHH----HHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLY----DILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTL  103 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~----~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l  103 (211)
                      .+.++||||||++.+++++|+    ++|++||.|.+|.+..   +++++|||||+|.+.++|++|++.|||. .|.|+.|
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~-~l~gr~l  102 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGY-PFQGNPL  102 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTC-CCTTSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCC-EeCCCEE
Confidence            457899999999999999876    6999999999998864   5889999999999999999999999998 9999999


Q ss_pred             EEEecCCCcc
Q 038096          104 RFALSGQDKN  113 (211)
Q Consensus       104 ~v~~a~~~~~  113 (211)
                      +|.||+.+..
T Consensus       103 ~V~~a~~~~~  112 (127)
T 2a3j_A          103 VITFSETPQS  112 (127)
T ss_dssp             EEEECCCCCH
T ss_pred             EEEEccCcch
Confidence            9999976543

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

Probab=99.80  E-value=3.3e-20  Score=126.54  Aligned_cols=73  Identities=26%  Similarity=0.431  Sum_probs=67.9

Q ss_pred             CCeEEEcCCCCCC------cHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCe-E
Q 038096           30 GCNVYIGNLDEKV------NERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNR-T  102 (211)
Q Consensus        30 ~~~lfVgnLp~~~------~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr-~  102 (211)
                      +++|||+|||..+      ++++|+++|++||.|.++.|+  +.+|+++|||||+|.+.++|++|++.|||. .++|+ +
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~-~~~g~~~   77 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGY-KLDKQHT   77 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSC-CCSSSSC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCc-ccCCcee
Confidence            4789999999999      789999999999999999988  467999999999999999999999999998 99999 8


Q ss_pred             EEE
Q 038096          103 LRF  105 (211)
Q Consensus       103 l~v  105 (211)
                      |+|
T Consensus        78 l~V   80 (81)
T 2krb_A           78 FRV   80 (81)
T ss_dssp             CCC
T ss_pred             EEe
Confidence            876

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

Probab=99.80  E-value=2.1e-19  Score=127.52  Aligned_cols=84  Identities=21%  Similarity=0.307  Sum_probs=76.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||+++++++|+++|+.|+   .+.++.++.++.++|||||+|.+.++|++||+.|||. .|+|+.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~V~   87 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDG-EIDGNKVTLD   87 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCC-eECCeEEEEE
Confidence            35589999999999999999999999874   6788888888999999999999999999999999998 9999999999


Q ss_pred             ecCCCccC
Q 038096          107 LSGQDKNA  114 (211)
Q Consensus       107 ~a~~~~~~  114 (211)
                      |++++...
T Consensus        88 ~a~~~~~~   95 (102)
T 2fc8_A           88 WAKPKGEG   95 (102)
T ss_dssp             ECCCCCSS
T ss_pred             EecCCCCC
Confidence            99876553

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

Probab=99.80  E-value=7.5e-20  Score=133.78  Aligned_cols=81  Identities=22%  Similarity=0.196  Sum_probs=75.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCC---eEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGR---VVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR  104 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~---i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~  104 (211)
                      .+.++|||+|||+++++++|+++|+.||.   |..|.|++++. |+++|||||+|.+.++|++||+ +|+. .|+|+.|+
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~-~~~gr~i~   91 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRE-SMGHRYIE   91 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTE-EETTEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCC-eECCeEEE
Confidence            34789999999999999999999999999   89999999987 9999999999999999999999 8998 99999999


Q ss_pred             EEecCCC
Q 038096          105 FALSGQD  111 (211)
Q Consensus       105 v~~a~~~  111 (211)
                      |.++..+
T Consensus        92 V~~a~~~   98 (118)
T 2db1_A           92 VFKSHRT   98 (118)
T ss_dssp             EEEECHH
T ss_pred             EEECCHH
Confidence            9998644

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

Probab=99.80  E-value=9.1e-21  Score=134.45  Aligned_cols=83  Identities=19%  Similarity=0.312  Sum_probs=76.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|.. .++.+..+|.++|||||+|.+.++|++||+ |||. .|+|+.|+|.+
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~-~~~g~~l~V~~   91 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGL-KVFGNEIKLEK   91 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGC-CBTTBCCEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCc-EECCcEEEEEE
Confidence            35789999999999999999999999999988 777888889999999999999999999999 9998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      +.+...
T Consensus        92 a~~~~~   97 (101)
T 1fj7_A           92 PKGRDG   97 (101)
T ss_dssp             CSCCCC
T ss_pred             cCCCCC
Confidence            976544

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

Probab=99.80  E-value=3.4e-19  Score=123.74  Aligned_cols=78  Identities=23%  Similarity=0.356  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|.        +|||||+|.+.++|++|++.||+. .++|+.|+|++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v~~   76 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHY-KLHGVNINVEA   76 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTC-BCSSCBCEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCC-ccCCcEEEEEE
Confidence            457999999999999999999999999999999987        589999999999999999999998 99999999999


Q ss_pred             cCCCccC
Q 038096          108 SGQDKNA  114 (211)
Q Consensus       108 a~~~~~~  114 (211)
                      +......
T Consensus        77 a~~~~~~   83 (90)
T 2dnq_A           77 SKNKSKA   83 (90)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            9776543

>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=99.80  E-value=8e-20  Score=130.36  Aligned_cols=81  Identities=17%  Similarity=0.208  Sum_probs=74.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ...++|||+|||+++++++|+++|+.||. ++|.|++|+ +++++|||||+|.+.++|++||+ +|+. .|+|+.|+|.+
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~-~~~gr~i~V~~   88 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKA-NMQHRYVELFL   88 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSC-CSSSSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCC-eECCcEEEEEE
Confidence            45789999999999999999999999995 499999998 89999999999999999999995 6998 99999999999


Q ss_pred             cCCCc
Q 038096          108 SGQDK  112 (211)
Q Consensus       108 a~~~~  112 (211)
                      +....
T Consensus        89 ~~~~~   93 (102)
T 1wez_A           89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            86544

>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=99.80  E-value=2.6e-19  Score=128.19  Aligned_cols=81  Identities=20%  Similarity=0.192  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCC-eeeCCeEEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGI-VTLYNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~-~~i~gr~l~v~  106 (211)
                      .++++|||+|||+++++++|+++|++||.|.+|.|+++      ||||||+|.+.++|++|++.|++. +.|+|++|+|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            45799999999999999999999999999999998764      699999999999999999988654 25999999999


Q ss_pred             ecCCCccC
Q 038096          107 LSGQDKNA  114 (211)
Q Consensus       107 ~a~~~~~~  114 (211)
                      |++.+...
T Consensus        87 ~a~~~~~~   94 (104)
T 1wex_A           87 YSTSKRIT   94 (104)
T ss_dssp             ECSSSSCC
T ss_pred             EccCcccc
Confidence            99765543

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

Probab=99.80  E-value=1.5e-19  Score=128.20  Aligned_cols=77  Identities=22%  Similarity=0.354  Sum_probs=71.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ....++|||+|||.++++++|+++|++||.|.++.|.      +++|||||+|.+.++|++|++.|||. .++|+.|+|.
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~~l~V~   96 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANF-PFQGRNLRTG   96 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTC-EETTEECCCC
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCC-eECCeEEEEE
Confidence            4457999999999999999999999999999999986      45799999999999999999999998 9999999999


Q ss_pred             ecCC
Q 038096          107 LSGQ  110 (211)
Q Consensus       107 ~a~~  110 (211)
                      |+++
T Consensus        97 ~a~~  100 (101)
T 2la4_A           97 WGKE  100 (101)
T ss_dssp             BCCC
T ss_pred             eccC
Confidence            9865

>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=99.80  E-value=8.3e-20  Score=136.91  Aligned_cols=80  Identities=20%  Similarity=0.167  Sum_probs=75.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCC---eEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGR---VVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR  104 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~---i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~  104 (211)
                      .+.++|||+|||+++++++|+++|+.||.   |..|.|++|+. |+++|||||+|.+.++|++||+ +|+. .|+|+.|+
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~-~l~gr~i~  118 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRE-SMGHRYIE  118 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEE-ESSSSEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCC-EECCEEEE
Confidence            45789999999999999999999999999   88999999988 9999999999999999999999 9998 99999999


Q ss_pred             EEecCC
Q 038096          105 FALSGQ  110 (211)
Q Consensus       105 v~~a~~  110 (211)
                      |.++..
T Consensus       119 V~~a~~  124 (136)
T 2hgl_A          119 VFKSHR  124 (136)
T ss_dssp             EEECCH
T ss_pred             EEECCh
Confidence            999854

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

Probab=99.80  E-value=3.4e-19  Score=142.65  Aligned_cols=84  Identities=23%  Similarity=0.424  Sum_probs=78.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||||||++++|++|+++|++||.|.+|+|++|+.|++++|||||+|.+.++|++||+.+++. .+.|+.|++.+
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~-~~~g~~i~~~~   91 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFD-VIKGKPVRIMW   91 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhh-hcCCccccccc
Confidence            45789999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cCCCc
Q 038096          108 SGQDK  112 (211)
Q Consensus       108 a~~~~  112 (211)
                      +....
T Consensus        92 ~~~~~   96 (213)
T 4f02_A           92 SQRDP   96 (213)
T ss_dssp             CCCCT
T ss_pred             ccccc
Confidence            86543

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

Probab=99.80  E-value=1.8e-19  Score=126.93  Aligned_cols=80  Identities=29%  Similarity=0.441  Sum_probs=72.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ...++|||+|||+++++++|+++|++||.|. +.++.    +.++|||||+|.+.++|++|++.|||. .|+|+.|+|.+
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~V~~   90 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGL-RLGTDTLRVAL   90 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTC-CSSSSCCEEEE
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCC-EECCcEEEEEE
Confidence            4478999999999999999999999999996 66664    478899999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      ++++..
T Consensus        91 a~~~~~   96 (97)
T 2e5j_A           91 ARQQRD   96 (97)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            977543

>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=99.80  E-value=1.6e-19  Score=126.91  Aligned_cols=82  Identities=26%  Similarity=0.534  Sum_probs=75.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHH----HHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLY----DILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTL  103 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~----~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l  103 (211)
                      .++++|||+|||+++++++|+    ++|++||.|..|.+..   +|.++|||||+|.+.++|++|++.|||. .++|+.|
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l   81 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGF-PFYDKPM   81 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTC-EETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCC-EECCcEE
Confidence            458999999999999999999    9999999999999874   4788999999999999999999999998 9999999


Q ss_pred             EEEecCCCcc
Q 038096          104 RFALSGQDKN  113 (211)
Q Consensus       104 ~v~~a~~~~~  113 (211)
                      +|.|+.++..
T Consensus        82 ~v~~a~~~~~   91 (97)
T 1nu4_A           82 RIQYAKTDSD   91 (97)
T ss_dssp             EEEECSSCCT
T ss_pred             EEEEccCCCc
Confidence            9999977543

>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=99.79  E-value=7.8e-19  Score=123.95  Aligned_cols=76  Identities=22%  Similarity=0.419  Sum_probs=70.7

Q ss_pred             CCCCCeEEEcCCCC-CCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEE
Q 038096           27 SNSGCNVYIGNLDE-KVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRF  105 (211)
Q Consensus        27 s~~~~~lfVgnLp~-~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v  105 (211)
                      .+++++|||+|||+ ++++++|+++|++||.|..+.|.        +|||||+|.+.++|++|++.|||. .++|+.|+|
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~~l~V   89 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQE-MNFGKKLIL   89 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTS-EETTEECEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCC-EECCEEEEE
Confidence            35689999999998 99999999999999999999983        699999999999999999999998 999999999


Q ss_pred             EecCCC
Q 038096          106 ALSGQD  111 (211)
Q Consensus       106 ~~a~~~  111 (211)
                      ++++..
T Consensus        90 ~~a~~~   95 (97)
T 2xnq_A           90 EVSSSN   95 (97)
T ss_dssp             EECCCC
T ss_pred             EecCCC
Confidence            998654

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

Probab=99.79  E-value=1.3e-18  Score=121.26  Aligned_cols=79  Identities=19%  Similarity=0.291  Sum_probs=72.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|++        +||||+|.+.++|++|++.|||. .|+|+.|+|.
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~V~   77 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNT-EFQGKRMHVQ   77 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTE-EETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCC-eeCCcEEEEE
Confidence            34579999999999999999999999999999999974        59999999999999999999998 9999999999


Q ss_pred             ecCCCccC
Q 038096          107 LSGQDKNA  114 (211)
Q Consensus       107 ~a~~~~~~  114 (211)
                      ++.+....
T Consensus        78 ~a~~~~~~   85 (92)
T 2dgt_A           78 LSTSRLRT   85 (92)
T ss_dssp             ESSCCCSC
T ss_pred             EccCCCCC
Confidence            99766543

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

Probab=99.79  E-value=5.2e-19  Score=127.37  Aligned_cols=77  Identities=27%  Similarity=0.369  Sum_probs=71.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|.        +|||||+|.+.++|++|++.|||. .++|+.|.|.+
T Consensus        29 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~-~~~g~~l~V~~   99 (108)
T 2jvo_A           29 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGK-SFANQPLEVVY   99 (108)
T ss_dssp             CSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTC-EETTEECEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCC-EECCeEEEEEE
Confidence            458999999999999999999999999999999987        599999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      ++....
T Consensus       100 a~~~~~  105 (108)
T 2jvo_A          100 SKLPAK  105 (108)
T ss_dssp             CSCCC-
T ss_pred             ecCCCC
Confidence            977644

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

Probab=99.79  E-value=4.7e-19  Score=127.93  Aligned_cols=77  Identities=14%  Similarity=0.145  Sum_probs=72.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||+++++++|+++|+.| .|.+|.|+.|+. |+++|||||+|.+.++|++|| .+|+. .|+|+.|.|..+.
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~-~~~gr~i~V~~a~   91 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRM-LMIQRYVEVSPAT   91 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTE-EETTEEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCC-eECCeEEEEEECC
Confidence            5799999999999999999999999 899999999986 999999999999999999999 68998 9999999998875


Q ss_pred             C
Q 038096          110 Q  110 (211)
Q Consensus       110 ~  110 (211)
                      .
T Consensus        92 ~   92 (109)
T 2dnn_A           92 E   92 (109)
T ss_dssp             H
T ss_pred             c
Confidence            4

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

Probab=99.66  E-value=7e-21  Score=138.52  Aligned_cols=87  Identities=21%  Similarity=0.346  Sum_probs=80.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEE--------EEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeC
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVD--------LYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLY   99 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~--------v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~   99 (211)
                      .+.++|||+|||+++++++|+++|++||.|..        |.|+.++.++.++|||||+|.+.++|++||+.|||. .|+
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~   83 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK-EFS   83 (116)
Confidence            45789999999999999999999999999998        999999999999999999999999999999999998 999


Q ss_pred             CeEEEEEecCCCccCC
Q 038096          100 NRTLRFALSGQDKNAQ  115 (211)
Q Consensus       100 gr~l~v~~a~~~~~~~  115 (211)
                      |+.|+|.++.++....
T Consensus        84 g~~l~V~~a~~~~~~~   99 (116)
T 2lcw_A           84 GNPIKVSFATRRADFN   99 (116)
Confidence            9999999997765543

>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=99.79  E-value=1.9e-18  Score=122.98  Aligned_cols=79  Identities=16%  Similarity=0.300  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+        +|||||+|.+.++|++||+.||+. .|+|+.|+|.|
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~   79 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGK-DLEGENIEIVF   79 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTE-EETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCC-ccCCCEEEEEE
Confidence            347899999999999999999999999999999986        369999999999999999999998 99999999999


Q ss_pred             cCCCccCC
Q 038096          108 SGQDKNAQ  115 (211)
Q Consensus       108 a~~~~~~~  115 (211)
                      +.+.....
T Consensus        80 a~~~~~~~   87 (103)
T 2dgu_A           80 AKPPDQKR   87 (103)
T ss_dssp             CCCCCCCC
T ss_pred             cCCCcccc
Confidence            97765543

>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=99.79  E-value=8.1e-20  Score=131.20  Aligned_cols=81  Identities=12%  Similarity=0.084  Sum_probs=75.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCC---eEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGR---VVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR  104 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~---i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~  104 (211)
                      .+.++|||+|||+++++++|+++|+.||.   |..|.|++|+. |+++|||||+|.+.++|++||+ +++. .|+|+.|+
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~-~~~gr~i~   85 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRM-YMGQRYVE   85 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTC-CSSSSCCC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcc-eeCCeEEE
Confidence            45799999999999999999999999998   89999999988 9999999999999999999999 8998 89999999


Q ss_pred             EEecCCC
Q 038096          105 FALSGQD  111 (211)
Q Consensus       105 v~~a~~~  111 (211)
                      |.++.+.
T Consensus        86 V~~a~~~   92 (107)
T 2lmi_A           86 VYEINNE   92 (107)
T ss_dssp             CEECCHH
T ss_pred             EEECCHH
Confidence            9998653

>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=99.79  E-value=5.8e-19  Score=127.94  Aligned_cols=82  Identities=24%  Similarity=0.362  Sum_probs=75.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ..+++|||+|||+++++++|+++|+.||.|..|.|+.+   +.++|||||+|.+.++|++|++.|||. .++|+.|.|.|
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v~~   81 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGF-NVSNRYLVVLY   81 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTC-BSSSCBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCC-EECCeEEEEEE
Confidence            44799999999999999999999999999999999876   456999999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      +.+...
T Consensus        82 a~~~~~   87 (115)
T 3lqv_A           82 YNANRA   87 (115)
T ss_dssp             CCHHHH
T ss_pred             ecCChh
Confidence            975443

>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=99.79  E-value=7.7e-19  Score=120.43  Aligned_cols=75  Identities=16%  Similarity=0.328  Sum_probs=70.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHc-CCCeeeCCeEEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF-SGIVTLYNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~l-ng~~~i~gr~l~v~  106 (211)
                      ...++|||+|||.++++++|+++|++||.|..|.++++      +|||||+|.+.++|++|++.| +|. .++|+.|+|+
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~-~~~g~~l~v~   82 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKL-IVNGRRLNVK   82 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTC-EETTEECCEE
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCe-eECCCEEEEE
Confidence            45789999999999999999999999999999999864      699999999999999999988 887 9999999999


Q ss_pred             ecC
Q 038096          107 LSG  109 (211)
Q Consensus       107 ~a~  109 (211)
                      ||+
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            974

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

Probab=99.79  E-value=1.2e-18  Score=120.89  Aligned_cols=78  Identities=22%  Similarity=0.425  Sum_probs=71.9

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|++        +||||+|.+.++|++|++.|||. .++|+.|+|.
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~   76 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGK-EVKGKRINVE   76 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCC-EECCcEEEEE
Confidence            34589999999999999999999999999999999974        59999999999999999999998 9999999999


Q ss_pred             ecCCCcc
Q 038096          107 LSGQDKN  113 (211)
Q Consensus       107 ~a~~~~~  113 (211)
                      ++.+...
T Consensus        77 ~a~~~~~   83 (90)
T 2dnp_A           77 LSTKGQK   83 (90)
T ss_dssp             ESCCCCC
T ss_pred             ECCCCCC
Confidence            9976644

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

Probab=99.79  E-value=3.7e-19  Score=126.07  Aligned_cols=78  Identities=28%  Similarity=0.453  Sum_probs=72.8

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQ  110 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~  110 (211)
                      ++|||+|||+++++++|+++|++||.|..|.|+.+     ++|||||+|.+.++|++|++.|||. .++|+.|+|.++..
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~V~~a~~   74 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGK-VICGSRVRVELSTG   74 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHS-CSSSCCCEEEESSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCC-eECCcEEEEEEccC
Confidence            58999999999999999999999999999999886     6899999999999999999999998 99999999999977


Q ss_pred             CccC
Q 038096          111 DKNA  114 (211)
Q Consensus       111 ~~~~  114 (211)
                      ....
T Consensus        75 ~~~~   78 (101)
T 2hvz_A           75 MPRR   78 (101)
T ss_dssp             CCCS
T ss_pred             CCCc
Confidence            6543

>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=99.79  E-value=3.1e-19  Score=129.34  Aligned_cols=82  Identities=18%  Similarity=0.235  Sum_probs=72.0

Q ss_pred             CCCCCeEEEcCCCCC-CcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCC-eeeCCeEEE
Q 038096           27 SNSGCNVYIGNLDEK-VNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGI-VTLYNRTLR  104 (211)
Q Consensus        27 s~~~~~lfVgnLp~~-~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~-~~i~gr~l~  104 (211)
                      ..++++|||+|||++ +++++|+++|++||.|.+|.|++      +||||||+|.+.++|++||+.|++. ..|+|++|+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            455899999999998 99999999999999999999964      4699999999999999999988642 269999999


Q ss_pred             EEecCCCccC
Q 038096          105 FALSGQDKNA  114 (211)
Q Consensus       105 v~~a~~~~~~  114 (211)
                      |.+|......
T Consensus        96 V~~a~~~~~~  105 (112)
T 1x4f_A           96 VDLSEKYKKL  105 (112)
T ss_dssp             EEEECSCSSS
T ss_pred             EEECcccccc
Confidence            9999766544

>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=99.78  E-value=5.6e-19  Score=124.79  Aligned_cols=80  Identities=20%  Similarity=0.465  Sum_probs=73.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..|.|.++      +|||||+|.+.++|++|++.|||. .|+|+.|+|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~-~~~g~~l~v~~   85 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNM-PLRGKQLRVRF   85 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTC-CBTTBCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCC-EeCCceEEEEE
Confidence            45789999999999999999999999999999999764      699999999999999999999998 89999999999


Q ss_pred             cCCCccC
Q 038096          108 SGQDKNA  114 (211)
Q Consensus       108 a~~~~~~  114 (211)
                      +.+....
T Consensus        86 a~~~~~~   92 (99)
T 2cpj_A           86 ACHSASL   92 (99)
T ss_dssp             SSCCSCC
T ss_pred             cCCCCCC
Confidence            9776543

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

Probab=99.78  E-value=2.1e-19  Score=127.58  Aligned_cols=80  Identities=20%  Similarity=0.387  Sum_probs=74.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ..++|||+|||+++++++|+++|++||.|..|.|+.++ +|.++|||||+|.+.++|++|++  ++. .++|+.|.|.++
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~-~~~g~~l~v~~a   83 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQI-NFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCC-EETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCC-eECCEEEEEEEC
Confidence            36899999999999999999999999999999999998 89999999999999999999999  887 999999999998


Q ss_pred             CCCc
Q 038096          109 GQDK  112 (211)
Q Consensus       109 ~~~~  112 (211)
                      ....
T Consensus        84 ~~~~   87 (102)
T 2xs2_A           84 IRKQ   87 (102)
T ss_dssp             EECC
T ss_pred             CcCc
Confidence            6543

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

Probab=99.78  E-value=2.7e-19  Score=125.57  Aligned_cols=80  Identities=19%  Similarity=0.311  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..+     ..++.++|||||+|.+.++|++|++.|+|. .|+|+.|+|.+
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~   87 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGA-EIDGRSVSLYY   87 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEE-EETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCC-EECCeEEEEEE
Confidence            347999999999999999999999999988766     346899999999999999999999999997 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      +.+...
T Consensus        88 a~~~~~   93 (96)
T 1fjc_A           88 TGEKGG   93 (96)
T ss_dssp             CSSSCC
T ss_pred             cCCCCC
Confidence            976543

>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=99.78  E-value=1.5e-18  Score=132.23  Aligned_cols=82  Identities=20%  Similarity=0.368  Sum_probs=78.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      +++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|++|++.|+|. .++|+.|.|.++.
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~-~~~g~~l~v~~~~   80 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGL-RLQTKTIKVSYAR   80 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEECC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCC-ccCCceEEEEecC
Confidence            689999999999999999999999999999999999989999999999999999999999999998 9999999999987


Q ss_pred             CCc
Q 038096          110 QDK  112 (211)
Q Consensus       110 ~~~  112 (211)
                      +..
T Consensus        81 ~~~   83 (167)
T 1fxl_A           81 PSS   83 (167)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            554

>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=99.78  E-value=1.1e-18  Score=133.44  Aligned_cols=83  Identities=30%  Similarity=0.482  Sum_probs=78.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ++++|||+|||+++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|++|++.|+|. .++|+.|.|.|+
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~-~~~g~~l~v~~~   80 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGI-TVRNKRLKVSYA   80 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEEC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCC-EeCCcEEEEEec
Confidence            3789999999999999999999999999999999999989999999999999999999999999998 999999999998


Q ss_pred             CCCc
Q 038096          109 GQDK  112 (211)
Q Consensus       109 ~~~~  112 (211)
                      .+..
T Consensus        81 ~~~~   84 (168)
T 1b7f_A           81 RPGG   84 (168)
T ss_dssp             CCCS
T ss_pred             CCCc
Confidence            7654

>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=99.78  E-value=1.6e-18  Score=124.79  Aligned_cols=76  Identities=32%  Similarity=0.482  Sum_probs=70.6

Q ss_pred             CCCeEEEcCCCCC-CcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           29 SGCNVYIGNLDEK-VNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        29 ~~~~lfVgnLp~~-~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ..++|||+|||++ +++++|+++|++||.|..|.|        ++|||||+|.+.++|++||+.|||. .|+|+.|+|.+
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~V~~   96 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGR-VLAGQTLDINM   96 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTC-EETTEECCEEE
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCC-EECCeEEEEEE
Confidence            4689999999999 999999999999999999988        4699999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      +...+.
T Consensus        97 a~~~~~  102 (110)
T 1wf1_A           97 AGEPKP  102 (110)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            975544

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

Probab=99.78  E-value=5e-19  Score=138.29  Aligned_cols=83  Identities=20%  Similarity=0.360  Sum_probs=78.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ..+++|||+|||+++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||+.|||. .|+|+.|+|.|
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~-~l~Gr~l~V~~  163 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGV-PLDGRPMDIQL  163 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTC-BCSSSBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCC-EECCEEEEEEE
Confidence            447899999999999999999999999999999999998 8999999999999999999999999998 99999999999


Q ss_pred             cCCCc
Q 038096          108 SGQDK  112 (211)
Q Consensus       108 a~~~~  112 (211)
                      |....
T Consensus       164 a~~~~  168 (177)
T 2f3j_A          164 VASQI  168 (177)
T ss_dssp             ESSGG
T ss_pred             ecCCC
Confidence            86543

>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=99.78  E-value=7.9e-19  Score=122.53  Aligned_cols=78  Identities=24%  Similarity=0.362  Sum_probs=69.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCC-eEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCC-CeeeCCeEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGR-VVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSG-IVTLYNRTLRF  105 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~-i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng-~~~i~gr~l~v  105 (211)
                      ...++|||+|||+++++++|+++|++||. |..+.+.       ++|||||+|.+.++|++|++.||| . .|+|+.|+|
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~-~~~g~~l~v   77 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKV-ELHGKIMEV   77 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTC-EETTEECEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCe-eECCEEEEE
Confidence            45789999999999999999999999999 5555552       469999999999999999999999 7 999999999


Q ss_pred             EecCCCcc
Q 038096          106 ALSGQDKN  113 (211)
Q Consensus       106 ~~a~~~~~  113 (211)
                      .|+.++..
T Consensus        78 ~~a~~~~~   85 (93)
T 2cqh_A           78 DYSVSKKL   85 (93)
T ss_dssp             EECCCCCC
T ss_pred             EEccCccc
Confidence            99976644

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

Probab=99.78  E-value=1.8e-18  Score=131.66  Aligned_cols=81  Identities=21%  Similarity=0.416  Sum_probs=77.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||.++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++.|||. .++|+.|+|.|
T Consensus        85 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~i~v~~  163 (166)
T 3md3_A           85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQ-DLNGRPLRINW  163 (166)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTC-EETTEECEEEE
T ss_pred             CCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCC-ccCCcEEEEEe
Confidence            45789999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cC
Q 038096          108 SG  109 (211)
Q Consensus       108 a~  109 (211)
                      |+
T Consensus       164 a~  165 (166)
T 3md3_A          164 AA  165 (166)
T ss_dssp             SC
T ss_pred             cC
Confidence            85

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

Probab=99.77  E-value=5e-18  Score=119.84  Aligned_cols=77  Identities=21%  Similarity=0.257  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcC--CCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQA--GRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRF  105 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~--G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v  105 (211)
                      .+.++|||+|||+++++++|+++|++|  |.|..|.+.        +|||||+|.+.++|++||+.|||. .|+|+.|+|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v   83 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGK-VLDGSPIEV   83 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSE-EETTEEEEE
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCC-EeCCcEEEE
Confidence            447899999999999999999999999  999999875        489999999999999999999998 999999999


Q ss_pred             EecCCCcc
Q 038096          106 ALSGQDKN  113 (211)
Q Consensus       106 ~~a~~~~~  113 (211)
                      .++++...
T Consensus        84 ~~a~~~~~   91 (99)
T 2cpd_A           84 TLAKPVDK   91 (99)
T ss_dssp             ECCCCCCC
T ss_pred             EECCCCCC
Confidence            99977654

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

Probab=99.77  E-value=6.8e-19  Score=129.40  Aligned_cols=80  Identities=13%  Similarity=0.217  Sum_probs=72.3

Q ss_pred             CeEEEcCC----CCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCC----HHH----HHHHHH--HcCCCe
Q 038096           31 CNVYIGNL----DEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYES----EEI----GHYAIK--LFSGIV   96 (211)
Q Consensus        31 ~~lfVgnL----p~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~----~~~----A~~Ai~--~lng~~   96 (211)
                      ++||||||    ++.+++++|+++|++||+|.+|.++.|+.||.++|||||+|.+    .++    |.+|+.  .+||. 
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~-   81 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGC-   81 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCE-
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCC-
Confidence            68999999    9999999999999999999999999999999999999999996    322    888988  78998 


Q ss_pred             eeCCeEEEEEecCCC
Q 038096           97 TLYNRTLRFALSGQD  111 (211)
Q Consensus        97 ~i~gr~l~v~~a~~~  111 (211)
                      .|+|++|+|.+.+..
T Consensus        82 ~I~Gr~irV~ln~~g   96 (136)
T 2j8a_A           82 FIMGFKFEVILNKHS   96 (136)
T ss_dssp             EETTEEEEEEECCTT
T ss_pred             eecCcEEEEEECccc
Confidence            999999999986543

>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=99.77  E-value=1.3e-18  Score=132.06  Aligned_cols=79  Identities=33%  Similarity=0.545  Sum_probs=73.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ...++|||+|||+++++++|+++|++||.|.+|.|+++     ++|||||+|.+.++|++||+.|||. .|+|+.|+|.|
T Consensus        71 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~  144 (150)
T 2i2y_A           71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGR-TLCGCRVRVEL  144 (150)
T ss_dssp             TTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSS-CSSSSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCC-EECCeEEEEEE
Confidence            45799999999999999999999999999999999876     5799999999999999999999998 89999999999


Q ss_pred             cCCCc
Q 038096          108 SGQDK  112 (211)
Q Consensus       108 a~~~~  112 (211)
                      +.+.+
T Consensus       145 a~~~~  149 (150)
T 2i2y_A          145 SNGEK  149 (150)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            97653

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

Probab=99.77  E-value=6.8e-18  Score=118.78  Aligned_cols=77  Identities=21%  Similarity=0.379  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+||  ++++++|+++|++||.|..|.|.      .++|||||+|.+.++|++||+.|||. .|+|+.|+|.|
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~-~~~g~~l~v~~   83 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGT-QVESVQLKVNI   83 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTE-EETTEEEEEEC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCC-eECCeEEEEEE
Confidence            45799999996  89999999999999999999984      56799999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      +.+...
T Consensus        84 a~~~~~   89 (97)
T 1x5p_A           84 ARKQPM   89 (97)
T ss_dssp             CSSCCC
T ss_pred             CCCCCC
Confidence            976544

>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=99.76  E-value=4e-18  Score=123.72  Aligned_cols=79  Identities=23%  Similarity=0.338  Sum_probs=70.6

Q ss_pred             CCCCCCeEEE--cCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee-----
Q 038096           26 NSNSGCNVYI--GNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL-----   98 (211)
Q Consensus        26 ~s~~~~~lfV--gnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i-----   98 (211)
                      ...++++|||  |||++++++++|+++|++||.|.+|.|+.+      ||||||+|.+.++|++|++.|||. .+     
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~-~~~~~lg   93 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGK-EVVDDLG   93 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTC-EEECTTS
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCC-EEccccC
Confidence            3456889999  889999999999999999999999988653      699999999999999999999998 77     


Q ss_pred             CCeEEEEEecCCC
Q 038096           99 YNRTLRFALSGQD  111 (211)
Q Consensus        99 ~gr~l~v~~a~~~  111 (211)
                      .|+.|.|.++..-
T Consensus        94 ~g~~l~v~~a~~~  106 (114)
T 2cq2_A           94 QKITLYLNFVEKV  106 (114)
T ss_dssp             CEEECEEEEESCC
T ss_pred             CCcEEEEEecccC
Confidence            6889999998643

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

Probab=99.76  E-value=5e-19  Score=130.47  Aligned_cols=80  Identities=18%  Similarity=0.156  Sum_probs=73.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCe----EEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRV----VDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTL  103 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i----~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l  103 (211)
                      .+.++|||+|||+++++++|+++|++||.|    ..|.|++|. +|+++|||||+|.+.++|++||+. |+. .|+|+.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~-~l~gR~i   97 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKD-LLGKRYI   97 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTE-ESSSCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCC-eeCCeEE
Confidence            347999999999999999999999999986    689999985 799999999999999999999997 887 9999999


Q ss_pred             EEEecCC
Q 038096          104 RFALSGQ  110 (211)
Q Consensus       104 ~v~~a~~  110 (211)
                      .|..+.+
T Consensus        98 ~V~~a~~  104 (123)
T 2dha_A           98 ELFRSTA  104 (123)
T ss_dssp             CCEEECH
T ss_pred             EEEECCH
Confidence            9988754

>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=99.76  E-value=1.6e-18  Score=119.99  Aligned_cols=76  Identities=22%  Similarity=0.314  Sum_probs=70.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ..++|||+|||+++++++|+++|++| .|.++.|.      +++|||||+|.+.++|++|++.|||. .++|+.|+|+++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~-~~~g~~l~V~~a   75 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQY-SFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTE-EETTEEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCC-eECCcEEEEEEc
Confidence            47899999999999999999999999 99999884      57899999999999999999999998 999999999998


Q ss_pred             CCCc
Q 038096          109 GQDK  112 (211)
Q Consensus       109 ~~~~  112 (211)
                      ..+.
T Consensus        76 ~~~~   79 (88)
T 1wg1_A           76 PTDA   79 (88)
T ss_dssp             CCCC
T ss_pred             CCCc
Confidence            6544

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

Probab=99.76  E-value=3e-18  Score=119.93  Aligned_cols=77  Identities=21%  Similarity=0.246  Sum_probs=69.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ..++|||+|||+++++++|+++|++||.|.+|  +.++.+++   ||||+|.+.++|++||+ |||. .|+|+.|.|.++
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~-~~~g~~l~V~~a   79 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQH-SLGGHRLRVRPR   79 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCC-EETTEECCCBCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCe-EECCEEEEEEEC
Confidence            36899999999999999999999999999987  55666565   99999999999999999 9998 999999999988


Q ss_pred             CCCc
Q 038096          109 GQDK  112 (211)
Q Consensus       109 ~~~~  112 (211)
                      ....
T Consensus        80 ~~~~   83 (94)
T 2e5g_A           80 EQKE   83 (94)
T ss_dssp             CCSC
T ss_pred             CcCC
Confidence            6543

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

Probab=99.76  E-value=7.9e-19  Score=123.46  Aligned_cols=78  Identities=21%  Similarity=0.385  Sum_probs=70.7

Q ss_pred             CCCCCeEEEcCCCC-CCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEE
Q 038096           27 SNSGCNVYIGNLDE-KVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRF  105 (211)
Q Consensus        27 s~~~~~lfVgnLp~-~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v  105 (211)
                      .++.++|||+|||+ ++++++|+++|++||.|..|.|.        +|||||+|.+.++|++|++.|||. .++|+.|+|
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~V   77 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQE-MNFGKKLIL   77 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCS-SCBTTTBCE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCC-eeCCcEEEE
Confidence            35689999999998 99999999999999999999984        599999999999999999999998 899999999


Q ss_pred             EecCCCcc
Q 038096          106 ALSGQDKN  113 (211)
Q Consensus       106 ~~a~~~~~  113 (211)
                      .++.....
T Consensus        78 ~~a~~~~~   85 (96)
T 2kvi_A           78 EVSSSNAR   85 (96)
T ss_dssp             EEEECCCC
T ss_pred             EEcCcCCC
Confidence            99876543

>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=99.76  E-value=2.3e-19  Score=135.01  Aligned_cols=81  Identities=20%  Similarity=0.228  Sum_probs=74.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ...++|||+|||++++|++|+++|++|| |++|.|++|+. |+++|||||+|.+.++|++|| .+|+. .|+|+.|+|.+
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~-~l~gR~i~V~~  119 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRA-NMQHRYIELFL  119 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSC-SSSSCCCCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCC-EECCEEEEEEE
Confidence            4578999999999999999999999999 77999999987 999999999999999999999 78998 99999999999


Q ss_pred             cCCCc
Q 038096          108 SGQDK  112 (211)
Q Consensus       108 a~~~~  112 (211)
                      +....
T Consensus       120 a~~~~  124 (139)
T 2hgn_A          120 NSTTG  124 (139)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            86543

>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=99.76  E-value=2.2e-19  Score=135.19  Aligned_cols=85  Identities=22%  Similarity=0.337  Sum_probs=73.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEE--EEccC---CCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDL--YIPRD---KETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRT  102 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v--~i~~d---~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~  102 (211)
                      .+.++|||+|||+++++++|+++|++||.|..+  .++.|   ..+|.++|||||+|.+.++|++||+.|||. .|+|+.
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~-~~~g~~  121 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGY-VLFGKP  121 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTB-EETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCC-EeCCcE
Confidence            457999999999999999999999999998764  11111   246899999999999999999999999998 999999


Q ss_pred             EEEEecCCCcc
Q 038096          103 LRFALSGQDKN  113 (211)
Q Consensus       103 l~v~~a~~~~~  113 (211)
                      |.|.+|+....
T Consensus       122 l~V~~a~~~~~  132 (143)
T 3egn_A          122 MVVQFARSARP  132 (143)
T ss_dssp             CEEEECCCSCC
T ss_pred             EEEEECCCCCC
Confidence            99999976544

>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=99.76  E-value=9.3e-19  Score=129.47  Aligned_cols=79  Identities=22%  Similarity=0.257  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeE--EEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVV--DLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRF  105 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~--~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v  105 (211)
                      .+.++|||+|||+++++++|+++|+.| .|+  .|.|++|+. |+++|||||+|.+.++|++||+. ++. .|+|+.|.|
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~-~l~gR~I~V  115 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKE-RIGHRYIEV  115 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTC-CBTTBCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCC-EECCEEEEE
Confidence            457899999999999999999999999 576  899999988 99999999999999999999986 666 899999999


Q ss_pred             EecCC
Q 038096          106 ALSGQ  110 (211)
Q Consensus       106 ~~a~~  110 (211)
                      .++..
T Consensus       116 ~~a~~  120 (126)
T 2hgm_A          116 FKSSQ  120 (126)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            88753

>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=99.76  E-value=2.6e-18  Score=151.62  Aligned_cols=83  Identities=22%  Similarity=0.316  Sum_probs=78.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +.++|||+|||+.+++++|+++|++||.|+.|.|+.++.||.++|||||+|.+.++|++||+.|||. .|+|+.|.|.|+
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~-~i~gr~i~V~~a  179 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGK-KIDGRRVLVDVE  179 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCC-EECCEEEEEEEe
Confidence            3589999999999999999999999999999999999999999999999999999999999999998 999999999999


Q ss_pred             CCCc
Q 038096          109 GQDK  112 (211)
Q Consensus       109 ~~~~  112 (211)
                      ....
T Consensus       180 ~~~~  183 (437)
T 3pgw_S          180 RGRT  183 (437)
T ss_pred             CCCC
Confidence            7543

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

Probab=99.76  E-value=1.9e-18  Score=121.22  Aligned_cols=78  Identities=27%  Similarity=0.306  Sum_probs=71.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEE-EEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDL-YIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v-~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ..++|||+|||+++++++|+++|++||.|..| .|+.++.++.    |||+|.+.++|++||+.|||. .|+|+.|+|.+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~-~~~g~~l~V~~   88 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNGF-QLENFTLKVAY   88 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTC-BCSSCBCEEEE
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCC-EECCcEEEEEE
Confidence            47899999999999999999999999999999 5888876543    999999999999999999998 99999999999


Q ss_pred             cCCC
Q 038096          108 SGQD  111 (211)
Q Consensus       108 a~~~  111 (211)
                      +.++
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            9765

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

Probab=99.76  E-value=3e-18  Score=124.33  Aligned_cols=79  Identities=20%  Similarity=0.294  Sum_probs=71.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCC---CCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKET---DKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR  104 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~t---g~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~  104 (211)
                      ...++|||+|||+++++++|+++|++||.|. +.++.++.+   |+++|||||+|.+.++|++||+.|+   .++|+.|.
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~---~~~G~~~~   81 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL---EEDGKLYL   81 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE---EETTEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh---hcCCcEEE
Confidence            3479999999999999999999999999999 999998887   7999999999999999999999984   58888888


Q ss_pred             EEecCC
Q 038096          105 FALSGQ  110 (211)
Q Consensus       105 v~~a~~  110 (211)
                      +..+..
T Consensus        82 ~~~~~~   87 (114)
T 2dnl_A           82 CVSSPT   87 (114)
T ss_dssp             EECCSS
T ss_pred             eccCCC
Confidence            876543

>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=99.76  E-value=1.8e-18  Score=125.08  Aligned_cols=75  Identities=12%  Similarity=0.074  Sum_probs=70.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||+++++++|+++|++||.|..|.|+.      ++|||||+|.+.++|++||+.|||. .|+|+.|+|.||.
T Consensus        10 ~~~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           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYS-KFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTC-BSSSSBCEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCC-EECCeEEEEEECC
Confidence            68999999999999999999999999999999864      5689999999999999999999998 9999999999986


Q ss_pred             CC
Q 038096          110 QD  111 (211)
Q Consensus       110 ~~  111 (211)
                      ..
T Consensus        83 ~~   84 (111)
T 1whx_A           83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.76  E-value=3.3e-18  Score=131.32  Aligned_cols=80  Identities=24%  Similarity=0.425  Sum_probs=76.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ..++|||+|||.++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.|||. .++|+.|.|+||
T Consensus        93 ~~~~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           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM-QLGDKKLLVQRA  171 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTC-EETTEECEEEEC
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCC-EECCeEEEEEeC
Confidence            3689999999999999999999999999999999999989999999999999999999999999998 999999999997


Q ss_pred             C
Q 038096          109 G  109 (211)
Q Consensus       109 ~  109 (211)
                      .
T Consensus       172 s  172 (172)
T 2g4b_A          172 S  172 (172)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.75  E-value=4.6e-18  Score=133.38  Aligned_cols=85  Identities=24%  Similarity=0.412  Sum_probs=80.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ...++|||+|||+++++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|++|++.|||. .|+|+.|+|.+
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~  190 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM-QLGDKKLLVQR  190 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTC-EETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCC-EECCEEEEEEE
Confidence            45799999999999999999999999999999999999989999999999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      +.+...
T Consensus       191 a~~~~~  196 (198)
T 2yh0_A          191 ASVGAK  196 (198)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            976543

>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=99.75  E-value=4.4e-18  Score=133.28  Aligned_cols=83  Identities=22%  Similarity=0.295  Sum_probs=76.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|+.||.|.+|.|+.++.+|.++|||||+|.+.++|++||+. ++. .++|+.|.|.+
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~-~~~g~~l~v~~   88 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPH-KVDGRVVEPKR   88 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSC-EETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCC-EECCEEeeeec
Confidence            4578999999999999999999999999999999999999999999999999999999999987 777 89999999999


Q ss_pred             cCCCc
Q 038096          108 SGQDK  112 (211)
Q Consensus       108 a~~~~  112 (211)
                      +....
T Consensus        89 ~~~~~   93 (196)
T 1l3k_A           89 AVSRE   93 (196)
T ss_dssp             CCC--
T ss_pred             ccCcc
Confidence            86543

>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=99.75  E-value=6.6e-18  Score=117.39  Aligned_cols=77  Identities=23%  Similarity=0.521  Sum_probs=63.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCC-eeeCCeEEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGI-VTLYNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~-~~i~gr~l~v~  106 (211)
                      .+.++|||||||+++++++|+++|++||.|.+|.|+++     +||||||+|.+.++|++    +++. +.+.|+.|.|.
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~   79 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHIS   79 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEE
Confidence            45899999999999999999999999999999999874     78999999999999984    3444 35679999999


Q ss_pred             ecCCCcc
Q 038096          107 LSGQDKN  113 (211)
Q Consensus       107 ~a~~~~~  113 (211)
                      +|.++..
T Consensus        80 ~a~~k~~   86 (89)
T 3d2w_A           80 NAEPKHN   86 (89)
T ss_dssp             ECC----
T ss_pred             EcCCCCc
Confidence            9976543

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

Probab=99.75  E-value=5.6e-18  Score=134.64  Aligned_cols=83  Identities=19%  Similarity=0.357  Sum_probs=78.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ...++|||+|||.++++++|+++|++||.|..|.|+.++.+|+++|||||+|.+.++|.+|++.|||. .|+|+.|.|.+
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~-~~~g~~i~V~~  201 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLF-DLGGQYLRVGK  201 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-BCSSSBCEEEE
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCC-EeCCcEEEEEE
Confidence            34689999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cCCC
Q 038096          108 SGQD  111 (211)
Q Consensus       108 a~~~  111 (211)
                      +...
T Consensus       202 a~~~  205 (216)
T 2qfj_A          202 AVTP  205 (216)
T ss_dssp             CSSC
T ss_pred             ecCC
Confidence            8654

>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=99.74  E-value=2.5e-18  Score=131.42  Aligned_cols=80  Identities=20%  Similarity=0.395  Sum_probs=76.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||.++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++ ++|. .++|+.|.|.||.
T Consensus        87 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~-~~~g~~i~V~~a~  164 (167)
T 2cjk_A           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFI-DFKDRKIEIKRAE  164 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEE-CSSSSCEEEEECC
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCE-EeCCeEEEEeecC
Confidence            6799999999999999999999999999999999999999999999999999999999998 7887 9999999999986


Q ss_pred             CC
Q 038096          110 QD  111 (211)
Q Consensus       110 ~~  111 (211)
                      ++
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.74  E-value=3.6e-18  Score=124.21  Aligned_cols=75  Identities=24%  Similarity=0.303  Sum_probs=66.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeE-----E
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRT-----L  103 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~-----l  103 (211)
                      ..++|||+|||+++++++|+++|++||.|..|.|+.+       |||||+|.+.++|++||+.|||. .|+|+.     |
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~-~~~gr~~~~~~i   86 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNT-KFRSHEGETAYI   86 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTC-BCCCTTSCCCBC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCC-EECCcEeeeEEE
Confidence            3689999999999999999999999999999999875       99999999999999999999998 999988     7


Q ss_pred             EEEecCCC
Q 038096          104 RFALSGQD  111 (211)
Q Consensus       104 ~v~~a~~~  111 (211)
                      +|..+.+.
T Consensus        87 ~v~~~~~~   94 (115)
T 3beg_B           87 RVKVDGPR   94 (115)
T ss_dssp             EEEECC--
T ss_pred             EeccCCCC
Confidence            77776553

>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=99.74  E-value=9.8e-18  Score=131.28  Aligned_cols=84  Identities=19%  Similarity=0.306  Sum_probs=75.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ..++|||+|||+++++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|++||.. +|. .|+|+.|.|.||
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~-~~~G~~i~v~~a  180 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYH-TVNGHNCEVRKA  180 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCC-EETTEECEEEEC
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCc-EECCEEEEEEec
Confidence            468999999999999999999999999999999999998999999999999999999999987 787 999999999999


Q ss_pred             CCCccC
Q 038096          109 GQDKNA  114 (211)
Q Consensus       109 ~~~~~~  114 (211)
                      .++...
T Consensus       181 ~~k~~~  186 (196)
T 1l3k_A          181 LSKQEM  186 (196)
T ss_dssp             C-----
T ss_pred             CChhHh
Confidence            776554

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

Probab=99.74  E-value=7.4e-18  Score=134.79  Aligned_cols=81  Identities=27%  Similarity=0.510  Sum_probs=75.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||+++++++|+++|++||.|..|.|++|.  +.++|||||+|.+.++|++||+.|||. .|+|+.|.|.+|.
T Consensus       103 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~-~~~g~~i~V~~a~  179 (213)
T 4f02_A          103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGM-LLNDRKVFVGRFK  179 (213)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEECC
T ss_pred             cccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCC-EECCEEEEEEEcC
Confidence            5789999999999999999999999999999999986  458999999999999999999999998 9999999999997


Q ss_pred             CCcc
Q 038096          110 QDKN  113 (211)
Q Consensus       110 ~~~~  113 (211)
                      ++..
T Consensus       180 ~~~~  183 (213)
T 4f02_A          180 SRKE  183 (213)
T ss_dssp             CHHH
T ss_pred             CCcc
Confidence            6543

>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=99.74  E-value=7.9e-18  Score=129.37  Aligned_cols=78  Identities=23%  Similarity=0.238  Sum_probs=70.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCC--eEEEEEe
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYN--RTLRFAL  107 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~g--r~l~v~~  107 (211)
                      ..+|||+||++.+++++|+++|++||.|.+|.|..+    .++|||||+|.+.++|++|++.|||. .|.|  +.|+|+|
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~-~i~g~g~~L~V~~  120 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQ-NIYNACCTLRIDF  120 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTB-CSSSSCSCEEEEE
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCC-EecCCCcEEEEEE
Confidence            456899999999999999999999999999998643    35799999999999999999999998 8865  9999999


Q ss_pred             cCCCc
Q 038096          108 SGQDK  112 (211)
Q Consensus       108 a~~~~  112 (211)
                      |++..
T Consensus       121 Ak~~~  125 (164)
T 1sjr_A          121 SKLTS  125 (164)
T ss_dssp             CSSSS
T ss_pred             ecCCc
Confidence            98653

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

Probab=99.73  E-value=1.7e-17  Score=122.99  Aligned_cols=77  Identities=25%  Similarity=0.294  Sum_probs=69.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccE-EEEEeCCHHHHHHHHHHcCCCeeeCC--eEEEEE
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGF-AFVEYESEEIGHYAIKLFSGIVTLYN--RTLRFA  106 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~-aFV~f~~~~~A~~Ai~~lng~~~i~g--r~l~v~  106 (211)
                      -..|||+||++.+++++|+++|++||.|.+|.|..+     .+|| |||+|.+.++|++|++.|||. .|.|  +.|+|+
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~-~i~g~~~~LrI~  101 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQ-NIYNACCTLRID  101 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTC-EEETTEEEEEEE
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCC-eecCCCcEEEEE
Confidence            356889999999999999999999999999988753     3688 999999999999999999999 8888  899999


Q ss_pred             ecCCCc
Q 038096          107 LSGQDK  112 (211)
Q Consensus       107 ~a~~~~  112 (211)
                      ||+...
T Consensus       102 ~ak~~~  107 (130)
T 3zzy_A          102 FSKLTS  107 (130)
T ss_dssp             ECSCSS
T ss_pred             ecCCCc
Confidence            997654

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

Probab=99.73  E-value=1.1e-17  Score=132.97  Aligned_cols=82  Identities=26%  Similarity=0.407  Sum_probs=75.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||.++++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|++|++.|+|. .|+|+.|.|.++.
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~-~~~g~~l~v~~~~  106 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSV-MLGGRNIKVGRPS  106 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSC-CCC-CCCEEECCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCC-eeCCeeEEEecCC
Confidence            689999999999999999999999999999999999989999999999999999999999999998 9999999999876


Q ss_pred             CCc
Q 038096          110 QDK  112 (211)
Q Consensus       110 ~~~  112 (211)
                      ...
T Consensus       107 ~~~  109 (216)
T 2qfj_A          107 NIG  109 (216)
T ss_dssp             CCG
T ss_pred             Ccc
Confidence            543

>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=99.73  E-value=6e-18  Score=116.92  Aligned_cols=79  Identities=20%  Similarity=0.429  Sum_probs=67.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|.+|.|+++     ++|||||+|.+.++|++|+..  . +.+.|+.|.|.+
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~-~~~~g~~l~v~~   74 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--D-LIIKGISVHISN   74 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--E-EEETTEEEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--C-ceeCCEEEEEEe
Confidence            45799999999999999999999999999999999865     679999999999999865332  2 467999999999


Q ss_pred             cCCCccC
Q 038096          108 SGQDKNA  114 (211)
Q Consensus       108 a~~~~~~  114 (211)
                      +.++...
T Consensus        75 a~~~~~~   81 (88)
T 1wf0_A           75 AEPKHNS   81 (88)
T ss_dssp             CCCCCCC
T ss_pred             cCCCCCC
Confidence            8766543

>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=99.73  E-value=2e-17  Score=132.03  Aligned_cols=78  Identities=19%  Similarity=0.253  Sum_probs=72.5

Q ss_pred             CCCeEEEcCCC-CCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           29 SGCNVYIGNLD-EKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        29 ~~~~lfVgnLp-~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ++++|||+||+ +.+++++|+++|++||.|.+|+|++++     +|||||+|.+.++|++||+.|||. .+.|+.|+|.+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~-~~~g~~l~v~~   76 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNN-FMFGQKMNVCV   76 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTC-EETTEECEEEE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCC-EECCceEEEEE
Confidence            47999999999 899999999999999999999998753     699999999999999999999998 99999999999


Q ss_pred             cCCCc
Q 038096          108 SGQDK  112 (211)
Q Consensus       108 a~~~~  112 (211)
                      ++.+.
T Consensus        77 s~~~~   81 (205)
T 3tyt_A           77 SKQPA   81 (205)
T ss_dssp             CSCSC
T ss_pred             ccCCc
Confidence            87543

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.3e-17  Score=116.10  Aligned_cols=76  Identities=13%  Similarity=0.268  Sum_probs=67.0

Q ss_pred             CCCCe-EEEcCCCCCCcHHH----HHHHHhcC-CCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCe
Q 038096           28 NSGCN-VYIGNLDEKVNERV----LYDILIQA-GRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNR  101 (211)
Q Consensus        28 ~~~~~-lfVgnLp~~~~e~~----L~~~F~~~-G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr  101 (211)
                      ++..+ |||+|||+++++++    |+++|++| |.|.+|       |+   |+|||+|.+.++|++|++.|||. .+.||
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~-~l~gr   74 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENE-DVFGN   74 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTC-CSSSS
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCC-ccCCc
Confidence            34555 99999999999988    55899999 599998       34   99999999999999999999998 99999


Q ss_pred             EEEEEecCCCccC
Q 038096          102 TLRFALSGQDKNA  114 (211)
Q Consensus       102 ~l~v~~a~~~~~~  114 (211)
                      .|+|++|+.....
T Consensus        75 ~i~v~~A~~~sd~   87 (96)
T 2diu_A           75 RIIVSFTPKNREL   87 (96)
T ss_dssp             CCEEESSCCSCCC
T ss_pred             eEEEEecCCCcce
Confidence            9999999776553

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

Probab=99.73  E-value=1.5e-17  Score=126.43  Aligned_cols=80  Identities=26%  Similarity=0.466  Sum_probs=74.4

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQ  110 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~  110 (211)
                      ++|||+|||.++++++|+++|++||.|.++.|+.++. ++++|||||+|.+.++|++|++.|+|. .+.|+.|.|.++..
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 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGK-QIENNIVKINWAFQ   78 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC--CCEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEECCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC-CCCCCEEEEEeCCHHHHHHHHHHcCCC-ccCCCeeEEEEcCC
Confidence            5899999999999999999999999999999999975 789999999999999999999999998 99999999999865


Q ss_pred             Cc
Q 038096          111 DK  112 (211)
Q Consensus       111 ~~  112 (211)
                      ..
T Consensus        79 ~~   80 (166)
T 3md3_A           79 SQ   80 (166)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.72  E-value=1.8e-17  Score=113.92  Aligned_cols=72  Identities=29%  Similarity=0.529  Sum_probs=66.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcC----C-------CeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQA----G-------RVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIV   96 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~----G-------~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~   96 (211)
                      .+.++|||+|||+++++++|+++|++|    |       .|.++.+.++      +|||||+|.+.++|++|+ .|||. 
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~-   75 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGI-   75 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTC-
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCC-
Confidence            347899999999999999999999999    8       9999999754      699999999999999999 99998 


Q ss_pred             eeCCeEEEEEe
Q 038096           97 TLYNRTLRFAL  107 (211)
Q Consensus        97 ~i~gr~l~v~~  107 (211)
                      .++|+.|+|+.
T Consensus        76 ~~~g~~l~V~r   86 (87)
T 2hzc_A           76 IFQGQSLKIRR   86 (87)
T ss_dssp             EETTEECEEEC
T ss_pred             EECCeEEEEeC
Confidence            99999999874

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

Probab=99.72  E-value=4.1e-17  Score=120.22  Aligned_cols=74  Identities=26%  Similarity=0.362  Sum_probs=66.6

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccE-EEEEeCCHHHHHHHHHHcCCCeeeCC--eEEEEEec
Q 038096           32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGF-AFVEYESEEIGHYAIKLFSGIVTLYN--RTLRFALS  108 (211)
Q Consensus        32 ~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~-aFV~f~~~~~A~~Ai~~lng~~~i~g--r~l~v~~a  108 (211)
                      .|||+||++.+++++|+++|++||.|.+|.|.. +     .|| |||+|.+.++|++|++.|||. .|.|  +.|+|.+|
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG~-~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGA-DIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTC-CCBTTBSEEEEECC
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCC-EecCCCeEEEEEEe
Confidence            468999999999999999999999999999865 2     286 999999999999999999998 8887  69999999


Q ss_pred             CCCc
Q 038096          109 GQDK  112 (211)
Q Consensus       109 ~~~~  112 (211)
                      ++..
T Consensus       100 k~~~  103 (124)
T 2e5i_A          100 RPTR  103 (124)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            7654

>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=99.72  E-value=2.6e-17  Score=125.65  Aligned_cols=80  Identities=30%  Similarity=0.456  Sum_probs=76.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCC--eEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYN--RTLRF  105 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~g--r~l~v  105 (211)
                      ...++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++.|||. .++|  ++|+|
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~~~l~V  165 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNV-IPEGGSQPLSV  165 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-CCTTCSSCCEE
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCC-EecCCCeEEEE
Confidence            45789999999999999999999999999999999999988999999999999999999999999998 8988  89999


Q ss_pred             Eec
Q 038096          106 ALS  108 (211)
Q Consensus       106 ~~a  108 (211)
                      .||
T Consensus       166 ~~A  168 (168)
T 1b7f_A          166 RLA  168 (168)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>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=99.72  E-value=1.8e-17  Score=126.54  Aligned_cols=81  Identities=23%  Similarity=0.377  Sum_probs=74.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ++++|||+|||+++++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|++|++.  +. .++|+.|.|.++
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~-~~~g~~i~v~~~   78 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QH-ILDGKVIDPKRA   78 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CC-EETTEECCCEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--cc-ccCCeEcccccc
Confidence            368999999999999999999999999999999999999999999999999999999999995  44 899999999997


Q ss_pred             CCCc
Q 038096          109 GQDK  112 (211)
Q Consensus       109 ~~~~  112 (211)
                      ....
T Consensus        79 ~~~~   82 (167)
T 2cjk_A           79 IPRD   82 (167)
T ss_dssp             CCHH
T ss_pred             cchh
Confidence            6543

>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=99.71  E-value=3.2e-17  Score=124.76  Aligned_cols=79  Identities=22%  Similarity=0.378  Sum_probs=74.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeE--EEEE
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRT--LRFA  106 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~--l~v~  106 (211)
                      ..++|||+|||..+++++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|.+|++.|||. .++|+.  |.|+
T Consensus        87 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~~~i~v~  165 (167)
T 1fxl_A           87 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ-KPSGATEPITVK  165 (167)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-CCTTCSSCCEEE
T ss_pred             CCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCC-ccCCCccceEEE
Confidence            4689999999999999999999999999999999999988999999999999999999999999998 999974  8888


Q ss_pred             ec
Q 038096          107 LS  108 (211)
Q Consensus       107 ~a  108 (211)
                      ||
T Consensus       166 ~A  167 (167)
T 1fxl_A          166 FA  167 (167)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>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=99.71  E-value=4.4e-17  Score=125.06  Aligned_cols=80  Identities=18%  Similarity=0.311  Sum_probs=73.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeC---CeEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLY---NRTLR  104 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~---gr~l~  104 (211)
                      ...++|||+|||.++++++|+++|++||.|..+.++++. +|.++|||||+|.+.++|++|++.|||. .+.   |+.|.
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~-~~~~g~~~~l~  170 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQA-QTMEGCSSPMV  170 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTS-CCCTTCSSCCE
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCC-cccCCCCCCeE
Confidence            357899999999999999999999999999999999996 4999999999999999999999999998 555   48999


Q ss_pred             EEecC
Q 038096          105 FALSG  109 (211)
Q Consensus       105 v~~a~  109 (211)
                      |.||.
T Consensus       171 V~~ad  175 (175)
T 3nmr_A          171 VKFAD  175 (175)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99974

>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=99.70  E-value=2.6e-17  Score=126.34  Aligned_cols=83  Identities=17%  Similarity=0.394  Sum_probs=74.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCC--CCccEEEEEeCCHHHHHHHHHHcCCCeeeC---CeEE
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETD--KPKGFAFVEYESEEIGHYAIKLFSGIVTLY---NRTL  103 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg--~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~---gr~l  103 (211)
                      +.++|||+|||+++++++|+++|++||.|.+|.|++++.++  +++|||||+|.+.++|++|++.|+|. .+.   ++.+
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~-~~~~~~~~~~   80 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNM-KVLPGMHHPI   80 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTT-CCCTTCSSCC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCc-EEccCCccce
Confidence            47899999999999999999999999999999999999877  89999999999999999999999997 555   4678


Q ss_pred             EEEecCCCc
Q 038096          104 RFALSGQDK  112 (211)
Q Consensus       104 ~v~~a~~~~  112 (211)
                      .+.++....
T Consensus        81 ~~~~~~~~~   89 (175)
T 3nmr_A           81 QMKPADSEK   89 (175)
T ss_dssp             EEEECGGGC
T ss_pred             EEccccccc
Confidence            888865443

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

Probab=99.70  E-value=1.1e-16  Score=114.72  Aligned_cols=81  Identities=17%  Similarity=0.069  Sum_probs=72.6

Q ss_pred             CCCeEEEcCCCC-----CCcHHHHHHHHhcCCCeEEEEEccCCCC-CCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeE
Q 038096           29 SGCNVYIGNLDE-----KVNERVLYDILIQAGRVVDLYIPRDKET-DKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRT  102 (211)
Q Consensus        29 ~~~~lfVgnLp~-----~~~e~~L~~~F~~~G~i~~v~i~~d~~t-g~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~  102 (211)
                      +++.|+|.||-.     +-++++|++.|++||.|.+|.|++++.+ +.++|||||+|.+.++|++|++.|||. .++|+.
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~-~~~Gr~   85 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGR-YFGGRV   85 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTC-EETTEE
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCC-EECCcE
Confidence            478999999962     2368999999999999999999998764 689999999999999999999999999 999999


Q ss_pred             EEEEecCC
Q 038096          103 LRFALSGQ  110 (211)
Q Consensus       103 l~v~~a~~  110 (211)
                      |.|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999864

>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=99.70  E-value=1.1e-16  Score=132.71  Aligned_cols=82  Identities=27%  Similarity=0.536  Sum_probs=75.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHH----HHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLY----DILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRT  102 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~----~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~  102 (211)
                      ..+.++|||+|||+++++++|+    ++|++||.|.+|.|++   +++++|||||+|.+.++|++||+.|||. .|.|+.
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~   81 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGF-PFYDKP   81 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCC-eeCCcE
Confidence            3558999999999999999976    8999999999999886   5889999999999999999999999998 999999


Q ss_pred             EEEEecCCCc
Q 038096          103 LRFALSGQDK  112 (211)
Q Consensus       103 l~v~~a~~~~  112 (211)
                      |+|.|++...
T Consensus        82 l~v~~a~~~~   91 (282)
T 3pgw_A           82 MRIQYAKTDS   91 (282)
T ss_pred             EEEEEeccCc
Confidence            9999987654

>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=99.69  E-value=1.2e-16  Score=126.38  Aligned_cols=80  Identities=18%  Similarity=0.195  Sum_probs=73.0

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||+++++++|+++|++||.|..|.|+++.. |.++|||||+|.+.++|++||+.++ . .++|+.|.|.|+.
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~-~~~kG~aFVeF~~~e~A~~A~~~~~-~-~~~Gr~l~V~~~~  185 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPG-Q-KYKETDLLILFKD  185 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTT-CCEEEEEEEEESSHHHHHHHHHCTT-C-EETTEECEEEETT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCC-CCcccEEEEEECCHHHHHHHHHhCC-C-eECCEEEEEEEhH
Confidence            58999999999999999999999999999999999874 8999999999999999999998765 4 7999999999986


Q ss_pred             CCc
Q 038096          110 QDK  112 (211)
Q Consensus       110 ~~~  112 (211)
                      .-.
T Consensus       186 ~y~  188 (193)
T 2voo_A          186 DYF  188 (193)
T ss_dssp             TC-
T ss_pred             HHH
Confidence            543

>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=99.68  E-value=1.3e-16  Score=122.91  Aligned_cols=77  Identities=19%  Similarity=0.324  Sum_probs=71.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ..++|||+|||.++++++|+++|++||.|..+     ..++.++|||||+|.+.++|.+|++.|||. .|+|+.|.|.||
T Consensus        98 ~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~i~v~~a  171 (175)
T 1fje_B           98 AARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGA-EIDGRSVSLYYT  171 (175)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEE-EETTEEEEEEEC
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCC-EECCeEEEEEec
Confidence            46899999999999999999999999988776     456899999999999999999999999998 999999999999


Q ss_pred             CCC
Q 038096          109 GQD  111 (211)
Q Consensus       109 ~~~  111 (211)
                      .++
T Consensus       172 ~~k  174 (175)
T 1fje_B          172 GEK  174 (175)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            654

>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=99.67  E-value=1.9e-16  Score=131.75  Aligned_cols=82  Identities=21%  Similarity=0.348  Sum_probs=75.8

Q ss_pred             CCCCeEEEcCCCCC-CcHHHHHHHHhcCCCeEEEEEccCCC-CCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEE
Q 038096           28 NSGCNVYIGNLDEK-VNERVLYDILIQAGRVVDLYIPRDKE-TDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRF  105 (211)
Q Consensus        28 ~~~~~lfVgnLp~~-~~e~~L~~~F~~~G~i~~v~i~~d~~-tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v  105 (211)
                      ...++|||+|||+. +++++|+++|+.||.|..|.|+.+.. ||.++|||||+|.+.++|.+|+ .|||. .|+|+.|.|
T Consensus       208 ~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~-~~~g~~i~V  285 (292)
T 2ghp_A          208 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRS-LLGNREISV  285 (292)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTE-EETTEEEEE
T ss_pred             CCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCC-EECCcEEEE
Confidence            45799999999999 99999999999999999999999887 6999999999999999999999 99998 999999999


Q ss_pred             EecCCC
Q 038096          106 ALSGQD  111 (211)
Q Consensus       106 ~~a~~~  111 (211)
                      .||.++
T Consensus       286 ~~a~~k  291 (292)
T 2ghp_A          286 SLADKK  291 (292)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999764

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

Probab=99.67  E-value=1.3e-16  Score=129.96  Aligned_cols=78  Identities=18%  Similarity=0.296  Sum_probs=69.9

Q ss_pred             CCCCeEEEcCCCCCC---------cHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee
Q 038096           28 NSGCNVYIGNLDEKV---------NERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL   98 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~---------~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i   98 (211)
                      .+.++||||||+..+         +|++|+++|++||.|.+|.|+.      ++|||||+|.+.++|+.|++.|+|. .|
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~-~l  204 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQ-TL  204 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTC-CC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCC-EE
Confidence            457999999999998         7999999999999999999985      4699999999999999999999998 78


Q ss_pred             ------------CCeEEEEEecCCCc
Q 038096           99 ------------YNRTLRFALSGQDK  112 (211)
Q Consensus        99 ------------~gr~l~v~~a~~~~  112 (211)
                                  .|+.|.|.||..+.
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             eccccccccccCCCCEEEEEEccCCC
Confidence                        89999999997653

>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=99.67  E-value=3.7e-16  Score=129.56  Aligned_cols=85  Identities=18%  Similarity=0.292  Sum_probs=80.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ++..++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|.+|++.|+|. .++|+.|.|.
T Consensus        92 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~-~~~g~~i~v~  170 (284)
T 3smz_A           92 QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGK-PLGPRTLYVH  170 (284)
T ss_dssp             CCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             cCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCC-EeCCcEEEEE
Confidence            355789999999999999999999999999999999999999999999999999999999999999998 9999999999


Q ss_pred             ecCCCc
Q 038096          107 LSGQDK  112 (211)
Q Consensus       107 ~a~~~~  112 (211)
                      ++....
T Consensus       171 ~a~~~~  176 (284)
T 3smz_A          171 WTDAGQ  176 (284)
T ss_dssp             ECCGGG
T ss_pred             ECCCCC
Confidence            986543

>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=99.66  E-value=2.4e-16  Score=127.27  Aligned_cols=78  Identities=22%  Similarity=0.318  Sum_probs=73.2

Q ss_pred             CCCCeEEEcCCCC-CCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           28 NSGCNVYIGNLDE-KVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~-~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      +++++|||+|||+ ++++++|+++|++||.|.+|.|++++     +|||||+|.+.++|++|++.|||. .+.|+.|.|.
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~-~~~g~~l~v~  105 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGH-KLHGKPIRIT  105 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTC-BCSSSBCEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCC-eECCeEEEEE
Confidence            4589999999999 99999999999999999999999875     699999999999999999999998 9999999999


Q ss_pred             ecCCC
Q 038096          107 LSGQD  111 (211)
Q Consensus       107 ~a~~~  111 (211)
                      ++...
T Consensus       106 ~a~~~  110 (229)
T 2adc_A          106 LSKHQ  110 (229)
T ss_dssp             CCSCC
T ss_pred             EecCc
Confidence            98755

>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=99.66  E-value=4.6e-16  Score=128.97  Aligned_cols=84  Identities=19%  Similarity=0.229  Sum_probs=78.3

Q ss_pred             CCCCeEEEcCCCCCC-cHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           28 NSGCNVYIGNLDEKV-NERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~-~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ...++|||+|||+.+ ++++|+++|+.||.|..+.|+.+. +|.++|||||+|.+.++|.+|++.|||. .++|+.|.|.
T Consensus       182 ~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v~  259 (284)
T 3smz_A          182 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGL-SLGGSHLRVS  259 (284)
T ss_dssp             TSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             CCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCC-ccCCeEEEEE
Confidence            457899999999995 999999999999999999999987 6999999999999999999999999998 9999999999


Q ss_pred             ecCCCcc
Q 038096          107 LSGQDKN  113 (211)
Q Consensus       107 ~a~~~~~  113 (211)
                      |+.++..
T Consensus       260 ~a~~~~~  266 (284)
T 3smz_A          260 FCAPGPP  266 (284)
T ss_dssp             ECCSSSC
T ss_pred             EecCCCc
Confidence            9977654

>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=99.65  E-value=7.4e-16  Score=127.60  Aligned_cols=76  Identities=20%  Similarity=0.326  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeC-CeEEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLY-NRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~-gr~l~v~  106 (211)
                      ...++|||+|||.++++++|+++|++||.|.+|.|+.++     +|||||+|.+.++|++|++.|||. .|+ |+.|+|.
T Consensus       205 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~-~~~~g~~l~v~  278 (282)
T 3pgw_A          205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGF-KITQNNAMKIS  278 (282)
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCc-EeCCCCEEEEE
Confidence            457899999999999999999999999999999998654     589999999999999999999998 898 9999999


Q ss_pred             ecC
Q 038096          107 LSG  109 (211)
Q Consensus       107 ~a~  109 (211)
                      ||+
T Consensus       279 ~ak  281 (282)
T 3pgw_A          279 FAK  281 (282)
T ss_pred             Eec
Confidence            985

>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=99.64  E-value=7.9e-17  Score=124.14  Aligned_cols=83  Identities=20%  Similarity=0.320  Sum_probs=73.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||+++++++|+++|..||.+.. .++.+..+|.++|||||+|.+.++|++||+ |||. .+.|+.|.|.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~-~~~g~~l~v~   86 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGL-KVFGNEIKLE   86 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGE-EETTEEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCC-EeCCeEEEEe
Confidence            345899999999999999999999999998766 445556679999999999999999999995 9998 9999999999


Q ss_pred             ecCCCc
Q 038096          107 LSGQDK  112 (211)
Q Consensus       107 ~a~~~~  112 (211)
                      ++....
T Consensus        87 ~~~~~~   92 (175)
T 1fje_B           87 KPKGRD   92 (175)
T ss_dssp             CCCCSS
T ss_pred             cCCCcc
Confidence            987643

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

Probab=99.64  E-value=3e-16  Score=123.43  Aligned_cols=77  Identities=22%  Similarity=0.325  Sum_probs=72.3

Q ss_pred             CCeEEEcCCCC-CCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           30 GCNVYIGNLDE-KVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        30 ~~~lfVgnLp~-~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +++|||+|||+ ++++++|+++|++||.|.+|.|++++     +|||||+|.+.++|++|++.|||. .++|+.|.|.++
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~-~~~g~~l~v~~a   76 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGH-KLHGKPIRITLS   76 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTC-CCSSCCCEEEEC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCC-eecCeEEEEEEe
Confidence            68999999999 99999999999999999999999875     699999999999999999999998 999999999998


Q ss_pred             CCCc
Q 038096          109 GQDK  112 (211)
Q Consensus       109 ~~~~  112 (211)
                      ....
T Consensus        77 ~~~~   80 (198)
T 1qm9_A           77 KHQN   80 (198)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            7653

>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=99.62  E-value=3.1e-16  Score=112.12  Aligned_cols=73  Identities=16%  Similarity=0.198  Sum_probs=65.5

Q ss_pred             EEcCCCCCCcHHHHHHHH------------hcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCe
Q 038096           34 YIGNLDEKVNERVLYDIL------------IQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNR  101 (211)
Q Consensus        34 fVgnLp~~~~e~~L~~~F------------~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr  101 (211)
                      .++||++.+++++|++.|            ++||.|.+|.|+++.. ++++|||||+|.+.++|++|++.|||. .++|+
T Consensus        19 ~~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~-~~~Gr   96 (104)
T 1jmt_A           19 SADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNR-WFNGQ   96 (104)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTC-EETTE
T ss_pred             ccCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCC-EECCE
Confidence            367888888888887766            9999999999999875 789999999999999999999999999 99999


Q ss_pred             EEEEEec
Q 038096          102 TLRFALS  108 (211)
Q Consensus       102 ~l~v~~a  108 (211)
                      .|+|.++
T Consensus        97 ~i~v~~s  103 (104)
T 1jmt_A           97 PIHAELS  103 (104)
T ss_dssp             ECCEEEC
T ss_pred             EEEEEEc
Confidence            9999986

>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=99.62  E-value=4.1e-15  Score=107.34  Aligned_cols=80  Identities=20%  Similarity=0.238  Sum_probs=68.9

Q ss_pred             CCCCeEEEcCCCCCCc-----------HHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCe
Q 038096           28 NSGCNVYIGNLDEKVN-----------ERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIV   96 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~-----------e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~   96 (211)
                      .++++|+|.||-....           +++|+++|++||.|.+|.| .++   .++|||||+|.+.++|++|++.|||. 
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~-   87 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGR-   87 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTC-
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCC-
Confidence            4479999999943332           6899999999999999966 543   37999999999999999999999998 


Q ss_pred             eeCCeEEEEEecCCCc
Q 038096           97 TLYNRTLRFALSGQDK  112 (211)
Q Consensus        97 ~i~gr~l~v~~a~~~~  112 (211)
                      .|+|+.|+|.++.+..
T Consensus        88 ~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           88 WFGGRQITAQAWDGTT  103 (112)
T ss_dssp             EETTEECEEEECCSCC
T ss_pred             EECCcEEEEEEeCCCC
Confidence            9999999999987644

>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=99.61  E-value=9.3e-16  Score=122.29  Aligned_cols=78  Identities=13%  Similarity=0.161  Sum_probs=69.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCe--EEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCe----
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRV--VDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNR----  101 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i--~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr----  101 (211)
                      +++++|||+|||+++++++|+++|++||.|  .++++..++  +..+|||||+|.+.++|.+||..|||. .|.|+    
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~-~~~g~~~~~  197 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHY-QMKNPNGPY  197 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTC-EECCSSSSS
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCC-CccCCCCCc
Confidence            457899999999999999999999999999  899998875  566799999999999999999999998 89887    


Q ss_pred             EEEEEec
Q 038096          102 TLRFALS  108 (211)
Q Consensus       102 ~l~v~~a  108 (211)
                      ++.|++|
T Consensus       198 p~~vk~~  204 (205)
T 3tyt_A          198 PYTLKLC  204 (205)
T ss_dssp             CEECEEE
T ss_pred             ceEEEec
Confidence            4666554

>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=99.61  E-value=3.3e-15  Score=106.90  Aligned_cols=81  Identities=21%  Similarity=0.161  Sum_probs=70.8

Q ss_pred             CCCeEEEcCC--CCCCc--------HHHHHHHHhcCCCeEEEEEccCCCC--CCCccEEEEEeCCHHHHHHHHHHcCCCe
Q 038096           29 SGCNVYIGNL--DEKVN--------ERVLYDILIQAGRVVDLYIPRDKET--DKPKGFAFVEYESEEIGHYAIKLFSGIV   96 (211)
Q Consensus        29 ~~~~lfVgnL--p~~~~--------e~~L~~~F~~~G~i~~v~i~~d~~t--g~~rg~aFV~f~~~~~A~~Ai~~lng~~   96 (211)
                      +++.|.+.|+  +.++.        +++|++.|++||.|.+|.|++++.+  +.++|||||+|.+.++|++|++.|||. 
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~-   82 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR-   82 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC-
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC-
Confidence            4788899988  33443        3689999999999999999998865  468999999999999999999999999 


Q ss_pred             eeCCeEEEEEecCC
Q 038096           97 TLYNRTLRFALSGQ  110 (211)
Q Consensus        97 ~i~gr~l~v~~a~~  110 (211)
                      .++||.|.|.++..
T Consensus        83 ~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           83 KFANRVVVTKYCDP   96 (105)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EeCCCEEEEEEeCH
Confidence            99999999999754

>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=99.60  E-value=2.6e-15  Score=124.94  Aligned_cols=83  Identities=18%  Similarity=0.400  Sum_probs=71.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCC-CeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAG-RVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G-~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ..++|||+|||+++++++|+++|+.|| .|..|.|+.++. |.++|||||+|.+.++|++|++.|+|. .++|+.|.|.+
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~  193 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGL-KIEGYTLVTKV  193 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTC-EETTEECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCC-EeCCcEEEEEE
Confidence            478999999999999999999999999 999999999876 889999999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      +.+...
T Consensus       194 a~~~~~  199 (292)
T 2ghp_A          194 SNPLEK  199 (292)
T ss_dssp             CCCC--
T ss_pred             CCCCcc
Confidence            876543

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

Probab=99.60  E-value=3.5e-15  Score=116.81  Aligned_cols=76  Identities=25%  Similarity=0.468  Sum_probs=67.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcC----C-------CeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCee
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQA----G-------RVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVT   97 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~----G-------~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~   97 (211)
                      ..++|||+|||+++++++|+++|+.|    |       .|.++.+      +.++|||||+|.+.++|++|| .|||. .
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~-~   74 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGI-I   74 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTE-E
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCC-E
Confidence            37999999999999999999999999    5       6677766      556799999999999999999 89998 9


Q ss_pred             eCCeEEEEEecCCCc
Q 038096           98 LYNRTLRFALSGQDK  112 (211)
Q Consensus        98 i~gr~l~v~~a~~~~  112 (211)
                      |+|+.|.|.++....
T Consensus        75 ~~g~~i~v~~~~~~~   89 (198)
T 2yh0_A           75 FQGQSLKIRRPHDYQ   89 (198)
T ss_dssp             ETTEEEEEECCCCCC
T ss_pred             EcCceEEEeCCCCCC
Confidence            999999999987654

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

Probab=99.60  E-value=1.9e-15  Score=118.76  Aligned_cols=78  Identities=19%  Similarity=0.203  Sum_probs=71.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCC-CeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeC-CeEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAG-RVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLY-NRTLRF  105 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G-~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~-gr~l~v  105 (211)
                      +++++|||+|||..+++++|+++|+.|| .|..+.|+.+     .+|+|||+|.+.++|.+|++.|||. .++ |+.|+|
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~-~~~~g~~l~v  191 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNH-DLGENHHLRV  191 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSS-CCSSCCSCCE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCC-ccCCCCeEEE
Confidence            4578999999999999999999999999 9999999764     2699999999999999999999998 899 999999


Q ss_pred             EecCCC
Q 038096          106 ALSGQD  111 (211)
Q Consensus       106 ~~a~~~  111 (211)
                      .|+++.
T Consensus       192 ~~a~~~  197 (198)
T 1qm9_A          192 SFSKST  197 (198)
T ss_dssp             EEECCC
T ss_pred             Eeeccc
Confidence            998653

>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=99.59  E-value=3.2e-15  Score=114.50  Aligned_cols=75  Identities=27%  Similarity=0.469  Sum_probs=67.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcC----C-------CeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCee
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQA----G-------RVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVT   97 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~----G-------~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~   97 (211)
                      +.++|||+|||+++++++|+++|++|    |       .|.++.+.      .++|||||+|.+.++|++|+ .+||. .
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~-~   74 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGI-I   74 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTC-E
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCc-E
Confidence            36899999999999999999999999    7       77888774      45799999999999999999 89998 9


Q ss_pred             eCCeEEEEEecCCC
Q 038096           98 LYNRTLRFALSGQD  111 (211)
Q Consensus        98 i~gr~l~v~~a~~~  111 (211)
                      ++|+.|.|.++...
T Consensus        75 ~~g~~i~v~~~~~~   88 (172)
T 2g4b_A           75 FQGQSLKIRRPHDY   88 (172)
T ss_dssp             ETTEECEEECCSSC
T ss_pred             ecCceeeecCCccc
Confidence            99999999987554

>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=99.59  E-value=3.3e-15  Score=122.91  Aligned_cols=85  Identities=20%  Similarity=0.244  Sum_probs=75.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeC---CeEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLY---NRTLR  104 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~---gr~l~  104 (211)
                      .++++|||+|||..+++++|+++|+.||.|..|.|+.| .+|.++|||||+|.+.++|.+||..||+...+.   ++.|.
T Consensus        94 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~  172 (261)
T 3sde_A           94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVI  172 (261)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCE
T ss_pred             ccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEE
Confidence            45789999999999999999999999999999999999 579999999999999999999999994431444   89999


Q ss_pred             EEecCCCcc
Q 038096          105 FALSGQDKN  113 (211)
Q Consensus       105 v~~a~~~~~  113 (211)
                      |.++.....
T Consensus       173 v~~~~~~~~  181 (261)
T 3sde_A          173 VEPMEQFDD  181 (261)
T ss_dssp             EEECCCEES
T ss_pred             EeeccccCc
Confidence            999876543

>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=99.59  E-value=1.2e-14  Score=117.32  Aligned_cols=78  Identities=19%  Similarity=0.203  Sum_probs=71.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCC-CeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeC-CeEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAG-RVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLY-NRTLRF  105 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G-~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~-gr~l~v  105 (211)
                      .++++|||+|||.++++++|+++|++|| .|..+.|+.+     .+|||||+|.+.++|.+|++.|||. .++ |+.|+|
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~-~~~~g~~l~v  222 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNH-DLGENHHLRV  222 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTC-BSSSSCBCEE
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCC-ccCCCCeEEE
Confidence            4579999999999999999999999999 9999999653     3699999999999999999999998 899 999999


Q ss_pred             EecCCC
Q 038096          106 ALSGQD  111 (211)
Q Consensus       106 ~~a~~~  111 (211)
                      .|+++.
T Consensus       223 ~~a~~~  228 (229)
T 2adc_A          223 SFSKST  228 (229)
T ss_dssp             EECSSC
T ss_pred             EEecCC
Confidence            998653

>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=99.59  E-value=4.5e-15  Score=122.10  Aligned_cols=77  Identities=25%  Similarity=0.536  Sum_probs=71.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|+.||.|..|.|.+      ++|||||+|.+.++|++|+..++|. .|.|+.|.|.+
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~A~~A~~~l~g~-~i~g~~l~v~~   92 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLESRTLAEIAKAELDGT-ILKSRPLRIRF   92 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTC-EETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEECCHHHHHHHHHHcCCc-EECCceeEeee
Confidence            4468999999999999999999999999999999964      4699999999999999999999998 99999999999


Q ss_pred             cCCC
Q 038096          108 SGQD  111 (211)
Q Consensus       108 a~~~  111 (211)
                      +.+.
T Consensus        93 a~~~   96 (261)
T 3sde_A           93 ATHG   96 (261)
T ss_dssp             CCCS
T ss_pred             cccC
Confidence            8654

>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=99.56  E-value=1e-14  Score=106.45  Aligned_cols=81  Identities=19%  Similarity=0.165  Sum_probs=71.1

Q ss_pred             CCCeEEEcCCC--CCC---cHHHHHHHHhcCCCeEEEEEccCCC----CCCCccEEEEEeCCHHHHHHHHHHcCCCeeeC
Q 038096           29 SGCNVYIGNLD--EKV---NERVLYDILIQAGRVVDLYIPRDKE----TDKPKGFAFVEYESEEIGHYAIKLFSGIVTLY   99 (211)
Q Consensus        29 ~~~~lfVgnLp--~~~---~e~~L~~~F~~~G~i~~v~i~~d~~----tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~   99 (211)
                      +++.|++.|+-  .++   -++||++.|++||.|.+|.|++++.    ++.++||+||+|.+.++|.+|++.|||. .++
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr-~f~   97 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGR-WFA   97 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTC-EET
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCC-EEC
Confidence            47899999984  222   3689999999999999999999865    4578899999999999999999999999 999


Q ss_pred             CeEEEEEecCC
Q 038096          100 NRTLRFALSGQ  110 (211)
Q Consensus       100 gr~l~v~~a~~  110 (211)
                      ||.|.|.++..
T Consensus        98 GR~i~v~~~~~  108 (118)
T 3ue2_A           98 GRKVVAEVYDQ  108 (118)
T ss_dssp             TEECEEEEECH
T ss_pred             CcEEEEEEcCh
Confidence            99999999754

>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=99.53  E-value=3.6e-14  Score=121.18  Aligned_cols=77  Identities=23%  Similarity=0.350  Sum_probs=66.4

Q ss_pred             CCCCCCeEEEcC--CCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee---CC
Q 038096           26 NSNSGCNVYIGN--LDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL---YN  100 (211)
Q Consensus        26 ~s~~~~~lfVgn--Lp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i---~g  100 (211)
                      .+.++++|||||  |++.++|++|+++|++||.|.+|.+..      +||||||+|.+.++|++||+.|||+ .+   .|
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~-~~~~~~g   86 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGK-EVVDDLG   86 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTC-EEECTTS
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCC-ccccccC
Confidence            356789999999  578999999999999999999988754      4699999999999999999999999 55   24


Q ss_pred             e--EEEEEecC
Q 038096          101 R--TLRFALSG  109 (211)
Q Consensus       101 r--~l~v~~a~  109 (211)
                      +  .|.+.++.
T Consensus        87 ~~~~ly~~~~~   97 (345)
T 3tht_A           87 QKITLYLNFVE   97 (345)
T ss_dssp             CEEECEEEECS
T ss_pred             CceEEEEEEee
Confidence            5  57788874

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

Probab=99.50  E-value=7.5e-14  Score=98.95  Aligned_cols=66  Identities=21%  Similarity=0.313  Sum_probs=58.3

Q ss_pred             CCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCCCcc
Q 038096           40 EKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDKN  113 (211)
Q Consensus        40 ~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~~~~  113 (211)
                      ..+++++|+++|++||.|.+|.|+     ++++|||||+|.+.++|++||+.++   .+.|+.|+|.|++....
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~---~~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEV---GLVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCC---BCSSSBCEEECSSCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcC---CCCCCeEEEEEccCCCC
Confidence            468999999999999999999987     4688999999999999999999865   46799999999876543

>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=99.40  E-value=5.5e-13  Score=96.67  Aligned_cols=76  Identities=13%  Similarity=0.169  Sum_probs=63.9

Q ss_pred             CCeEEEcCCCC--CC--------cHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeC
Q 038096           30 GCNVYIGNLDE--KV--------NERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLY   99 (211)
Q Consensus        30 ~~~lfVgnLp~--~~--------~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~   99 (211)
                      ++.|.+.|+=.  +.        -++||++.|++||.|.+|.|.++.    .+|||||+|.+.++|++|++.|||. .++
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~-~f~   81 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGR-WFA   81 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTC-EET
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCC-EEC
Confidence            56777777632  11        135889999999999999997653    5899999999999999999999999 999


Q ss_pred             CeEEEEEecCC
Q 038096          100 NRTLRFALSGQ  110 (211)
Q Consensus       100 gr~l~v~~a~~  110 (211)
                      |+.|.|.++..
T Consensus        82 GR~i~v~~~~~   92 (114)
T 3s6e_A           82 GKMITAAYVPL   92 (114)
T ss_dssp             TEECEEEEECH
T ss_pred             CEEEEEEEEcH
Confidence            99999999853

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

Probab=99.33  E-value=8.7e-12  Score=85.94  Aligned_cols=76  Identities=21%  Similarity=0.298  Sum_probs=64.7

Q ss_pred             CCCCeEEEcCCC----CCCcH----HHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeC
Q 038096           28 NSGCNVYIGNLD----EKVNE----RVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLY   99 (211)
Q Consensus        28 ~~~~~lfVgnLp----~~~~e----~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~   99 (211)
                      ++..+|+|.-++    .++..    .+|.+.|++||.|..++|+.|+        +||+|.+.++|.+||+ |||. .++
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~-~v~   74 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGK-ELL   74 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTC-EET
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCe-EeC
Confidence            557888888766    22333    5789999999999999998864        8999999999999999 9998 999


Q ss_pred             CeEEEEEecCCCcc
Q 038096          100 NRTLRFALSGQDKN  113 (211)
Q Consensus       100 gr~l~v~~a~~~~~  113 (211)
                      |+.|+|+++.++..
T Consensus        75 Gr~LkV~lkt~dW~   88 (91)
T 2dnr_A           75 NRTITIALKSPSGP   88 (91)
T ss_dssp             TEEEEEEECCCSSC
T ss_pred             CeEEEEEeCCCCcc
Confidence            99999999887654

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

Probab=99.28  E-value=1e-11  Score=90.53  Aligned_cols=76  Identities=12%  Similarity=0.126  Sum_probs=66.7

Q ss_pred             CCCCeEEEcCCCCC-CcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCC-HHHHHHHHHHcC-CCeeeCCeEEE
Q 038096           28 NSGCNVYIGNLDEK-VNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYES-EEIGHYAIKLFS-GIVTLYNRTLR  104 (211)
Q Consensus        28 ~~~~~lfVgnLp~~-~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~-~~~A~~Ai~~ln-g~~~i~gr~l~  104 (211)
                      +.++.|||+||+.+ +++++|+++|++||.|..|.+..+..      .|||.|.+ .++|.+|++.+| +.++|.|..++
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~   89 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   89 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEE
Confidence            56899999999999 99999999999999999999988764      59999999 899999999985 22489998888


Q ss_pred             EEecC
Q 038096          105 FALSG  109 (211)
Q Consensus       105 v~~a~  109 (211)
                      +....
T Consensus        90 ~evL~   94 (121)
T 1owx_A           90 WEVLE   94 (121)
T ss_dssp             EEECC
T ss_pred             EEECC
Confidence            87654

>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=99.12  E-value=7.8e-11  Score=81.59  Aligned_cols=71  Identities=13%  Similarity=0.168  Sum_probs=61.6

Q ss_pred             CCCCeEEEcCCCCC-----CcH----HHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee
Q 038096           28 NSGCNVYIGNLDEK-----VNE----RVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL   98 (211)
Q Consensus        28 ~~~~~lfVgnLp~~-----~~e----~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i   98 (211)
                      ++..+|+|.-++..     +..    .+|.+.|.+||.|..++|..|+        +||+|.+.++|.+||+ |||. .+
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~-~v   82 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGM-KV   82 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGS-EE
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCe-ee
Confidence            66889999888632     222    4689999999999999999874        9999999999999999 9998 99


Q ss_pred             CCeEEEEEec
Q 038096           99 YNRTLRFALS  108 (211)
Q Consensus        99 ~gr~l~v~~a  108 (211)
                      +||.|+|++.
T Consensus        83 ~Gr~L~V~~k   92 (95)
T 1ufw_A           83 KGRAVKISGP   92 (95)
T ss_dssp             TTEEEEEECC
T ss_pred             CCeEEEEecc
Confidence            9999999874

>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=99.12  E-value=1.3e-10  Score=93.02  Aligned_cols=68  Identities=21%  Similarity=0.139  Sum_probs=60.8

Q ss_pred             CcHHHHHHHHhcCCCeEEEEEccC----CCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCC
Q 038096           42 VNERVLYDILIQAGRVVDLYIPRD----KETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQ  110 (211)
Q Consensus        42 ~~e~~L~~~F~~~G~i~~v~i~~d----~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~  110 (211)
                      -.+++|++.|++||.|.++.|.++    ..++.++|++||+|.+.++|++|++.|||. .++||.|.+.++..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr-~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGR-WFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTC-BSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCc-eECCeEEEEEEcCH
Confidence            356799999999999999999844    455699999999999999999999999999 99999999999753

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

Probab=98.60  E-value=2.9e-07  Score=65.13  Aligned_cols=73  Identities=11%  Similarity=0.201  Sum_probs=67.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcC-----CCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEE
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQA-----GRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTL  103 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~-----G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l  103 (211)
                      ..++|-+=|||..+++..++.++..+     |.|+.+.+..|.      +-|+|+|.+...|.+|.-.|+|. +|.|++|
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~-ef~gr~L   92 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGS-QFQGKVI   92 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSE-EETTEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCe-eecCeEE
Confidence            36888888999999999999999999     999999998886      68999999999999999999998 9999999


Q ss_pred             EEEec
Q 038096          104 RFALS  108 (211)
Q Consensus       104 ~v~~a  108 (211)
                      +|.-.
T Consensus        93 r~gTv   97 (117)
T 2l9w_A           93 RSGTI   97 (117)
T ss_dssp             EEECH
T ss_pred             EecCH
Confidence            98653

>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=97.70  E-value=0.00039  Score=48.73  Aligned_cols=73  Identities=3%  Similarity=0.011  Sum_probs=62.0

Q ss_pred             CCeEEEcCCCCCC-c----HHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEE
Q 038096           30 GCNVYIGNLDEKV-N----ERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR  104 (211)
Q Consensus        30 ~~~lfVgnLp~~~-~----e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~  104 (211)
                      -++|+|.||+.++ .    .+.++++|..|+++....+.+.-      .-..|.|.+.++|.+|-..|++. .++|+.|+
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~-~f~g~~~r   77 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKT-EFLGKEMK   77 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTS-EETTEECE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccc-eecCceeE
Confidence            5789999999765 2    25778999999999887776543      35689999999999999999998 99999999


Q ss_pred             EEecC
Q 038096          105 FALSG  109 (211)
Q Consensus       105 v~~a~  109 (211)
                      |-++.
T Consensus        78 ~YFgq   82 (104)
T 1wey_A           78 LYFAQ   82 (104)
T ss_dssp             EECCC
T ss_pred             EEecC
Confidence            99986

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

Probab=97.63  E-value=0.0015  Score=45.66  Aligned_cols=70  Identities=13%  Similarity=0.093  Sum_probs=58.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhc-----CCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEE
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQ-----AGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTL  103 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~-----~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l  103 (211)
                      .+++|.|.|||..+.++.|+-+|+.     -|.|..+....        +-|+|+|.+.+.|++.|+.-.  ..|++..|
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~--H~L~~~~L   76 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQAD--HELHGAQL   76 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSC--CBSSSSBC
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCc--ceecCeEE
Confidence            4789999999999999999999987     36788886642        578999999999999998633  26888888


Q ss_pred             EEEec
Q 038096          104 RFALS  108 (211)
Q Consensus       104 ~v~~a  108 (211)
                      .|...
T Consensus        77 sV~P~   81 (104)
T 2dhx_A           77 SLRPA   81 (104)
T ss_dssp             EEEEC
T ss_pred             EEEcC
Confidence            88664

>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=97.50  E-value=0.0013  Score=45.06  Aligned_cols=78  Identities=15%  Similarity=0.101  Sum_probs=60.6

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCC--CccEEEEEeCCHHHHHHHHHHcCCCeeeCCe----EEE
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDK--PKGFAFVEYESEEIGHYAIKLFSGIVTLYNR----TLR  104 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~--~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr----~l~  104 (211)
                      ++|.|.+||+.++|+++.+.++....+........+.+..  .-+-|+|.|.+.+++..-.+.++|.+-++.+    ...
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            5899999999999999999999998877766665554322  3467899999999999999999998444432    334


Q ss_pred             EEec
Q 038096          105 FALS  108 (211)
Q Consensus       105 v~~a  108 (211)
                      |++|
T Consensus        82 VE~A   85 (91)
T 1uw4_A           82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            5554

>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=97.29  E-value=0.00062  Score=47.05  Aligned_cols=54  Identities=17%  Similarity=0.209  Sum_probs=46.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHc
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF   92 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~l   92 (211)
                      ...+++ +.|.++...||.++|+.||. ..|.++.|       --|||.|.+++.|..|+..+
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidD-------TsAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDD-------TSAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEET-------TEEEEECSCHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcC-------CeEEEEecCHHHHHHHHHhc
Confidence            344556 99999999999999999994 46777776       37999999999999999876

>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=97.22  E-value=0.00044  Score=47.92  Aligned_cols=54  Identities=17%  Similarity=0.190  Sum_probs=46.7

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFS   93 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~ln   93 (211)
                      ..++| +.|.++...||.++|+.|| -..|.++.|       --|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidD-------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDD-------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEET-------TEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcC-------CeEEEEecCHHHHHHHHHhcc
Confidence            34556 9999999999999999999 567888877       479999999999999999764

>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=97.01  E-value=0.0051  Score=44.11  Aligned_cols=72  Identities=10%  Similarity=0.098  Sum_probs=57.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCC-eEEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYN-RTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~g-r~l~v~  106 (211)
                      ...+-|-|-+.|... -+.+.+.|++||.|++....      ....+-.|.|.++.+|++||.. ||. .|+| -.|-|.
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~k-NG~-ii~g~~mIGV~   92 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSK-DGR-IFGESIMIGVK   92 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHTT-TTC-EETTTEECEEE
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHHh-CCe-EecCCEEEEEE
Confidence            346778888999875 56777889999999998762      2347999999999999999987 898 7875 566776


Q ss_pred             ec
Q 038096          107 LS  108 (211)
Q Consensus       107 ~a  108 (211)
                      +.
T Consensus        93 p~   94 (119)
T 1wwh_A           93 PC   94 (119)
T ss_dssp             EC
T ss_pred             EC
Confidence            64

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

Probab=96.61  E-value=0.0098  Score=41.06  Aligned_cols=79  Identities=11%  Similarity=0.016  Sum_probs=55.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCC--CccEEEEEeCCHHHHHHHHHHcCCCeeeCCe----EE
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDK--PKGFAFVEYESEEIGHYAIKLFSGIVTLYNR----TL  103 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~--~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr----~l  103 (211)
                      +-+|.|..||+.+||+++.+.++..-.+........+.+.+  .-.-|+|.|.+.++...-.+.++|.+-++.+    +.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            57899999999999999888777654443333333222211  2356899999999999999999998444433    44


Q ss_pred             EEEec
Q 038096          104 RFALS  108 (211)
Q Consensus       104 ~v~~a  108 (211)
                      .|++|
T Consensus        89 ~VE~A   93 (97)
T 2l08_A           89 VVEFA   93 (97)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            56665

>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=96.43  E-value=0.0018  Score=48.15  Aligned_cols=35  Identities=11%  Similarity=0.042  Sum_probs=29.0

Q ss_pred             EEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCC
Q 038096           59 DLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGI   95 (211)
Q Consensus        59 ~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~   95 (211)
                      .+.|+.+.  ++++|||||+|.+.++|++|++.+++.
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhccc
Confidence            45666665  468999999999999999999888764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.39  E-value=0.0065  Score=44.23  Aligned_cols=77  Identities=9%  Similarity=0.148  Sum_probs=54.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEE-EEEccCC--------CCC-----CCccEEEEEeCCHHHHHHHHHHcCCC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVD-LYIPRDK--------ETD-----KPKGFAFVEYESEEIGHYAIKLFSGI   95 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~-v~i~~d~--------~tg-----~~rg~aFV~f~~~~~A~~Ai~~lng~   95 (211)
                      ..-|.|-+.|.... ..+-+.|++||.|.+ .....+.        .+.     ....+-.|+|.+..+|.+||.. ||.
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-NGA   84 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-TTC
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-CCe
Confidence            45666778887655 456677999999977 2222100        000     1357889999999999999987 898


Q ss_pred             eeeCCeEEEEEecC
Q 038096           96 VTLYNRTLRFALSG  109 (211)
Q Consensus        96 ~~i~gr~l~v~~a~  109 (211)
                       .|+|..|-|.+..
T Consensus        85 -ii~G~mIGV~Py~   97 (132)
T 3p3d_A           85 -VFNGVLLGVIPYT   97 (132)
T ss_dssp             -EETTEECEEEECC
T ss_pred             -EeCcEEEEEEECC
Confidence             8999988888754

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.24  E-value=0.0021  Score=56.58  Aligned_cols=56  Identities=21%  Similarity=0.158  Sum_probs=42.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHH
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL   91 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~   91 (211)
                      .+.|||. .+..+++++|.++|++||.|.++..-.++.     -||.|+|.+.++++.++..
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g-----~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFG-----LYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSS-----EEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCC-----eEEEEEeCCHHHHHHHHhc
Confidence            4789997 799999999999999999999998876542     7999999999999877654

>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=95.66  E-value=0.004  Score=45.95  Aligned_cols=41  Identities=10%  Similarity=0.054  Sum_probs=36.8

Q ss_pred             CCCccEEEEEeCCHHHHHHHHHHc-CCCeeeCCeEEEEEecCCC
Q 038096           69 DKPKGFAFVEYESEEIGHYAIKLF-SGIVTLYNRTLRFALSGQD  111 (211)
Q Consensus        69 g~~rg~aFV~f~~~~~A~~Ai~~l-ng~~~i~gr~l~v~~a~~~  111 (211)
                      ..-+|+++|+|.+.++|++|++.+ ||. .++| .|.+.++...
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~-~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDN-GVDG-EWTYDDATKT   51 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHH-TCCC-EEEEETTTTE
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCC-CCCC-ceecccccCc
Confidence            467899999999999999999999 998 9999 9999987643

>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=90.55  E-value=0.62  Score=41.37  Aligned_cols=55  Identities=16%  Similarity=0.196  Sum_probs=45.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFS   93 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~ln   93 (211)
                      ...++|+ ++..+...+|.+.|+.||. .+|.++.|       ..|||.|.+.+.|..+++.++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widd-------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDD-------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSS-------SEEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcC-------CeEEEEECCHHHHHHHHHHHH
Confidence            3456676 8888899999999999995 46777665       469999999999999999884

---

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	211
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-13
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-13
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-13
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	8e-11
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-10
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-10
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-10
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-10
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	8e-10
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	8e-10
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-09
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:) 3e-09
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-09
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	4e-09
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	4e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	4e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	5e-09
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	6e-09
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	7e-09
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-08
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-08
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-08
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	5e-08
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	7e-08
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	7e-08
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	9e-08
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-07
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-07
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-07
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-07
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	4e-07
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	5e-07
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	5e-07
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	6e-07
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	6e-07
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	6e-07
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-06
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-06
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-06
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-06
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	7e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	9e-06
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-05
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-05
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-05
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	3e-05
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	4e-05
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	6e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	6e-05
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-04
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	2e-04
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-04
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	3e-04
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-04
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-04
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	4e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	6e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.001
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	0.001
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.001
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	0.002
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	0.003
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.004
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.004

>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 = 61.1 bits (148), Expect = 3e-13
 Identities = 16/90 (17%), Positives = 37/90 (41%), Gaps = 1/90 (1%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKE-TDKPKGFAFVEYESEEIG 85
             +   + + N+  + N+R + ++    G +  + +P+    T   +GF FV++ +++  
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 86  HYAIKLFSGIVTLYNRTLRFALSGQDKNAQ 115
             A         LY R L    +  +   Q
Sbjct: 65  KKAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>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 = 60.7 bits (147), Expect = 3e-13
 Identities = 26/81 (32%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 25  GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
           G S    N+Y+ NL   + +  L  I  + G +V   I RDK T +P+G AFV Y   E 
Sbjct: 1   GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 60

Query: 85  GHYAIKLFSG-IVTLYNRTLR 104
              AI   +  I    ++ L 
Sbjct: 61  AQEAISALNNVIPEGGSQPLS 81

>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 = 60.3 bits (146), Expect = 3e-13
 Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 1/80 (1%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
           ++Y+G+L   V E +LY+    AG ++ + + RD  T +  G+A+V ++       A+  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 92  FSGIVTLYNRTLRFALSGQD 111
            +  V +  + +R   S +D
Sbjct: 62  MNFDV-IKGKPVRIMWSQRD 80

>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 = 54.3 bits (130), Expect = 8e-11
 Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 30  GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
             N+Y+  L + + ++ L  +  Q GR++   I  D+ T   +G  F+ ++       AI
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 65

Query: 90  KLFSGIVTLYNRTLR 104
           K  +G       T  
Sbjct: 66  KGLNGQK-PSGATEP 79

>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 = 54.2 bits (130), Expect = 1e-10
 Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 30  GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
            C +Y+GNL     E  +Y++  ++G +  + +  DK      GF FVEY S      A+
Sbjct: 7   SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 66

Query: 90  KLFSGIVTLYNRTLR 104
           +  +G   L +R +R
Sbjct: 67  RYINGTR-LDDRIIR 80

>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 = 53.4 bits (128), Expect = 2e-10
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
           C ++IG L  +  +  L +   Q G V +  + RD  T + +GF FV +  +      + 
Sbjct: 1   CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

Query: 91  LFSGIVTLYNRTLR 104
                  L ++T+ 
Sbjct: 61  Q--SRHELDSKTID 72

>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 = 53.4 bits (128), Expect = 2e-10
 Identities = 17/87 (19%), Positives = 32/87 (36%), Gaps = 5/87 (5%)

Query: 29  SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
              ++ +  L  K  E+ L +     G V+ + + +D +T   KGF FV +   E     
Sbjct: 7   KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 66

Query: 89  IKLFSGIVTLYNRTLR--FALSGQDKN 113
           +        +  R        S Q ++
Sbjct: 67  MS---QRHMIDGRWCDCKLPNSKQSQD 90

>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 = 53.9 bits (129), Expect = 2e-10
 Identities = 21/90 (23%), Positives = 34/90 (37%), Gaps = 4/90 (4%)

Query: 28  NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
                +YI NL  K+    +YDI  + G +  + +       + +G A+V YE       
Sbjct: 5   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKN 61

Query: 88  AIKLFSGIVTLYNRTLRFALSGQDKNAQNS 117
           A    SG   + NR L       ++  Q  
Sbjct: 62  ACDHLSG-FNVCNRYLVVLYYNANRAFQKM 90

>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 = 52.4 bits (125), Expect = 4e-10
 Identities = 14/84 (16%), Positives = 29/84 (34%), Gaps = 1/84 (1%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           S        + + N+   V+   + D       +      +  E   P G A V +ES +
Sbjct: 3   SSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD 62

Query: 84  IGHYAIKLFSGIVTLYNRTLRFAL 107
               A+   +    + +R ++  L
Sbjct: 63  EATAAVIDLNDRP-IGSRKVKLVL 85

>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 = 51.6 bits (123), Expect = 8e-10
 Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 6/72 (8%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +YIGNL   V    L  +       +   +          G+AFV+Y  +     AI+  
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQVL------LKSGYAFVDYPDQNWAIRAIETL 57

Query: 93  SGIVTLYNRTLR 104
           SG V L+ + + 
Sbjct: 58  SGKVELHGKIME 69

>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 = 52.0 bits (124), Expect = 8e-10
 Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 3/92 (3%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDL--YIPRDKETDKPKGFAFVEYESEEIGHYA 88
           C ++IG + +      + + + +    V          +  K +GFAFVEYES      A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 89  IK-LFSGIVTLYNRTLRFALSGQDKNAQNSSM 119
            + L  G + L+   +    +  + +     M
Sbjct: 62  RRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVM 93

>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 = 51.2 bits (122), Expect = 2e-09
 Identities = 24/97 (24%), Positives = 38/97 (39%), Gaps = 2/97 (2%)

Query: 17  RNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAF 76
           R     +S        V+   L  ++  R L D     G+V D+ I  D+ + + KG A+
Sbjct: 5   REPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAY 64

Query: 77  VEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDKN 113
           VE+   +    AI L      L    +    S  +KN
Sbjct: 65  VEFCEIQSVPLAIGLTG--QRLLGVPIIVQASQAEKN 99

>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 = 50.8 bits (121), Expect = 3e-09
 Identities = 16/91 (17%), Positives = 36/91 (39%), Gaps = 2/91 (2%)

Query: 18  NKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFV 77
           N  Q   G  ++  +V +    ++  E V  ++  + G V ++ +  +   D   G  +V
Sbjct: 15  NSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYV 73

Query: 78  EYESEEIGHYAIKLFSGIVTLYNRTLRFALS 108
           ++  EE    A+   +       + +   LS
Sbjct: 74  KFRREEDAEKAVIDLNNRW-FNGQPIHAELS 103

>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 = 50.4 bits (120), Expect = 3e-09
 Identities = 34/79 (43%), Positives = 53/79 (67%), Gaps = 1/79 (1%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
             N    VY+G LDEKV+E +L+++ +QAG VV+ ++P+D+ T + +G+ FVE+ SEE  
Sbjct: 5   ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 64

Query: 86  HYAIKLFSGIVTLYNRTLR 104
            YAIK+   I  LY + +R
Sbjct: 65  DYAIKIMDMI-KLYGKPIR 82

>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 = 49.7 bits (118), Expect = 4e-09
 Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 1/79 (1%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
           N +  C + +  L     ER L ++  + G + D+ I  D+++ + +GFAFV +E+ +  
Sbjct: 5   NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 64

Query: 86  HYAIKLFSGIVTLYNRTLR 104
             A +  +G + L  R +R
Sbjct: 65  KEAKERANG-MELDGRRIR 82

>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 = 49.6 bits (118), Expect = 4e-09
 Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 29  SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
           S  N+ +  L + + +R LY +    G +    I RD +T    G+AFV++ SE     A
Sbjct: 1   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 89  IKLFSGIVTLYNRTLR 104
           IK+ +GI T+ N+ L+
Sbjct: 61  IKVLNGI-TVRNKRLK 75

>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 = 49.6 bits (118), Expect = 4e-09
 Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 2/72 (2%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           ++IG L  +  +  L     Q G + D  + RD  T + +GF FV Y + E    A+   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68

Query: 93  SGIVTLYNRTLR 104
                +  R + 
Sbjct: 69  PH--KVDGRVVE 78

>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 = 50.1 bits (119), Expect = 4e-09
 Identities = 19/87 (21%), Positives = 33/87 (37%), Gaps = 4/87 (4%)

Query: 28  NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
           N+ C +Y+GNL   +  + + D+  + G + D+ +           FAFVE+E       
Sbjct: 12  NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAED 68

Query: 88  AIKLFSGIVTLYNRTLRFALSGQDKNA 114
           A+    G        LR       +  
Sbjct: 69  AVYGRDGYD-YDGYRLRVEFPRSGRGT 94

>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 = 49.2 bits (117), Expect = 4e-09
 Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 2/72 (2%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           ++IG L     ++ L D   + G VVD  +  D  T + +GF FV ++  E     +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ- 60

Query: 93  SGIVTLYNRTLR 104
                L  + + 
Sbjct: 61  -KEHKLNGKVID 71

>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 = 49.6 bits (118), Expect = 4e-09
 Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 4/84 (4%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           ++IG L   +N+  + ++L   G +    + +D  T   KG+AF EY    +   AI   
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 93  SGIVTLYNRTLR--FALSGQDKNA 114
           +G+  L ++ L    A S   KNA
Sbjct: 64  NGM-QLGDKKLLVQRA-SVGAKNA 85

>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 = 49.4 bits (117), Expect = 5e-09
 Identities = 27/83 (32%), Positives = 45/83 (54%), Gaps = 4/83 (4%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLY-IPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
           ++IGNLD +++E++LYD     G ++    I RD +T   KG+AF+ + S +    AI+ 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 92  FSGIVTLYNRTLR--FALSGQDK 112
            +G   L NR +   +A     K
Sbjct: 61  MNGQ-YLCNRPITVSYAFKKDSK 82

>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 = 49.3 bits (117), Expect = 6e-09
 Identities = 30/78 (38%), Positives = 47/78 (60%), Gaps = 1/78 (1%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
           + +   +Y+G L E+V+++VL+   I  G + D+ IP D ET+K +GFAFVE+E  E   
Sbjct: 2   ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61

Query: 87  YAIKLFSGIVTLYNRTLR 104
            AI   +    L+ RT+R
Sbjct: 62  AAIDNMNESE-LFGRTIR 78

>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 = 49.6 bits (118), Expect = 7e-09
 Identities = 19/87 (21%), Positives = 31/87 (35%), Gaps = 6/87 (6%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
           M+G S     + + NL   V   VL+ I  + G V+ +           +  A ++Y   
Sbjct: 1   MAGQSPV-LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFT----KNNQFQALLQYADP 55

Query: 83  EIGHYAIKLFSGI-VTLYNRTLRFALS 108
               +A     G  +     TLR   S
Sbjct: 56  VSAQHAKLSLDGQNIYNACCTLRIDFS 82

>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 = 48.2 bits (114), Expect = 2e-08
 Identities = 31/94 (32%), Positives = 41/94 (43%), Gaps = 2/94 (2%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           SG+S SG  +++ NL    +E  L  +    G + +L+ P D  T KPKGFAFV +   E
Sbjct: 3   SGSSGSG-RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

Query: 84  IGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNS 117
               A     G      R L    S   K A  S
Sbjct: 62  HAVKAYAEVDG-QVFQGRMLHVLPSTIKKEASQS 94

>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 = 46.9 bits (111), Expect = 3e-08
 Identities = 14/59 (23%), Positives = 29/59 (49%)

Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
          +++G L     E  + +     G V  + +P D +T+K +GF F+ ++ EE     ++ 
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

>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 = 47.4 bits (112), Expect = 3e-08
 Identities = 17/84 (20%), Positives = 41/84 (48%), Gaps = 3/84 (3%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
           S  G  +++ ++ E+  E  + +     G + ++++  D+ T   KG+A VEYE+ +   
Sbjct: 4   SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 63

Query: 87  YAIKLFSGIVTLYNRTLR--FALS 108
            A +  +G   +  +T++  +   
Sbjct: 64  AAKEALNGAE-IMGQTIQVDWCFV 86

>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 = 47.4 bits (112), Expect = 5e-08
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
             ++IG L  +  E  L +   Q G++ D  + RD  + + +GF FV + S      A+ 
Sbjct: 21  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 80

Query: 91  LFSGIVTLYNRTLR 104
                 ++  R + 
Sbjct: 81  ARPH--SIDGRVVE 92

>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 = 46.1 bits (109), Expect = 7e-08
 Identities = 17/76 (22%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           + + NLD  V++  + ++  + G +    +  D+ + +  G A V +E +     A+K +
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 61

Query: 93  SGIVTLYNRTLRFALS 108
           +G V L  R +   L 
Sbjct: 62  NG-VPLDGRPMNIQLV 76

>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 = 46.5 bits (110), Expect = 7e-08
 Identities = 13/84 (15%), Positives = 39/84 (46%), Gaps = 7/84 (8%)

Query: 21  QIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE 80
            +++ +S   C VY G +   + ++++       G+++++ +  +K       ++FV + 
Sbjct: 9   DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFS 62

Query: 81  SEEIGHYAIKLFSGIVTLYNRTLR 104
           + E   +AI   +G   +    ++
Sbjct: 63  THESAAHAIVSVNGTT-IEGHVVK 85

>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 = 46.3 bits (109), Expect = 9e-08
 Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 7/77 (9%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPR-----DKETDKPKGFAFVEYESEEIGHY 87
           +Y+GN+   + E  + D      R+  L           + ++ K FAF+E+ S +    
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 88  AIKLFSGIVTLYNRTLR 104
           A+      +    ++L+
Sbjct: 64  AMAFDG--IIFQGQSLK 78

>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 = 45.8 bits (108), Expect = 1e-07
 Identities = 21/78 (26%), Positives = 31/78 (39%), Gaps = 4/78 (5%)

Query: 34  YIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKE---TDKPKGFAFVEYESEEIGHYAIK 90
           +I NL+    E  L  +  + G +    I + K         GF FVEY+  E    A+K
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 91  LFSGIVTLYNRTLRFALS 108
              G  T+    L   +S
Sbjct: 62  QLQG-HTVDGHKLEVRIS 78

>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 = 45.9 bits (108), Expect = 1e-07
 Identities = 19/86 (22%), Positives = 47/86 (54%), Gaps = 1/86 (1%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
             +++G L    NE+ L  +  + G++ ++ + +D+ET + +GF FV +E+ +    A+ 
Sbjct: 6   GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 65

Query: 91  LFSGIVTLYNRTLRFALSGQDKNAQN 116
             +G  ++  R +R   +G+  + ++
Sbjct: 66  AMNGK-SVDGRQIRVDQAGKSSDNRS 90

>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 = 45.5 bits (107), Expect = 1e-07
 Identities = 17/76 (22%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 29  SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
           S  N+ +  L + + +     +    G +    + RDK T +  G+ FV Y   +    A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 89  IKLFSGIVTLYNRTLR 104
           I   +G+  L  +T++
Sbjct: 61  INTLNGLR-LQTKTIK 75

>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 = 45.9 bits (108), Expect = 2e-07
 Identities = 15/91 (16%), Positives = 30/91 (32%), Gaps = 4/91 (4%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
             +++G L     +  L       G + +  +  D++T K +G+ FV          A K
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 70

Query: 91  LFSGIVTLYNRTLR--FALSGQDKNAQNSSM 119
             +    +  R      A  G    +  +  
Sbjct: 71  DPNP--IIDGRKANVNLAYLGAKPRSLQTGF 99

>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 = 44.7 bits (105), Expect = 2e-07
 Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 2/72 (2%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +++G L        +     Q G+V D  +  DK T++ +GF FV +ESE+I     ++ 
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI- 60

Query: 93  SGIVTLYNRTLR 104
                + N+ + 
Sbjct: 61  -HFHEINNKMVE 71

>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 = 46.9 bits (110), Expect = 2e-07
 Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 4/83 (4%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
             +++G + E   E  L D   Q G++  + I  D+ + K +GFAFV ++  +     + 
Sbjct: 98  KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 157

Query: 91  LFSGIVTLYNRTLR--FALSGQD 111
                 T+         ALS Q+
Sbjct: 158 QKYH--TVNGHNCEVRKALSKQE 178

>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 = 46.5 bits (109), Expect = 4e-07
 Identities = 22/92 (23%), Positives = 38/92 (41%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           ++IG L  +  +  L     Q G + D  + RD  T + +GF FV Y + E    A+   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68

Query: 93  SGIVTLYNRTLRFALSGQDKNAQNSSMTTTPL 124
              V       + A+S +D     + +T   +
Sbjct: 69  PHKVDGRVVEPKRAVSREDSQRPGAHLTVKKI 100

>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 = 45.2 bits (107), Expect = 3e-07
 Identities = 24/100 (24%), Positives = 43/100 (43%), Gaps = 16/100 (16%)

Query: 24  SGNSNS------GCNVYIGNLD-EKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAF 76
           SG+S           V+IGNL+   V +  +  I  + G++V   + +        GFAF
Sbjct: 3   SGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAF 54

Query: 77  VEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQN 116
           V+Y +E     A+    G   +  + L   L+ + K  ++
Sbjct: 55  VQYVNERNARAAVAGEDGR-MIAGQVLDINLAAEPKVNRS 93

>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 = 44.7 bits (105), Expect = 3e-07
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 27  SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
           ++    + + NL E   E  L ++    G +  +Y+ +DK T + KGFAF+ +   E   
Sbjct: 5   ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 64

Query: 87  YAIKLFSGIVTLYNRTLR 104
            AI   SG     +  L 
Sbjct: 65  RAIAGVSGFG-YDHLILN 81

>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 = 44.0 bits (103), Expect = 4e-07
 Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 1/78 (1%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
           C +++ N      +R + D+L     V           +  + FA+++  S+E   Y ++
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 91  LFSGIVTLYNRTLRFALS 108
             +G+  +   TL   +S
Sbjct: 62  KLNGLK-IEGYTLVTKVS 78

>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 = 43.9 bits (103), Expect = 5e-07
 Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 2/72 (2%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +++G + E   E  L D   Q G++  + I  D+ + K +GFAFV ++  +     +   
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 64

Query: 93  SGIVTLYNRTLR 104
               T+      
Sbjct: 65  Y--HTVNGHNCE 74

>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 = 44.4 bits (104), Expect = 5e-07
 Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 3/84 (3%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
             +Y+ NL  +V ER L  +  +        I     T + +G AF+ + ++EI   A+ 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 91  LFSGIVTLYNRTLR--FALSGQDK 112
           L +G   LY + L   F  + + +
Sbjct: 79  LVNGYK-LYGKILVIEFGKNKKQR 101

>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 = 44.4 bits (104), Expect = 6e-07
 Identities = 28/100 (28%), Positives = 39/100 (39%), Gaps = 10/100 (10%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIP--------RDKETDKPKGFAFV 77
             +    +Y+  L++ V    L D   Q G V               DKET KPKG A V
Sbjct: 4   EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 63

Query: 78  EYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNS 117
            YE       A++ F G        L+ +L+ + K   NS
Sbjct: 64  SYEDPPTAKAAVEWFDGKD-FQGSKLKVSLA-RKKPPMNS 101

>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 = 44.0 bits (103), Expect = 6e-07
 Identities = 20/87 (22%), Positives = 37/87 (42%), Gaps = 5/87 (5%)

Query: 23  MSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE 82
           +  +   G  V+I NL     E  L ++L Q G +  + +    +T+  KG AF ++ ++
Sbjct: 1   LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 60

Query: 83  EIGHYAIKLFSGI-----VTLYNRTLR 104
           E     +   S       + L  R L+
Sbjct: 61  EAAQKCLAAASLEAEGGGLKLDGRQLK 87

>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 = 44.3 bits (104), Expect = 6e-07
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 30  GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
           G N++I +L ++  ++ L  + +  G VV   +  DK+T+  K F FV Y++      AI
Sbjct: 18  GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 77

Query: 90  KLFSGIVTLYNRTLR 104
           +  +G   +  + L+
Sbjct: 78  QSMNGFQ-IGMKRLK 91

>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 = 43.1 bits (101), Expect = 1e-06
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 4/83 (4%)

Query: 22  IMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYES 81
           +M  +      +Y+GNL   V E ++  +  Q G      +  +  ++ P  + FVE+  
Sbjct: 1   MMEDDGQPR-TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYE 57

Query: 82  EEIGHYAIKLFSGIVTLYNRTLR 104
                 A+   +G   +  + ++
Sbjct: 58  HRDAAAALAAMNGRK-ILGKEVK 79

>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 = 43.1 bits (101), Expect = 1e-06
 Identities = 22/81 (27%), Positives = 42/81 (51%), Gaps = 3/81 (3%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           S   +   N++I NLD+ ++ + LYD     G ++   +  D+     KG+ FV +E++E
Sbjct: 2   SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQE 59

Query: 84  IGHYAIKLFSGIVTLYNRTLR 104
               AI+  +G + L +R + 
Sbjct: 60  AAERAIEKMNG-MLLNDRKVF 79

>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 = 43.1 bits (101), Expect = 1e-06
 Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 2/85 (2%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQA-GRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
             +YI NL+EK+ +  L   L     R   +       + K +G AFV ++       A+
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 90  KLFSGIVTLYNRTLRFALSGQDKNA 114
           +   G    Y++ +R   +  D + 
Sbjct: 64  RSMQGFP-FYDKPMRIQYAKTDSDI 87

>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 = 42.1 bits (98), Expect = 2e-06
 Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 1/72 (1%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +YI  L     ++ L  +    G++V      DK T+K KG+ FV+++S      A+   
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 93  SGIVTLYNRTLR 104
                +  +  +
Sbjct: 61  KA-SGVQAQMAK 71

>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 = 41.9 bits (98), Expect = 3e-06
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 7/83 (8%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
             +++GNL   + E  +  +  + G+  +++I +DK       F F+  E+  +   A  
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKV 62

Query: 91  LFSGIVTLYNRTLRFALSGQDKN 113
                + L  + LR   +    +
Sbjct: 63  ELDN-MPLRGKQLRVRFACHSAS 84

>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 = 40.9 bits (95), Expect = 7e-06
 Identities = 19/92 (20%), Positives = 34/92 (36%), Gaps = 8/92 (8%)

Query: 17  RNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAF 76
           +N + I   ++     +++ N+   V+E  L  +    G VV       K   K +  A 
Sbjct: 1   KNFQNIFPPSAT----LHLSNIPPSVSEEDLKVLFSSNGGVV----KGFKFFQKDRKMAL 52

Query: 77  VEYESEEIGHYAIKLFSGIVTLYNRTLRFALS 108
           ++  S E    A+          N  LR + S
Sbjct: 53  IQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 84

>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 = 40.9 bits (95), Expect = 9e-06
 Identities = 32/95 (33%), Positives = 49/95 (51%), Gaps = 3/95 (3%)

Query: 32  NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
           +V++GN+  +  E  L DI  + G VV   +  D+ET KPKG+ F EY+ +E    A++ 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 92  FSGIVTLYNRTLR--FALSGQDKNAQNSSMTTTPL 124
            +G      R LR   A S ++K    S  T  P+
Sbjct: 70  LNGR-EFSGRALRVDNAASEKNKEELKSLGTGAPV 103

>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 = 40.4 bits (94), Expect = 1e-05
 Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 6/84 (7%)

Query: 24  SGNSNS---GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE 80
           SGNS S      +++ N+  +  +  L  +  Q G+++D+ I  ++     KGF FV +E
Sbjct: 2   SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFE 59

Query: 81  SEEIGHYAIKLFSGIVTLYNRTLR 104
           +      A +   G V +  R + 
Sbjct: 60  NSADADRAREKLHGTV-VEGRKIE 82

>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 = 40.0 bits (93), Expect = 2e-05
 Identities = 20/96 (20%), Positives = 35/96 (36%), Gaps = 11/96 (11%)

Query: 25  GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
           G+S S   V++G     + E  L +   Q G V+D            + FAFV +  ++I
Sbjct: 1   GSSGS-SGVFVGRCTGDMTEDELREFFSQYGDVMD-----VFIPKPFRAFAFVTFADDQI 54

Query: 85  GHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSS 118
                        +   ++    A    + N+  SS
Sbjct: 55  AQSLCGEDL---IIKGISVHISNAEPKHNSNSGPSS 87

>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 = 15/79 (18%), Positives = 32/79 (40%), Gaps = 7/79 (8%)

Query: 32  NVYIGNLDEKVNE---RVLYDILIQAGRVVDLYIPRDKETDK---PKGFAFVEYESEEIG 85
            V++  L +++ +       +   + G++  + I           P   A+V Y   E  
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 86  HYAIKLFSGIVTLYNRTLR 104
             AI+  + +V +  RTL+
Sbjct: 70  LRAIQCVNNVV-VDGRTLK 87

>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 = 39.6 bits (92), Expect = 3e-05
 Identities = 16/81 (19%), Positives = 31/81 (38%), Gaps = 6/81 (7%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           S    +   +   NL   + E  L ++   A       I    +  K KG A++E++SE 
Sbjct: 10  SKKVRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKSEA 64

Query: 84  IGHYAIKLFSGIVTLYNRTLR 104
                ++   G   +  R++ 
Sbjct: 65  DAEKNLEEKQGAE-IDGRSVS 84

>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 = 39.4 bits (91), Expect = 3e-05
 Identities = 8/65 (12%), Positives = 25/65 (38%)

Query: 27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
          +++    +I N+   + +  +   L       +          +  G A V++++E+   
Sbjct: 5  NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDAR 64

Query: 87 YAIKL 91
           + +L
Sbjct: 65 KSERL 69

>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 = 38.5 bits (89), Expect = 4e-05
 Identities = 16/76 (21%), Positives = 29/76 (38%), Gaps = 9/76 (11%)

Query: 29  SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
            G  +Y+   D  +   +L       G ++DL +   +        AFV YE  E    A
Sbjct: 4   KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQA 55

Query: 89  IKLFSGIVTLYNRTLR 104
           +   +G   + +  L+
Sbjct: 56  VAELNGTQ-VESVQLK 70

>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 = 38.5 bits (89), Expect = 6e-05
 Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 7/72 (9%)

Query: 33  VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
           +Y+ NL    +E ++                  +   K + +AFV + + E    A+K  
Sbjct: 11  LYVRNLMLSTSEEMIEKEFNNIKPG------AVERVKKIRDYAFVHFSNREDAVEAMKAL 64

Query: 93  SGIVTLYNRTLR 104
           +G V L    + 
Sbjct: 65  NGKV-LDGSPIE 75

>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 = 38.2 bits (88), Expect = 6e-05
 Identities = 21/102 (20%), Positives = 39/102 (38%), Gaps = 15/102 (14%)

Query: 25  GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
           G+S S   + + NL +  N + ++D+L            +    D+ K  AFV   + E 
Sbjct: 1   GSSGS-SGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQ 52

Query: 85  GHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSS 126
              AI++F    +   + L   L          ++  +  SS
Sbjct: 53  AQNAIQMFHQY-SFRGKDLIVQL------QPTDALLCSGPSS 87

>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 = 38.2 bits (88), Expect = 1e-04
 Identities = 25/103 (24%), Positives = 41/103 (39%), Gaps = 10/103 (9%)

Query: 24  SGNSNSG------CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFV 77
           SG+S S          ++GNL   V E  + +                   ++ KGF + 
Sbjct: 3   SGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYA 62

Query: 78  EYESEEIGHYAIKLFSGIVTLYNRTLR--FALSGQDKNAQNSS 118
           E+E  +    A+ L     +L N+ +R   A   QDK++  SS
Sbjct: 63  EFEDLDSLLSALSLNE--ESLGNKRIRVDVADQAQDKDSGPSS 103

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

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 = 37.6 bits (86), Expect = 2e-04
 Identities = 19/89 (21%), Positives = 31/89 (34%), Gaps = 2/89 (2%)

Query: 16  SRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFA 75
           S  KR        +G  VY+  L  +   + + D   +   V D          K  G  
Sbjct: 4   SGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEG 63

Query: 76  FVEYESEEIGHYAIKLFSGIVTLYNRTLR 104
           FVE+ +E     A+        + NR ++
Sbjct: 64  FVEFRNEADYKAALCRHKQ--YMGNRFIQ 90

>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 = 36.5 bits (84), Expect = 2e-04
 Identities = 5/62 (8%), Positives = 13/62 (20%), Gaps = 7/62 (11%)

Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
            V +    +     +L                          +  + Y+S+     A+ 
Sbjct: 5  TWVTVFGFPQASASYILLQF-------AQYGNILKHVMSNTGNWMHIRYQSKLQARKALS 57

Query: 91 LF 92
            
Sbjct: 58 KD 59

>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 = 3e-04
 Identities = 16/81 (19%), Positives = 34/81 (41%), Gaps = 4/81 (4%)

Query: 30  GCNVYIGNLDEKV-NERVLYDILIQ-AGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
           G  + I NL  ++ +E +L +                 KE       AF+ +E+++    
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 88  AIKLFSGIVTLYNRTLRFALS 108
           A+++ +    L NR +  +L+
Sbjct: 64  ALQM-NR-SLLGNREISVSLA 82

>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 = 36.7 bits (84), Expect = 3e-04
 Identities = 3/69 (4%), Positives = 13/69 (18%), Gaps = 11/69 (15%)

Query: 27 SNSGCNVYIGNLDEKVNERV-----LYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYES 81
          S+    +     ++ V            +     +       +            + + +
Sbjct: 2  SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSN 55

Query: 82 EEIGHYAIK 90
                A  
Sbjct: 56 PLSAADARL 64

>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 = 37.2 bits (85), Expect = 3e-04
 Identities = 21/89 (23%), Positives = 42/89 (47%), Gaps = 3/89 (3%)

Query: 26  NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
             +   N+ +  +   V+E  L  +  + G +  + I  D+ET + +G+ FV+++S    
Sbjct: 38  EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97

Query: 86  HYAIKLFSGIVTLYNRTLR--FALSGQDK 112
             AI   +G   + N+ L+   A SG  +
Sbjct: 98  QQAIAGLNGFN-ILNKRLKVALAASGHQR 125

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

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 = 36.1 bits (82), Expect = 4e-04
 Identities = 17/85 (20%), Positives = 36/85 (42%), Gaps = 3/85 (3%)

Query: 20  RQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEY 79
             +    S +  N++IGNL+   +   L   + +     D     D  T   + F +V++
Sbjct: 3   HMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDF 61

Query: 80  ESEEIGHYAIKLFSGIVTLYNRTLR 104
           ES E    A++L    + ++   ++
Sbjct: 62  ESAEDLEKALELTG--LKVFGNEIK 84

>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 = 35.7 bits (82), Expect = 6e-04
 Identities = 12/58 (20%), Positives = 19/58 (32%), Gaps = 5/58 (8%)

Query: 47  LYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR 104
           L     + G++  L +        P G A V +   E   Y I+   G      R + 
Sbjct: 36  LRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLDG-RWFGGRQIT 88

>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 = 35.3 bits (81), Expect = 0.001
 Identities = 16/90 (17%), Positives = 28/90 (31%), Gaps = 7/90 (7%)

Query: 33  VYIGNLDEKVNERVLYDILIQAG----RVVDLYIPRDKET--DKPKGFAFVEYESEEIGH 86
           V    L +      + + +         V  + IPR  +       G  FVE+ S     
Sbjct: 13  VLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQ 72

Query: 87  YAIKLFSGIVTLYNRTLRFALSGQDKNAQN 116
            A++  +G     NR +       D   + 
Sbjct: 73  KAMQGLTGRK-FANRVVVTKYCDPDSYHRR 101

>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 = 35.1 bits (80), Expect = 0.001
 Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 7/79 (8%)

Query: 31  CNVYIGNLD-EKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
             + + NL+ E+V  + L+ +    G V  + I  +K+       A V+         A+
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLAM 57

Query: 90  KLFSGIVTLYNRTLRFALS 108
              +G   L+ + +R  LS
Sbjct: 58  SHLNG-HKLHGKPIRITLS 75

>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 = 34.9 bits (79), Expect = 0.001
 Identities = 16/111 (14%), Positives = 32/111 (28%), Gaps = 7/111 (6%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
             +  S   +   NL        + +   + G +  + +P           A VE+    
Sbjct: 4   GSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPL 57

Query: 84  IGHYAIKLFSGIVTLYNR-TLRFALSGQDKNAQNSSMTTTPLSSRKSRSDP 133
               A +  +     +    L +A  G    A     +     + K+ S P
Sbjct: 58  EARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGP 108

>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 = 34.4 bits (78), Expect = 0.002
 Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 2/78 (2%)

Query: 31  CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
            N+YI NL   ++E+ L + +++    V         +   +G  F   ES E     I 
Sbjct: 19  TNLYISNLPLSMDEQELEN-MLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIG 77

Query: 91  LFSGIVTLYNRTLRFALS 108
            F+G   +       A +
Sbjct: 78  HFNG-KFIKTPPGVSAPT 94

>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 = 33.5 bits (76), Expect = 0.003
 Identities = 17/95 (17%), Positives = 36/95 (37%), Gaps = 7/95 (7%)

Query: 21  QIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE 80
           +I  G +N    +++G L    +   L     + G +  +   +         FA+++YE
Sbjct: 8   KIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYE 61

Query: 81  SEEIGHYAIKLFSG-IVTLYNRTLRFALSGQDKNA 114
           S +    A     G  +   +R LR   +    ++
Sbjct: 62  SLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPSS 96

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {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: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.6 bits (76), Expect = 0.004
 Identities = 15/94 (15%), Positives = 32/94 (34%), Gaps = 4/94 (4%)

Query: 24  SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
           S  S +G  V++  L  +  E  +Y+       +            +  G A VE+ + E
Sbjct: 9   SFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIE--IGPDGRVTGEADVEFATHE 66

Query: 84  IGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNS 117
               A+        + +R +   L+     + + 
Sbjct: 67  DAVAAMAKDK--ANMQHRYVELFLNSTAGTSGSG 98

>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 = 33.6 bits (76), Expect = 0.004
 Identities = 18/93 (19%), Positives = 36/93 (38%), Gaps = 10/93 (10%)

Query: 24  SGNSNSG---CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE 80
           SG+ +       V++  L E V E  L + L + G +  + +   K        A VE+E
Sbjct: 6   SGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFE 59

Query: 81  SEEIGHYAIKLFSGI-VTLYNRTLRFALSGQDK 112
           + +     +   + + V +  +   F  S   +
Sbjct: 60  NIDSAKECVTFAADVPVYIAGQQAFFNYSTSKR 92

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	211
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.91
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.91
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.9
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.9
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.9
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.9
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.9
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.9
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.9
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.9
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.89
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.89
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.89
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.89
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.89
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.88
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.88
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.88
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.88
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.88
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.88
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.88
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.88
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.87
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.87
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.87
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.87
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.87
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.87
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.87
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.87
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.86
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.86
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.86
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.86
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.86
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.86
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.85
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.84
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.84
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.84
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.84
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.83
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.83
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.83
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.83
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.82
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.82
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.82
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.82
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.81
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.81
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.81
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.81
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.81
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.81
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.8
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.8
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.8
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.8
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.79
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.79
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.79
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.78
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.78
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.77
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.77
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.77
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.76
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.76
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.75
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.74
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.73
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.73
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.73
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.73
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.71
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	99.66
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.62
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.6
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.6
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.56
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.52
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.44
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.51
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.4
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.37
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.44

>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=99.91  E-value=3e-24  Score=148.14  Aligned_cols=84  Identities=37%  Similarity=0.580  Sum_probs=79.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ..++|||+|||+++++++|+++|++||.|.+|.|+.|+.+|.++|||||+|.+.++|++|++.|||. .|+|+.|+|+||
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~-~i~g~~l~v~~a   82 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES-ELFGRTIRVNLA   82 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTE-EETTEEEEEEEC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCC-EECCEEEEEEEe
Confidence            3789999999999999999999999999999999999999999999999999999999999999998 999999999999


Q ss_pred             CCCcc
Q 038096          109 GQDKN  113 (211)
Q Consensus       109 ~~~~~  113 (211)
                      ++.+.
T Consensus        83 ~p~~~   87 (89)
T d2cqba1          83 KPMRI   87 (89)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76543

>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=99.91  E-value=3.6e-24  Score=145.36  Aligned_cols=80  Identities=30%  Similarity=0.495  Sum_probs=77.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      +++|||+|||+++++++|+++|++||.|.++.|++++.+|+++|||||+|.+.++|++||+.|||. .++|+.|+|+||+
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~-~~~g~~l~v~~a~   80 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGI-TVRNKRLKVSYAR   80 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCC-EECCEEEEEEEcC
Confidence            678999999999999999999999999999999999999999999999999999999999999998 9999999999996


Q ss_pred             C
Q 038096          110 Q  110 (211)
Q Consensus       110 ~  110 (211)
                      +
T Consensus        81 p   81 (82)
T d1b7fa1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.90  E-value=5.5e-24  Score=147.98  Aligned_cols=85  Identities=40%  Similarity=0.744  Sum_probs=80.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ++.++|||||||.++++++|+++|++||.|.++.|++|+.||.++|||||+|.+.++|++||+.|||. .|+|+.|+|+|
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~-~~~g~~l~V~~   85 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMI-KLYGKPIRVNK   85 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSC-BCSSCBCEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCC-EECCEEEEEEE
Confidence            44789999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      |.++..
T Consensus        86 A~~~~~   91 (93)
T d1x5ua1          86 ASAHNK   91 (93)
T ss_dssp             TTTTSC
T ss_pred             cCCCCC
Confidence            977653

>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=99.90  E-value=6.1e-24  Score=143.69  Aligned_cols=78  Identities=23%  Similarity=0.456  Sum_probs=75.8

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCC
Q 038096           32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQ  110 (211)
Q Consensus        32 ~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~  110 (211)
                      .|||||||+++++++|+++|++||.|.+++|++|+.||+++|||||+|.+.++|++|++.|||. .++|+.|+|.||+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~-~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFD-VIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTC-EETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCC-EECCEEEEEEEeCC
Confidence            6999999999999999999999999999999999999999999999999999999999999998 99999999999864

>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=99.90  E-value=7e-24  Score=145.98  Aligned_cols=84  Identities=20%  Similarity=0.363  Sum_probs=79.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      +.++++|||+|||.++++++|+++|++||.|.+|+|++|+.||+++|||||+|.+.++|++|++.|||. .++|+.|+|+
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~-~l~g~~l~V~   82 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGA-EIMGQTIQVD   82 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCC-EECCEEEEEE
Confidence            455889999999999999999999999999999999999999999999999999999999999999998 9999999999


Q ss_pred             ecCCC
Q 038096          107 LSGQD  111 (211)
Q Consensus       107 ~a~~~  111 (211)
                      ||.++
T Consensus        83 ~a~~k   87 (88)
T d1rk8a_          83 WCFVK   87 (88)
T ss_dssp             ESEEC
T ss_pred             EecCC
Confidence            98643

>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=99.90  E-value=1.3e-23  Score=146.04  Aligned_cols=83  Identities=28%  Similarity=0.508  Sum_probs=79.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ++++|||+|||+++++++|+++|++||.|.+|.|++++.++.++|||||+|.+.++|+.||+.|||. .++|+.|+|+||
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~-~~~gr~i~V~~a   84 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGT-RLDDRIIRTDWD   84 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTS-EETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEEc
Confidence            4799999999999999999999999999999999999999999999999999999999999999998 999999999998


Q ss_pred             CCCc
Q 038096          109 GQDK  112 (211)
Q Consensus       109 ~~~~  112 (211)
                      ....
T Consensus        85 ~~~~   88 (93)
T d1h2vz_          85 AGFK   88 (93)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            6543

>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=99.90  E-value=7.9e-24  Score=146.27  Aligned_cols=84  Identities=25%  Similarity=0.423  Sum_probs=79.8

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||+|||.++++++|+++|++||.|.++.|++|+.+|.++|||||+|.+.++|++||+.|||. .++|+.|+|+
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~-~~~g~~i~v~   83 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGF-GYDHLILNVE   83 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTC-EETTEECEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCC-EECCEEEEEE
Confidence            345789999999999999999999999999999999999999999999999999999999999999998 9999999999


Q ss_pred             ecCCC
Q 038096          107 LSGQD  111 (211)
Q Consensus       107 ~a~~~  111 (211)
                      ||++.
T Consensus        84 ~akp~   88 (90)
T d2cq0a1          84 WAKPS   88 (90)
T ss_dssp             ESSCC
T ss_pred             eeeCC
Confidence            99764

>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=99.90  E-value=2.3e-23  Score=146.41  Aligned_cols=85  Identities=28%  Similarity=0.355  Sum_probs=80.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ...++|||+|||+++++++|+++|++||.|.+|.|++|+.|++++|||||+|.+.++|++||+.|||. .|+|+.|+|.+
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~-~~~gr~i~V~~   84 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQ-VFQGRMLHVLP   84 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTE-ESSSCEEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCC-EECCEEEEEEE
Confidence            44788999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      |..+..
T Consensus        85 a~~~~~   90 (99)
T d1whwa_          85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             CCCCCc
Confidence            987654

>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=99.90  E-value=1.7e-23  Score=141.96  Aligned_cols=80  Identities=20%  Similarity=0.375  Sum_probs=77.0

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||.++++++|+++|++||.|.+|+|++|..+|.++|||||+|.+.++|++|++.|||. .++|+.|+|.||+
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~-~~~g~~l~v~~Ak   80 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGL-RLQTKTIKVSYAR   80 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEEee
Confidence            468999999999999999999999999999999999999999999999999999999999999998 9999999999986


Q ss_pred             C
Q 038096          110 Q  110 (211)
Q Consensus       110 ~  110 (211)
                      +
T Consensus        81 P   81 (82)
T d1fxla1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.90  E-value=1e-23  Score=149.11  Aligned_cols=85  Identities=25%  Similarity=0.434  Sum_probs=80.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      +++++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|++||+.|||. .|+|+.|+|+|
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~-~~~g~~i~V~~   94 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGF-QIGMKRLKVQL   94 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTC-EETTEECEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCC-EECCEEEEEEE
Confidence            45789999999999999999999999999999999999999999999999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      |+++..
T Consensus        95 a~~k~~  100 (102)
T d2cpza1          95 KRSKND  100 (102)
T ss_dssp             CCCSCC
T ss_pred             eCCCCC
Confidence            987654

>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=99.89  E-value=1.4e-23  Score=143.52  Aligned_cols=81  Identities=23%  Similarity=0.409  Sum_probs=77.5

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQ  110 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~  110 (211)
                      .+|||+|||+++++++|+++|++||+|.+++|++|+.||.++|||||+|.+.++|++|++.|||. .|+|+.|.|.||..
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~~   80 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM-QLGDKKLLVQRASV   80 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSC-CCSSSCCEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEECCC
Confidence            47999999999999999999999999999999999999999999999999999999999999998 99999999999975


Q ss_pred             Cc
Q 038096          111 DK  112 (211)
Q Consensus       111 ~~  112 (211)
                      ..
T Consensus        81 ~~   82 (85)
T d2u2fa_          81 GA   82 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.89  E-value=1.9e-23  Score=142.85  Aligned_cols=79  Identities=20%  Similarity=0.368  Sum_probs=75.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCe--EEEEE
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNR--TLRFA  106 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr--~l~v~  106 (211)
                      ++++|||||||.++++++|+++|++||.|.+++|++|+.+|.++|||||+|.+.++|++|++.|||. .++|+  +|+|+
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~-~~~G~~~~i~V~   83 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ-KPSGATEPITVK   83 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-CCTTCSSCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCC-EeCCCCEEEEEE
Confidence            4789999999999999999999999999999999999999999999999999999999999999998 89884  69999


Q ss_pred             ec
Q 038096          107 LS  108 (211)
Q Consensus       107 ~a  108 (211)
                      ||
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>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=99.89  E-value=6.4e-23  Score=152.55  Aligned_cols=84  Identities=24%  Similarity=0.420  Sum_probs=79.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ..++|||||||+++++++|+++|++||.|.+|.|++|+.||+++|||||+|.+.++|++||+.|||. .|+|+.|+|++|
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~-~~~gr~l~V~~a  119 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGF-NILNKRLKVALA  119 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTE-ECSSCEEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCC-EECCEEEEEEEc
Confidence            3578999999999999999999999999999999999999999999999999999999999999998 999999999999


Q ss_pred             CCCcc
Q 038096          109 GQDKN  113 (211)
Q Consensus       109 ~~~~~  113 (211)
                      .....
T Consensus       120 ~~~~~  124 (139)
T d1u6fa1         120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            76544

>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=99.89  E-value=3.5e-23  Score=141.48  Aligned_cols=80  Identities=30%  Similarity=0.456  Sum_probs=75.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCC--eEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYN--RTLRF  105 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~g--r~l~v  105 (211)
                      .++++|||+|||+++++++|+++|++||.|.+++|++|+.+|+++|||||+|.+.++|++||+.|||. .+.|  ++|+|
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~~~~l~V   82 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNV-IPEGGSQPLSV   82 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-CCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCC-EeCCCCeEEEE
Confidence            34788999999999999999999999999999999999999999999999999999999999999998 7876  78999


Q ss_pred             Eec
Q 038096          106 ALS  108 (211)
Q Consensus       106 ~~a  108 (211)
                      +||
T Consensus        83 ~~A   85 (85)
T d1b7fa2          83 RLA   85 (85)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            986

>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=99.89  E-value=6.1e-23  Score=142.89  Aligned_cols=84  Identities=18%  Similarity=0.404  Sum_probs=77.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCC-CCCCCccEEEEEeCCHHHHHHHHHHc-CCCeeeCCeEEEEE
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDK-ETDKPKGFAFVEYESEEIGHYAIKLF-SGIVTLYNRTLRFA  106 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~-~tg~~rg~aFV~f~~~~~A~~Ai~~l-ng~~~i~gr~l~v~  106 (211)
                      ..++|||+|||+++++++|+++|++||.|..|.|+++. .+|.++|||||+|.+.++|++||+.| ||. .|+|++|+|+
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~-~~~Gr~l~V~   85 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHST-HLYGRRLVLE   85 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCC-BSSSCBCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCc-EECCEEEEEE
Confidence            47889999999999999999999999999999999886 47999999999999999999999988 887 8999999999


Q ss_pred             ecCCCcc
Q 038096          107 LSGQDKN  113 (211)
Q Consensus       107 ~a~~~~~  113 (211)
                      ||+.+..
T Consensus        86 ~A~~~~~   92 (94)
T d2cpha1          86 WADSEVT   92 (94)
T ss_dssp             ECCCCCC
T ss_pred             EcCCCCC
Confidence            9977653

>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=99.88  E-value=3.3e-23  Score=143.01  Aligned_cols=84  Identities=23%  Similarity=0.510  Sum_probs=79.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +.++|||||||+++++++|+++|++||.|..+.++.+..+|.++|||||+|.++++|++||+.|||. .|+|+.|+|+||
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~-~~~g~~l~V~~a   82 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGK-SVDGRQIRVDQA   82 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTC-CTTSCCCEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCC-EECCEEEEEEEc
Confidence            4788999999999999999999999999999999999999999999999999999999999999998 999999999998


Q ss_pred             CCCcc
Q 038096          109 GQDKN  113 (211)
Q Consensus       109 ~~~~~  113 (211)
                      .+...
T Consensus        83 ~~~~~   87 (90)
T d1x5sa1          83 GKSSD   87 (90)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            76543

>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=99.88  E-value=1.3e-22  Score=140.19  Aligned_cols=81  Identities=20%  Similarity=0.246  Sum_probs=75.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ..++|||+|||+++++++|+++|++||.|.+|.|++|+.||.++|||||+|.+.++|++||+.+  . .|+|+.|.|++|
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~-~l~Gr~i~v~~a   83 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--H-MIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--E-EETTEEEEEECC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--C-ccCCEEeEEEeC
Confidence            4789999999999999999999999999999999999999999999999999999999999853  3 799999999998


Q ss_pred             CCCc
Q 038096          109 GQDK  112 (211)
Q Consensus       109 ~~~~  112 (211)
                      .++.
T Consensus        84 ~~k~   87 (90)
T d2cqga1          84 NSKQ   87 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            7654

>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=99.88  E-value=1e-23  Score=141.59  Aligned_cols=76  Identities=24%  Similarity=0.378  Sum_probs=73.0

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      |+|||+|||+++++++|+++|++||.|.++.|++|+.||+++|||||+|.+.++|++||+ +++. .|+|+.|.|++|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~-~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRH-ELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTC-CCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCC-EECCeEEEEEEC
Confidence            689999999999999999999999999999999999999999999999999999999997 5888 899999999876

>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=99.88  E-value=5.1e-23  Score=139.32  Aligned_cols=80  Identities=19%  Similarity=0.331  Sum_probs=70.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||+++++++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|++|++.|||. .++|++|+|++|+
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~-~~~g~~i~V~~a~   79 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGL-KIEGYTLVTKVSN   79 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTC-EETTEECEEEECC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCC-EECCEEEEEEEcc
Confidence            379999999999999999999999999999988888888999999999999999999999999998 9999999999986


Q ss_pred             C
Q 038096          110 Q  110 (211)
Q Consensus       110 ~  110 (211)
                      |
T Consensus        80 P   80 (81)
T d2ghpa1          80 P   80 (81)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.88  E-value=1.9e-22  Score=142.65  Aligned_cols=81  Identities=17%  Similarity=0.259  Sum_probs=76.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ..++|||||||+++++++|+++|++||.|.+|.|++|+.||+++|||||+|.+.++|++||+.+|+  .|+|+.|+|++|
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~--~l~Gr~l~V~~a   86 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP--IIDGRKANVNLA   86 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC--EETTEECEEEES
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC--cCCCEEEEEEEc
Confidence            357899999999999999999999999999999999999999999999999999999999999876  599999999998


Q ss_pred             CCC
Q 038096          109 GQD  111 (211)
Q Consensus       109 ~~~  111 (211)
                      ...
T Consensus        87 ~~~   89 (103)
T d2cqda1          87 YLG   89 (103)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            654

>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=99.88  E-value=2.3e-22  Score=138.83  Aligned_cols=84  Identities=15%  Similarity=0.340  Sum_probs=76.6

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ..+.++|||||||.++++++|+++|++||.|.+|.|+.|+.++  +|||||+|.+.++|++|++.|||. .|+|+.|+|.
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~-~~~g~~i~v~   81 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGR-KILGKEVKVN   81 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTE-EETTEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCC-EECCEEEEEE
Confidence            3457899999999999999999999999999999999987654  799999999999999999999998 9999999999


Q ss_pred             ecCCCcc
Q 038096          107 LSGQDKN  113 (211)
Q Consensus       107 ~a~~~~~  113 (211)
                      ||++...
T Consensus        82 ~a~~~~~   88 (90)
T d2cqia1          82 WATTPSS   88 (90)
T ss_dssp             ECCCTTC
T ss_pred             EcCCCCC
Confidence            9976543

>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=99.88  E-value=9.5e-23  Score=138.61  Aligned_cols=77  Identities=26%  Similarity=0.434  Sum_probs=73.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRF  105 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v  105 (211)
                      .++++|||+|||+++++++|+++|++||.|.+|.|++|+.+|+++|||||+|.+.++|++||+.|||. .|+|+.|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGM-ELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTE-EETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCC-EECCEEeEC
Confidence            34689999999999999999999999999999999999999999999999999999999999999998 999999987

>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=99.88  E-value=8.5e-23  Score=138.81  Aligned_cols=80  Identities=31%  Similarity=0.592  Sum_probs=75.0

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCeEEE-EEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCCC
Q 038096           33 VYIGNLDEKVNERVLYDILIQAGRVVDL-YIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQD  111 (211)
Q Consensus        33 lfVgnLp~~~~e~~L~~~F~~~G~i~~v-~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~~  111 (211)
                      |||+|||+++++++|+++|++||.|.++ .|++++.||+++|||||+|.+.++|++||+.|+|. .++|++|+|+||.++
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 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQ-YLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTC-EETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCc-EECCEEEEEEEecCC
Confidence            7999999999999999999999999765 78999999999999999999999999999999998 999999999999765


Q ss_pred             cc
Q 038096          112 KN  113 (211)
Q Consensus       112 ~~  113 (211)
                      ..
T Consensus        80 ~~   81 (83)
T d1x5ta1          80 DS   81 (83)
T ss_dssp             CC
T ss_pred             Cc
Confidence            43

>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=99.87  E-value=2.6e-22  Score=134.90  Aligned_cols=76  Identities=21%  Similarity=0.357  Sum_probs=73.1

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        32 ~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      +|||+|||+++++++|+++|++||.|.+++|..++ +|+++|||||+|.+.++|++|++.|||. .++|+.|+|++|.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGV-PLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTC-EETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEEee
Confidence            69999999999999999999999999999999986 6999999999999999999999999998 9999999999974

>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=99.87  E-value=2.3e-22  Score=137.15  Aligned_cols=78  Identities=23%  Similarity=0.304  Sum_probs=74.0

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||||||+++++++|+++|++||.|.++.|++|+.||+++|||||+|.+.++|++||+. ++. .|+|+.|+|+.|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~-~~~-~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPH-KVDGRVVEPKRAV   83 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSC-EETTEECEEEECC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHh-CCC-EECCEEEEEEeee
Confidence            57899999999999999999999999999999999999999999999999999999999985 777 8999999999874

>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=99.87  E-value=1.1e-22  Score=135.74  Aligned_cols=75  Identities=23%  Similarity=0.342  Sum_probs=71.0

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        32 ~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +|||||||++++|++|+++|++||.|.++.|++|+.|++++|||||+|.+.++|++||+ +++. .|+|+.|.|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~-~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEH-KLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCC-CBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCC-EECCCEEEeeEC
Confidence            59999999999999999999999999999999999999999999999999999999998 5777 899999998654

>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=99.87  E-value=1.2e-22  Score=143.25  Aligned_cols=80  Identities=25%  Similarity=0.375  Sum_probs=75.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||+++++++|+++|+.||.|.+|.|++|+.||+++|||||+|.+.++|++|++ |||. .|+|+.|+|.+|.
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~-~~~G~~l~V~~a~   95 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQ-RLLGVPIIVQASQ   95 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTE-EETTEEEEEEEHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCC-EECCEEEEEEECC
Confidence            4789999999999999999999999999999999999999999999999999999999996 8998 9999999999975


Q ss_pred             CC
Q 038096          110 QD  111 (211)
Q Consensus       110 ~~  111 (211)
                      ..
T Consensus        96 ~~   97 (101)
T d2cq4a1          96 AE   97 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            43

>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=99.87  E-value=2.3e-22  Score=137.27  Aligned_cols=78  Identities=27%  Similarity=0.444  Sum_probs=72.8

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCC---CCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETD---KPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        33 lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg---~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      |||+|||+++++++|+++|++||.|.++.|++++.++   .++|||||+|.+.++|++|++.|||. .++|+.|.|+||+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~-~~~g~~i~V~~a~   79 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGH-TVDGHKLEVRISE   79 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTC-EETTEECEEECSS
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEECC
Confidence            7999999999999999999999999999999988765   46899999999999999999999998 9999999999985


Q ss_pred             CC
Q 038096          110 QD  111 (211)
Q Consensus       110 ~~  111 (211)
                      ..
T Consensus        80 ~~   81 (85)
T d2cpfa1          80 RA   81 (85)
T ss_dssp             CS
T ss_pred             CC
Confidence            43

>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=99.87  E-value=8.6e-23  Score=144.60  Aligned_cols=83  Identities=34%  Similarity=0.568  Sum_probs=78.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||+++++++|+++|++||.|.+|.|++++.||+++|||||+|.+.++|++||+.|||. .|+|+.|+|.||.
T Consensus         8 ~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_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGR-EFSGRALRVDNAA   86 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSB-SCSSSCBEEEETT
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCC-EECCEEEEEEECC
Confidence            468999999999999999999999999999999999999999999999999999999999999998 9999999999987


Q ss_pred             CCcc
Q 038096          110 QDKN  113 (211)
Q Consensus       110 ~~~~  113 (211)
                      .+..
T Consensus        87 ~~~~   90 (104)
T d1p1ta_          87 SEKN   90 (104)
T ss_dssp             CTTH
T ss_pred             CCCC
Confidence            6543

>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=99.87  E-value=7.8e-22  Score=137.88  Aligned_cols=84  Identities=26%  Similarity=0.398  Sum_probs=77.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcC------CCeeeCCe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFS------GIVTLYNR  101 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~ln------g~~~i~gr  101 (211)
                      .++++|||||||+++++++|+++|++||.|.++.++.++.++.++|||||+|.+.++|.+||+.+|      |. .++|+
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~-~~~gr   84 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGL-KLDGR   84 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCE-ESSSC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCc-EECCE
Confidence            457899999999999999999999999999999999999999999999999999999999999886      54 79999


Q ss_pred             EEEEEecCCCc
Q 038096          102 TLRFALSGQDK  112 (211)
Q Consensus       102 ~l~v~~a~~~~  112 (211)
                      .|+|+||.++.
T Consensus        85 ~l~v~~a~~k~   95 (98)
T d1x4ha1          85 QLKVDLAVTRD   95 (98)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEECCCCC
Confidence            99999997653

>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=99.87  E-value=3.7e-22  Score=141.20  Aligned_cols=82  Identities=21%  Similarity=0.283  Sum_probs=76.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||||||+++++++|+++|++||.|..+.|++|+.++.++|||||+|.+.++|++||+ +++. .|+|+.|.|.+|.
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~-~l~G~~i~V~~a~   97 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPH-SIDGRVVEPKRAV   97 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSE-EETTEEEEEECCS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCC-eECCEEEEEEECc
Confidence            4789999999999999999999999999999999999999999999999999999999996 6887 8999999999987


Q ss_pred             CCcc
Q 038096          110 QDKN  113 (211)
Q Consensus       110 ~~~~  113 (211)
                      ++..
T Consensus        98 ~ke~  101 (103)
T d1x4ba1          98 AREE  101 (103)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            6543

>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=99.87  E-value=1.2e-21  Score=135.92  Aligned_cols=82  Identities=18%  Similarity=0.286  Sum_probs=75.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ...++|||+|||+++++++|+++|++||.|.+|.++.++.  .++|||||+|.+.++|++||+.|||. .|+|+.|+|+|
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~-~~~g~~l~V~~   85 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGT-VVEGRKIEVNN   85 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTC-EETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCC-EECCEEEEEEe
Confidence            3478899999999999999999999999999999999874  47899999999999999999999998 99999999999


Q ss_pred             cCCCc
Q 038096          108 SGQDK  112 (211)
Q Consensus       108 a~~~~  112 (211)
                      |+++.
T Consensus        86 A~~r~   90 (93)
T d2cq3a1          86 ATARV   90 (93)
T ss_dssp             CCSSC
T ss_pred             cCcCC
Confidence            97653

>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=99.86  E-value=4e-22  Score=137.28  Aligned_cols=81  Identities=27%  Similarity=0.505  Sum_probs=75.0

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      ..+|||+|||+++++++|+++|++||.|..+.|+.++.  .++|||||+|.+.++|++||+.|||. .|+|+.|+|.+|+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~-~~~g~~i~V~~a~   84 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGM-LLNDRKVFVGRFK   84 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEE-EETTEEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCC-EECCEEEEEEECC
Confidence            46799999999999999999999999999999999874  57899999999999999999999998 9999999999997


Q ss_pred             CCcc
Q 038096          110 QDKN  113 (211)
Q Consensus       110 ~~~~  113 (211)
                      +++.
T Consensus        85 ~~~~   88 (89)
T d1cvja2          85 SRKE   88 (89)
T ss_dssp             CTTT
T ss_pred             CCCC
Confidence            6543

>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=99.86  E-value=7e-22  Score=132.94  Aligned_cols=77  Identities=21%  Similarity=0.332  Sum_probs=73.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      .++|||||||+++++++|+++|++||.|..+.+..++.++.++|||||+|.+.++|++|++ ++|. .|+|+.|+|+.|
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-QKYH-TVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCC-EETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCC-EECCEEEEEEEC
Confidence            4799999999999999999999999999999999999999999999999999999999996 7998 999999999876

>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=99.86  E-value=1.3e-22  Score=135.52  Aligned_cols=75  Identities=19%  Similarity=0.353  Sum_probs=70.5

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        32 ~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +|||||||+++++++|+++|++||.|.+|.|++|+.|++++|||||+|.+.++|++||+. ++. .|+|+.|.|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~-~~~-~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYH-NVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSC-CBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCC-EECCEEeEEEEC
Confidence            699999999999999999999999999999999999999999999999999999999976 555 799999998865

>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=99.86  E-value=9.9e-22  Score=138.14  Aligned_cols=85  Identities=31%  Similarity=0.436  Sum_probs=78.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeE--------EEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVV--------DLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL   98 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~--------~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i   98 (211)
                      ..+.++|||+|||+++++++|+++|++||.|.        .+.+.+++.+|+++|||||+|.++++|++||+.|||. .|
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~-~~   83 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK-DF   83 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC-EE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCC-EE
Confidence            34578999999999999999999999999874        5778888899999999999999999999999999998 99


Q ss_pred             CCeEEEEEecCCCc
Q 038096           99 YNRTLRFALSGQDK  112 (211)
Q Consensus        99 ~gr~l~v~~a~~~~  112 (211)
                      +|+.|+|++|++..
T Consensus        84 ~gr~i~V~~a~~~~   97 (101)
T d2cpea1          84 QGSKLKVSLARKKP   97 (101)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCEEEEEEEcCCCC
Confidence            99999999997654

>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=99.86  E-value=8e-22  Score=134.92  Aligned_cols=81  Identities=23%  Similarity=0.372  Sum_probs=70.8

Q ss_pred             CCCeEEEcCCCCCCc-HHHHHHHHhcCCCeEEEEEccC-CCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           29 SGCNVYIGNLDEKVN-ERVLYDILIQAGRVVDLYIPRD-KETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~-e~~L~~~F~~~G~i~~v~i~~d-~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ++++|||+|||++++ +++|+++|++||.|.+|.|..+ +.+++++|||||+|.+.++|++||+ |||. .|+|+.|+|+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~-~~~gr~l~V~   80 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRS-LLGNREISVS   80 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTE-EETTEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCC-EECCEEEEEE
Confidence            478999999999875 6679999999999999998764 5789999999999999999999996 8998 9999999999


Q ss_pred             ecCCC
Q 038096          107 LSGQD  111 (211)
Q Consensus       107 ~a~~~  111 (211)
                      +|.++
T Consensus        81 ~a~~k   85 (86)
T d2ghpa3          81 LADKK   85 (86)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            98754

>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=99.86  E-value=5.7e-22  Score=131.99  Aligned_cols=75  Identities=24%  Similarity=0.384  Sum_probs=72.3

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        32 ~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +|||||||++++|++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++ +||. .|+|+.|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~-~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFH-EINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSC-CBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCC-EECCeEEEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999997 8998 999999999986

>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=99.85  E-value=5.3e-21  Score=133.15  Aligned_cols=81  Identities=23%  Similarity=0.423  Sum_probs=74.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .++++|||+|||+++++++|+++|++||.|..+.+..+   +.++|||||+|.+.++|++||+.|||. .|+|++|+|+|
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~-~~~g~~l~V~~   87 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGY-DYDGYRLRVEF   87 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTC-EETTEECEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEe
Confidence            44789999999999999999999999999999988654   567899999999999999999999998 99999999999


Q ss_pred             cCCCc
Q 038096          108 SGQDK  112 (211)
Q Consensus       108 a~~~~  112 (211)
                      |+..+
T Consensus        88 a~~~r   92 (95)
T d1x4aa1          88 PRSGR   92 (95)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            97653

>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=99.84  E-value=6.2e-21  Score=136.97  Aligned_cols=79  Identities=25%  Similarity=0.350  Sum_probs=73.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      .+++|||+|||.++++++|+++|++||.|.+|.+..+   +.++|||||+|.+.++|..||+.|||. .|+|+.|.|.++
T Consensus         6 ~~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           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGF-NVCNRYLVVLYY   81 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEEc
Confidence            3789999999999999999999999999999999865   567999999999999999999999998 999999999998


Q ss_pred             CCC
Q 038096          109 GQD  111 (211)
Q Consensus       109 ~~~  111 (211)
                      ...
T Consensus        82 ~~~   84 (114)
T d2f9da1          82 NAN   84 (114)
T ss_dssp             CHH
T ss_pred             CCC
Confidence            643

>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=99.84  E-value=4.4e-21  Score=133.75  Aligned_cols=84  Identities=20%  Similarity=0.420  Sum_probs=74.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCC-eEEEEEccCC-CCCCCccEEEEEeCCHHHHHHHHHHcCCC-eeeCCeEEEEE
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGR-VVDLYIPRDK-ETDKPKGFAFVEYESEEIGHYAIKLFSGI-VTLYNRTLRFA  106 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~-i~~v~i~~d~-~tg~~rg~aFV~f~~~~~A~~Ai~~lng~-~~i~gr~l~v~  106 (211)
                      +|+|||||||.++++++|+++|++||. |..+.|++|. .+++++|||||+|.+.++|..|++.|++. +.++|+.|+|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            478999999999999999999999996 8999999886 46899999999999999999999998643 36789999999


Q ss_pred             ecCCCcc
Q 038096          107 LSGQDKN  113 (211)
Q Consensus       107 ~a~~~~~  113 (211)
                      ||+++..
T Consensus        81 ~A~p~~~   87 (96)
T d2disa1          81 WAEPEID   87 (96)
T ss_dssp             ESCSSCS
T ss_pred             EcCCCCC
Confidence            9976544

>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=99.84  E-value=4.1e-22  Score=140.44  Aligned_cols=85  Identities=25%  Similarity=0.381  Sum_probs=79.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .++++|||+|||.++++++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|++||+.|||. .|.|+.|+|+|
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~-~~~g~~l~V~~   94 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGY-KLYGKILVIEF   94 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTC-BCSSCBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCC-EECCEEEEEEe
Confidence            34789999999999999999999999999999999888888999999999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      |+++..
T Consensus        95 ak~k~~  100 (102)
T d2cpxa1          95 GKNKKQ  100 (102)
T ss_dssp             CCCCSC
T ss_pred             CCCccc
Confidence            987654

>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=99.84  E-value=9.2e-21  Score=132.21  Aligned_cols=77  Identities=18%  Similarity=0.451  Sum_probs=72.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      +..++|||+|||.++++++|+++|++||.|.+|+|+.+      +|||||+|.+.++|++||..|||. .|+|+.|+|.|
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~-~i~g~~l~v~~   88 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGT-TIEGHVVKCYW   88 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEE
Confidence            45789999999999999999999999999999999876      599999999999999999999998 99999999999


Q ss_pred             cCCC
Q 038096          108 SGQD  111 (211)
Q Consensus       108 a~~~  111 (211)
                      +++.
T Consensus        89 ak~~   92 (96)
T d1x4ga1          89 GKES   92 (96)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8654

>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=99.83  E-value=3.7e-21  Score=135.45  Aligned_cols=80  Identities=28%  Similarity=0.343  Sum_probs=73.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +.++|||+|||.++++++|+++|++||.|..+.+..+. ++.++|||||+|.+.++|++||+.|||. .|.|+++.|.++
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~-~i~gr~~~v~~~   94 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGK-FIKTPPGVSAPT   94 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTC-CCCCCTTSCCCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCC-EECCcCCccCCC
Confidence            46899999999999999999999999999999998885 6899999999999999999999999999 999998888776


Q ss_pred             CC
Q 038096          109 GQ  110 (211)
Q Consensus       109 ~~  110 (211)
                      ++
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            43

>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=99.83  E-value=5.6e-21  Score=131.51  Aligned_cols=77  Identities=17%  Similarity=0.248  Sum_probs=70.6

Q ss_pred             CCCeEEEcCCCCCCcHHHH---HHHHhcCCCeEEEEEccCCCCCCC---ccEEEEEeCCHHHHHHHHHHcCCCeeeCCeE
Q 038096           29 SGCNVYIGNLDEKVNERVL---YDILIQAGRVVDLYIPRDKETDKP---KGFAFVEYESEEIGHYAIKLFSGIVTLYNRT  102 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L---~~~F~~~G~i~~v~i~~d~~tg~~---rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~  102 (211)
                      +.++|||+|||+++++++|   +++|++||.|..|.|++|+.++.+   +|||||+|.+.++|++||+.|||. .++|+.
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~-~~~gr~   85 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNV-VVDGRT   85 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTE-EETTEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCC-EECCEE
Confidence            3578999999999999999   678999999999999999877655   499999999999999999999998 999999


Q ss_pred             EEEE
Q 038096          103 LRFA  106 (211)
Q Consensus       103 l~v~  106 (211)
                      |+|+
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9985

>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=99.83  E-value=9.1e-22  Score=136.08  Aligned_cols=80  Identities=20%  Similarity=0.328  Sum_probs=73.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ....+|||+|||+++++++|+++|+.||.|..+.|+.+ .+|+++|||||+|.+.++|++||+ |||. .|+|+.|+|.+
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~-~~~g~~i~V~~   87 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGL-KVFGNEIKLEK   87 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGE-EETTEEEEEEC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCc-EECCEEEEEEe
Confidence            34678999999999999999999999999998888654 579999999999999999999996 8998 99999999999


Q ss_pred             cCC
Q 038096          108 SGQ  110 (211)
Q Consensus       108 a~~  110 (211)
                      |+.
T Consensus        88 ak~   90 (91)
T d1fjeb1          88 PKG   90 (91)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            864

>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=99.83  E-value=2e-20  Score=127.58  Aligned_cols=77  Identities=19%  Similarity=0.263  Sum_probs=72.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||.++++++|+++|+.||.|..|.|..+. +|+++|||||+|.+.++|++||+ ++|. .+.|+.|.|.|++
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~-~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQ-KYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCC-EETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCC-EECCEEEEEEEcC
Confidence            5899999999999999999999999999999998875 69999999999999999999996 6887 9999999999964

>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=99.82  E-value=2.9e-20  Score=131.32  Aligned_cols=83  Identities=20%  Similarity=0.411  Sum_probs=73.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCC-CCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDK-ETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~-~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      +.++|||+|||+++++++|+++|+.|| |+++.++.+. .+++++|||||+|.+.++|++|+ .||+. .|+|+.|+|.+
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~-~~~gr~l~V~~   90 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEE-SLGNKRIRVDV   90 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTC-EETTEECEEEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCC-EECCEEEEEEE
Confidence            468999999999999999999999999 7788777765 46889999999999999998777 48998 99999999999


Q ss_pred             cCCCccC
Q 038096          108 SGQDKNA  114 (211)
Q Consensus       108 a~~~~~~  114 (211)
                      |.++...
T Consensus        91 a~~~~~~   97 (104)
T d1wi8a_          91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9776543

>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=99.82  E-value=6.3e-21  Score=128.67  Aligned_cols=77  Identities=26%  Similarity=0.335  Sum_probs=69.1

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQ  110 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~  110 (211)
                      ++|||||||.++++++|+++|++||.|..+.+..      .+|||||+|.+.++|++|++.|||.+.++|+.|+|+||.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            4799999999999999999999999987766643      5699999999999999999999997579999999999987


Q ss_pred             Ccc
Q 038096          111 DKN  113 (211)
Q Consensus       111 ~~~  113 (211)
                      ++.
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            654

>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=99.82  E-value=3.2e-20  Score=129.93  Aligned_cols=77  Identities=29%  Similarity=0.424  Sum_probs=69.2

Q ss_pred             CCCCeEEEcCCC-CCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           28 NSGCNVYIGNLD-EKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp-~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      ...++|||+||+ ..+++++|+++|++||.|.+|.|        ++|||||+|.+.++|++||+.|||. .|+|+.|+|+
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~-~~~g~~l~V~   83 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGR-MIAGQVLDIN   83 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTC-EETTEECEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCC-EECCEEEEEE
Confidence            346789999997 67889999999999999999988        3599999999999999999999998 9999999999


Q ss_pred             ecCCCcc
Q 038096          107 LSGQDKN  113 (211)
Q Consensus       107 ~a~~~~~  113 (211)
                      ||...+.
T Consensus        84 ~a~~~~~   90 (98)
T d1wf2a_          84 LAAEPKV   90 (98)
T ss_dssp             ETTSCCC
T ss_pred             ECCCCCC
Confidence            9976443

>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=99.82  E-value=4.1e-20  Score=126.18  Aligned_cols=77  Identities=18%  Similarity=0.197  Sum_probs=70.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||+++++++|+++|++||.|..+.+      ++++|||||+|.+.++|.+||..|||. .|+|+.|+|+||+
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~------~~~rg~afV~f~~~~~A~~Ai~~l~~~-~i~g~~i~V~~ak   80 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAMKALNGK-VLDGSPIEVTLAK   80 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEE------EECSSEEEEEESSHHHHHHHHHHHSSE-EETTEEEEEECCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEE------ccccEEEEEEeCCHHHHHHHHHHcCCC-EECCEEEEEEecc
Confidence            578999999999999999999999999988776      356799999999999999999999998 9999999999997


Q ss_pred             CCcc
Q 038096          110 QDKN  113 (211)
Q Consensus       110 ~~~~  113 (211)
                      +..+
T Consensus        81 P~~~   84 (86)
T d2cpda1          81 PVDK   84 (86)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=99.81  E-value=4.9e-20  Score=125.03  Aligned_cols=77  Identities=18%  Similarity=0.310  Sum_probs=70.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee-CCeEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL-YNRTLRF  105 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i-~gr~l~v  105 (211)
                      .+++++|||+|||.++++++|+++|++||.|.+|++++++     +|||||+|.+.++|++|++.|+|. .| +|+.|+|
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~-~~~~~~~i~v   78 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGF-KITPTHAMKI   78 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTC-BSSTTCBCEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCc-EeCCCcEEEE
Confidence            3568999999999999999999999999999999998653     589999999999999999999998 67 5689999


Q ss_pred             EecC
Q 038096          106 ALSG  109 (211)
Q Consensus       106 ~~a~  109 (211)
                      .||+
T Consensus        79 ~~ak   82 (83)
T d2b0ga1          79 TFAK   82 (83)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9985

>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=99.81  E-value=4.1e-20  Score=126.68  Aligned_cols=78  Identities=22%  Similarity=0.222  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee-CCeEEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL-YNRTLRFA  106 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i-~gr~l~v~  106 (211)
                      +++++|||+|||.++++++|+++|++||.|..+.+..    ++.+|||||+|.+.++|.+|+..|||. .+ +|+.|+|+
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~-~i~~g~~l~v~   82 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNH-DLGENHHLRVS   82 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTC-BSSSSCBCEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCC-EecCCCEEEEE
Confidence            4578999999999999999999999999998887755    456799999999999999999999998 77 58999999


Q ss_pred             ecCC
Q 038096          107 LSGQ  110 (211)
Q Consensus       107 ~a~~  110 (211)
                      |++.
T Consensus        83 ~sk~   86 (88)
T d2adca2          83 FSKS   86 (88)
T ss_dssp             ECSS
T ss_pred             eCCC
Confidence            9864

>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=99.81  E-value=3e-20  Score=127.01  Aligned_cols=76  Identities=21%  Similarity=0.488  Sum_probs=70.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||.++++++|+++|++||.|.+|.+.++      +|||||+|.+.++|++|++.|||. .|+|+.|+|+||.
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~-~i~g~~l~V~~A~   80 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNM-PLRGKQLRVRFAC   80 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTC-CBTTBCCEEEESS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEECC
Confidence            578999999999999999999999999999999765      489999999999999999999998 9999999999986


Q ss_pred             CCc
Q 038096          110 QDK  112 (211)
Q Consensus       110 ~~~  112 (211)
                      ...
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            653

>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=99.81  E-value=4.9e-21  Score=126.51  Aligned_cols=71  Identities=23%  Similarity=0.385  Sum_probs=68.2

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEE
Q 038096           33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR  104 (211)
Q Consensus        33 lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~  104 (211)
                      |||+|||.++++++|+++|++||.|..+++.+++.++.++|||||+|.+.++|++|++.|||. .|+|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~-~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKAS-GVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHH-TCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCC-EECCEECc
Confidence            799999999999999999999999999999999999999999999999999999999999998 89998764

>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=99.81  E-value=3.1e-20  Score=129.45  Aligned_cols=80  Identities=19%  Similarity=0.287  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+.++|||+|||+++++++|+++|++||.|..+..     ++.++|||||+|.+.++|++|++.|||. .|+|+.|+|.|
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~-~~~gr~i~V~~   87 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGA-EIDGRSVSLYY   87 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEE-EETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCC-EECCEEEEEEE
Confidence            34789999999999999999999999998876643     5789999999999999999999999998 99999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      +.++..
T Consensus        88 a~~k~~   93 (96)
T d1fjca_          88 TGEKGG   93 (96)
T ss_dssp             CSSSCC
T ss_pred             eCCCCC
Confidence            977654

>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=99.81  E-value=2.9e-20  Score=132.58  Aligned_cols=76  Identities=12%  Similarity=0.069  Sum_probs=70.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      +++|||+|||+++++++|+++|+.||.|..|.|.      .++|||||+|.+.++|++||+.|||. .|.|+.|.|+|+.
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~-~~~gr~l~v~~a~   82 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYS-KFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTC-BSSSSBCEEEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCC-ccCCCeEEEEECC
Confidence            6789999999999999999999999999999884      45699999999999999999999998 9999999999986


Q ss_pred             CCc
Q 038096          110 QDK  112 (211)
Q Consensus       110 ~~~  112 (211)
                      ...
T Consensus        83 ~~~   85 (111)
T d1whxa_          83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            543

>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=99.81  E-value=3.7e-20  Score=127.80  Aligned_cols=80  Identities=26%  Similarity=0.541  Sum_probs=72.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHH----HHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEE
Q 038096           29 SGCNVYIGNLDEKVNERVLYD----ILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLR  104 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~----~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~  104 (211)
                      ++++|||||||++++++||++    +|++||.|.+|.+..   ++.++|||||+|.+.++|.+|++.+||. .++|+.|.
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~-~~~g~~l~   77 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGF-PFYDKPMR   77 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTC-EETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCC-EECCEEEE
Confidence            368999999999999998864    689999999998865   4678999999999999999999999998 99999999


Q ss_pred             EEecCCCc
Q 038096          105 FALSGQDK  112 (211)
Q Consensus       105 v~~a~~~~  112 (211)
                      |.||+.+.
T Consensus        78 v~~ak~~~   85 (91)
T d1nu4a_          78 IQYAKTDS   85 (91)
T ss_dssp             EEECSSCC
T ss_pred             EEEeCCCc
Confidence            99997654

>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=99.80  E-value=3.6e-20  Score=126.44  Aligned_cols=80  Identities=16%  Similarity=0.183  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      +..+.|||+|||++++++||+++|+.||.+....++.+..+++++|+|||+|.+.++|++||+.||+. .|+|++|+|++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~-~l~gr~i~v~l   85 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDR-PIGSRKVKLVL   85 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTC-EETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCC-EECCEEEEEEE
Confidence            34677999999999999999999999999977434444467999999999999999999999999998 99999999987


Q ss_pred             c
Q 038096          108 S  108 (211)
Q Consensus       108 a  108 (211)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.80  E-value=7.3e-20  Score=130.13  Aligned_cols=76  Identities=22%  Similarity=0.326  Sum_probs=69.9

Q ss_pred             CCeEEEcCCCC-CCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           30 GCNVYIGNLDE-KVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        30 ~~~lfVgnLp~-~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +++|||+||++ .+++++|+++|+.||.|..|.|++++     +|||||+|.+.++|++||+.|||. .|+|+.|+|.|+
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~-~l~g~~l~v~~s   75 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGH-KLHGKPIRITLS   75 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTC-BCSSSBCEEECC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEEC
Confidence            57899999965 59999999999999999999998874     699999999999999999999998 999999999998


Q ss_pred             CCC
Q 038096          109 GQD  111 (211)
Q Consensus       109 ~~~  111 (211)
                      +..
T Consensus        76 ~~~   78 (109)
T d2adca1          76 KHQ   78 (109)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            643

>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=99.80  E-value=5.6e-20  Score=123.62  Aligned_cols=74  Identities=22%  Similarity=0.386  Sum_probs=68.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ++++|||+||+  +++++|+++|++||.|.++.+.++      +|||||+|.+.++|.+|++.|||. .++|+.|+|+||
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~-~~~g~~l~V~~a   74 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGT-QVESVQLKVNIA   74 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTC-BCSSCBCEEEEC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCC-EECCEEEEEEEe
Confidence            37899999986  899999999999999999998654      589999999999999999999998 999999999999


Q ss_pred             CCC
Q 038096          109 GQD  111 (211)
Q Consensus       109 ~~~  111 (211)
                      +++
T Consensus        75 ~~~   77 (79)
T d2bz2a1          75 RKQ   77 (79)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            654

>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=99.80  E-value=9.5e-20  Score=124.98  Aligned_cols=76  Identities=24%  Similarity=0.325  Sum_probs=66.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||+|||++++++||+++|++|| +..+.+      +..+|||||+|.+.++|++||+.||+. .|+|++|+|++++
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~-~~~G~~l~V~~a~   76 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQY-SFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTE-EETTEEEEEEECC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCC-EECCEEEEEEEcC
Confidence            67899999999999999999999999 333333      456799999999999999999999998 9999999999986


Q ss_pred             CCcc
Q 038096          110 QDKN  113 (211)
Q Consensus       110 ~~~~  113 (211)
                      .+..
T Consensus        77 ~~~~   80 (88)
T d1wg1a_          77 TDAL   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            5543

>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=99.79  E-value=3.5e-19  Score=124.21  Aligned_cols=80  Identities=20%  Similarity=0.338  Sum_probs=72.2

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCC--eEE
Q 038096           26 NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYN--RTL  103 (211)
Q Consensus        26 ~s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~g--r~l  103 (211)
                      .+.+.++|||+|||.++++++|+++|++||.|..+++.++      ++||||+|.+.++|++|++.||+. .|.|  ++|
T Consensus        13 ~~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~-~i~g~~~~l   85 (97)
T d1whya_          13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGF-PLGGPDRRL   85 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTC-BCSSSSCBC
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCC-EeCCCceEE
Confidence            4566899999999999999999999999999999999764      589999999999999999999998 8876  489


Q ss_pred             EEEecCCCc
Q 038096          104 RFALSGQDK  112 (211)
Q Consensus       104 ~v~~a~~~~  112 (211)
                      +|+||+.++
T Consensus        86 ~v~~ak~~~   94 (97)
T d1whya_          86 RVDFAKSGP   94 (97)
T ss_dssp             EEEECCCCC
T ss_pred             EEEeCCCCC
Confidence            999997654

>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=99.79  E-value=9.9e-20  Score=124.84  Aligned_cols=77  Identities=21%  Similarity=0.449  Sum_probs=68.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      .+++|||+|||++++|++|+++|++||.|.+|++..     .++|||||+|.+.++|++||.  ++. .|+|+.|+|.+|
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~--~~~-~i~g~~l~v~~a   75 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG--EDL-IIKGISVHISNA   75 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT--CEE-EETTEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh--CCC-EECCEEeEEEeC
Confidence            478999999999999999999999999999998754     467999999999999999985  675 899999999999


Q ss_pred             CCCcc
Q 038096          109 GQDKN  113 (211)
Q Consensus       109 ~~~~~  113 (211)
                      .++..
T Consensus        76 ~~k~~   80 (88)
T d1wf0a_          76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76543

>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=99.79  E-value=2.6e-19  Score=119.12  Aligned_cols=71  Identities=30%  Similarity=0.359  Sum_probs=64.7

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCCC
Q 038096           33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQD  111 (211)
Q Consensus        33 lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~~  111 (211)
                      |||+|||.++++++|+++|++|| +..+.+      ++++|||||+|.+.++|++|++.|||. .+.|++|+|+|+..+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~-~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQS-RLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTE-ESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCc-cCCCCEEEEEEeCCC
Confidence            79999999999999999999999 555554      567899999999999999999999998 999999999998654

>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=99.79  E-value=3e-19  Score=118.85  Aligned_cols=74  Identities=16%  Similarity=0.213  Sum_probs=68.0

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ++|||+|||+++++++|+++|+.||.|..+.+..++.  ..++||||+|.+.++|++||. +|+. .|+|+.|.|..+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTHK-VVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTTC-EETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHH-hcCc-EECCEEEEEEEC
Confidence            4799999999999999999999999999999999875  345899999999999999995 7998 999999999864

>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=99.78  E-value=4.4e-19  Score=125.25  Aligned_cols=84  Identities=17%  Similarity=0.113  Sum_probs=75.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      .+...|||+|||++++|+||+++|..+|.|..+.++.+..++.++|||||+|.++++|++|++ +|+. .|+||.|.|.+
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~-~i~gR~i~V~~   90 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKE-RIGHRYIEIFK   90 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTC-CSSSSCCEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCC-EEcceEEEEEE
Confidence            346689999999999999999999999999887677777789999999999999999999996 7888 89999999999


Q ss_pred             cCCCcc
Q 038096          108 SGQDKN  113 (211)
Q Consensus       108 a~~~~~  113 (211)
                      +.+...
T Consensus        91 ~~~~~~   96 (104)
T d1wg5a_          91 SSRAEV   96 (104)
T ss_dssp             ECTTTS
T ss_pred             CCHHHh
Confidence            876543

>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=99.78  E-value=3.9e-20  Score=126.65  Aligned_cols=73  Identities=22%  Similarity=0.199  Sum_probs=67.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecCC
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQ  110 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~~  110 (211)
                      ++|||+|||+++++++|+++|++||.|.++.|..|       |||||+|.+.++|++||+.|||. .|+|+.|+|.+++.
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~-~~~g~~i~v~~~~~   72 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNT-KFRSHEGETAYIRV   72 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTC-BCCCTTSCCCBCEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCC-EECCcEeEEeEEec
Confidence            47999999999999999999999999999998764       89999999999999999999999 99999998887654


Q ss_pred             C
Q 038096          111 D  111 (211)
Q Consensus       111 ~  111 (211)
                      +
T Consensus        73 ~   73 (87)
T d3begb1          73 K   73 (87)
T ss_dssp             E
T ss_pred             C
Confidence            3

>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=99.77  E-value=2.3e-19  Score=126.26  Aligned_cols=83  Identities=18%  Similarity=0.221  Sum_probs=73.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      +..+.+|||+|||+++|+++|+++|..+| +..+.++.+.. +..+|||||+|.+.++|++|++ +|+. .|+||.|+|.
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~-g~~~G~afVeF~~~~~a~~Al~-~~~~-~i~gR~I~V~   87 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEFATHEDAVAAMA-KDKA-NMQHRYVELF   87 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSS-SCEEEEEEEECSSSHHHHHHHT-TSSC-CSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecC-CcceEEEEEEECCHHHHHHHHH-cCCC-EECCEEEEEE
Confidence            35578999999999999999999999998 45777777764 8999999999999999999997 7998 9999999999


Q ss_pred             ecCCCcc
Q 038096          107 LSGQDKN  113 (211)
Q Consensus       107 ~a~~~~~  113 (211)
                      ++.....
T Consensus        88 ~s~~~~~   94 (102)
T d1weza_          88 LNSTAGT   94 (102)
T ss_dssp             EECCCCC
T ss_pred             EcCCCCC
Confidence            9876543

>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=99.77  E-value=3.1e-19  Score=125.73  Aligned_cols=79  Identities=11%  Similarity=0.037  Sum_probs=71.0

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      ..+|||+|||+++++++|+++|..||.|..+.++.+..+|+++|||||+|.+.++|++||+ +|+. .|+|+.|.|.++.
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~-~i~gr~i~V~~~~   85 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRK-KLNGREAFVHVVT   85 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSE-EETTEEEEEEEEC
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCC-eECCcEEEEEECC
Confidence            5779999999999999999999999999875555555679999999999999999999996 8998 9999999999875


Q ss_pred             C
Q 038096          110 Q  110 (211)
Q Consensus       110 ~  110 (211)
                      .
T Consensus        86 ~   86 (103)
T d2cpya1          86 L   86 (103)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=99.77  E-value=2.1e-18  Score=118.04  Aligned_cols=79  Identities=19%  Similarity=0.286  Sum_probs=70.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHc--CCCeeeCCeEEE
Q 038096           27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF--SGIVTLYNRTLR  104 (211)
Q Consensus        27 s~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~l--ng~~~i~gr~l~  104 (211)
                      ..++++|||+|||.++++++|+++|++||.|.++.+..+      +|||||+|.+.++|++|++.+  ++. .+.|+.|+
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~-~~~g~~l~   77 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTP-HLRNQPIY   77 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCC-EETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCC-ccCCCEEE
Confidence            356899999999999999999999999999999998764      489999999999999999866  455 89999999


Q ss_pred             EEecCCCc
Q 038096          105 FALSGQDK  112 (211)
Q Consensus       105 v~~a~~~~  112 (211)
                      |.|++.+.
T Consensus        78 v~~sk~~~   85 (88)
T d2cq1a1          78 IQYSNHKE   85 (88)
T ss_dssp             EEECSCSS
T ss_pred             EEECCCCC
Confidence            99986543

>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=99.76  E-value=4.6e-19  Score=123.92  Aligned_cols=75  Identities=19%  Similarity=0.198  Sum_probs=69.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      ..+|||+|||+++++++|+++|++||.|+.+.|.+       +|||||+|.+.++|++||+.|||. .|.|+.|+|.+++
T Consensus        15 ~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~-~~~g~~i~v~~~~   86 (98)
T d1wg4a_          15 DFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDT-KFRSHEGETSYIR   86 (98)
T ss_dssp             SCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSE-EEECTTSCEEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCC-EeCCeEEEEEEEe
Confidence            67899999999999999999999999999999864       489999999999999999999998 9999999999986


Q ss_pred             CCc
Q 038096          110 QDK  112 (211)
Q Consensus       110 ~~~  112 (211)
                      .+.
T Consensus        87 ~~~   89 (98)
T d1wg4a_          87 VYP   89 (98)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            544

>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=99.76  E-value=4.6e-19  Score=125.99  Aligned_cols=78  Identities=21%  Similarity=0.171  Sum_probs=70.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee--CCeEEEEEe
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL--YNRTLRFAL  107 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i--~gr~l~v~~  107 (211)
                      ..+|||+||++.+++++|+++|++||.|.+|.|..++    .+|||||+|.+.++|++||+.|||. .|  .|+.|+|.+
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~-~l~~~~~~l~v~~   81 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQ-NIYNACCTLRIDF   81 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSC-CSSTTCCCCEEEE
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCC-EeccCCcEEEEEe
Confidence            5789999999999999999999999999999998753    5799999999999999999999998 77  467899999


Q ss_pred             cCCCc
Q 038096          108 SGQDK  112 (211)
Q Consensus       108 a~~~~  112 (211)
                      ++...
T Consensus        82 s~~~~   86 (108)
T d2adba1          82 SKLTS   86 (108)
T ss_dssp             CSSCS
T ss_pred             cCCcc
Confidence            86543

>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=99.75  E-value=8.9e-18  Score=118.41  Aligned_cols=78  Identities=19%  Similarity=0.178  Sum_probs=70.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHc--CCCeeeCCeEEEE
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF--SGIVTLYNRTLRF  105 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~l--ng~~~i~gr~l~v  105 (211)
                      .++++|||+|||.+++|++|+++|++||.|..+.+.++      ||+|||+|.+.++|++|++.+  ++. .+.|++|+|
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~-~~~g~~l~v   85 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPV-YIAGQQAFF   85 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCC-BSSSSBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCc-EEeeEEEEE
Confidence            55899999999999999999999999999999999654      589999999999999999987  454 789999999


Q ss_pred             EecCCCc
Q 038096          106 ALSGQDK  112 (211)
Q Consensus       106 ~~a~~~~  112 (211)
                      .|++.+.
T Consensus        86 ~~s~~~~   92 (104)
T d1wexa_          86 NYSTSKR   92 (104)
T ss_dssp             EECSSSS
T ss_pred             EEcCCCc
Confidence            9997654

>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=99.74  E-value=3e-18  Score=120.93  Aligned_cols=79  Identities=3%  Similarity=-0.011  Sum_probs=69.3

Q ss_pred             CCCCeEEEcCCCCCC-c----HHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeE
Q 038096           28 NSGCNVYIGNLDEKV-N----ERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRT  102 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~-~----e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~  102 (211)
                      ...++|||+||+.++ +    +++|+++|+.||.|.++.+++      ++|+|||+|.+.++|++|++.|||. .|+|+.
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~-~~~g~~   75 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKT-EFLGKE   75 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTS-EETTEE
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhccc-ccCCCE
Confidence            347899999999876 3    357999999999999999975      4689999999999999999999998 999999


Q ss_pred             EEEEecCCCcc
Q 038096          103 LRFALSGQDKN  113 (211)
Q Consensus       103 l~v~~a~~~~~  113 (211)
                      |+|.||+....
T Consensus        76 l~v~~a~~~~~   86 (104)
T d1weya_          76 MKLYFAQTLHI   86 (104)
T ss_dssp             CEEECCCCSSC
T ss_pred             eEEeecccCCC
Confidence            99999965543

>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=99.73  E-value=8.4e-18  Score=115.33  Aligned_cols=79  Identities=18%  Similarity=0.221  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCCCCC-CcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHc--CCCeeeCCeEEE
Q 038096           28 NSGCNVYIGNLDEK-VNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF--SGIVTLYNRTLR  104 (211)
Q Consensus        28 ~~~~~lfVgnLp~~-~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~l--ng~~~i~gr~l~  104 (211)
                      ..++.|||+|||.. ++++||.++|+.||.|.++.++.++      ++|||+|.+.++|+.|++.+  ++. .+.|++|+
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~-~~~gr~l~   78 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPA-LVFGKPVR   78 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCC-EETTEECE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCC-ccCCceEE
Confidence            45789999999975 8899999999999999999997654      79999999999999999966  665 89999999


Q ss_pred             EEecCCCcc
Q 038096          105 FALSGQDKN  113 (211)
Q Consensus       105 v~~a~~~~~  113 (211)
                      |+||+..+.
T Consensus        79 V~~s~~~~~   87 (89)
T d1x4da1          79 VHLSQKYKR   87 (89)
T ss_dssp             EEEECCCTT
T ss_pred             EEECCCccc
Confidence            999975543

>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=99.73  E-value=9.4e-19  Score=125.15  Aligned_cols=80  Identities=20%  Similarity=0.179  Sum_probs=71.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        29 ~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      ...+|||+|||+++++++|+++|+.+|.+..+.++.+..+|.++|||||+|.+.++|++|++ +||. .|+|+.|.|..+
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~-~i~gR~i~V~~~   94 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQ-YMGNRFIQVHPI   94 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSB-CSTTSCBEEEEE
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCC-cCCCEEEEEEEc
Confidence            47799999999999999999999999999776566666679999999999999999999996 8998 899999999887


Q ss_pred             CC
Q 038096          109 GQ  110 (211)
Q Consensus       109 ~~  110 (211)
                      ..
T Consensus        95 ~~   96 (112)
T d1wela1          95 TK   96 (112)
T ss_dssp             CH
T ss_pred             Ch
Confidence            53

>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=99.73  E-value=8.6e-18  Score=129.17  Aligned_cols=83  Identities=19%  Similarity=0.293  Sum_probs=77.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEe
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFAL  107 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~  107 (211)
                      ...++|||+|||+.+++++|+++|+.||.|..+.|+.|..+|.++|||||+|.+.++|.+||+ +++. .++|+.|+|.+
T Consensus        95 ~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~-~~~G~~i~V~~  172 (183)
T d1u1qa_          95 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYH-TVNGHNCEVRK  172 (183)
T ss_dssp             CCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCE-EETTEEEEEEE
T ss_pred             cccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCC-eECCEEEEEEe
Confidence            447899999999999999999999999999999999999999999999999999999999997 5787 89999999999


Q ss_pred             cCCCc
Q 038096          108 SGQDK  112 (211)
Q Consensus       108 a~~~~  112 (211)
                      |.++.
T Consensus       173 A~~k~  177 (183)
T d1u1qa_         173 ALSKQ  177 (183)
T ss_dssp             CCCHH
T ss_pred             cCCcc
Confidence            87654

>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=99.73  E-value=3.5e-18  Score=119.54  Aligned_cols=79  Identities=20%  Similarity=0.289  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCCC-CcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHH--HcCCCeeeCCeEEE
Q 038096           28 NSGCNVYIGNLDEK-VNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK--LFSGIVTLYNRTLR  104 (211)
Q Consensus        28 ~~~~~lfVgnLp~~-~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~--~lng~~~i~gr~l~  104 (211)
                      ..+++|||+|||.+ +++++|.++|++||.|.++.++++      +|+|||+|.+.++|.+|++  .+++. .++|+.|+
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~-~~~gr~l~   88 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKAL-WFQGRCVK   88 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCC-CSSSSCCE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCc-eECCEEEE
Confidence            34789999999975 899999999999999999999765      4899999999999999997  46776 89999999


Q ss_pred             EEecCCCcc
Q 038096          105 FALSGQDKN  113 (211)
Q Consensus       105 v~~a~~~~~  113 (211)
                      |.+|+..+.
T Consensus        89 V~~s~~~~~   97 (99)
T d1x4fa1          89 VDLSEKYKK   97 (99)
T ss_dssp             EEEECSCSS
T ss_pred             EEEcCCccc
Confidence            999976543

>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=99.71  E-value=1.1e-19  Score=125.12  Aligned_cols=77  Identities=23%  Similarity=0.395  Sum_probs=68.1

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEc-----cCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEE
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIP-----RDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRF  105 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~-----~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v  105 (211)
                      ++|||||||++++|++|+++|++||.|..+.+.     .+..+++++|||||+|.+.++|++|++ |||. .++|+.|+|
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~-~~~Gr~l~V   79 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGI-IFQGQSLKI   79 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSC-CSSSSCCCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCc-EECCEEEEE
Confidence            689999999999999999999999988776554     344678899999999999999999995 9998 999999999


Q ss_pred             EecC
Q 038096          106 ALSG  109 (211)
Q Consensus       106 ~~a~  109 (211)
                      ++++
T Consensus        80 ~r~k   83 (90)
T d1u2fa_          80 RRPH   83 (90)
T ss_dssp             BCTT
T ss_pred             CCCC
Confidence            7654

>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=99.66  E-value=8.4e-18  Score=118.62  Aligned_cols=76  Identities=17%  Similarity=0.213  Sum_probs=71.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEec
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS  108 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a  108 (211)
                      +.++|.++..+++|++|+++|++||.|.+|.|+++. +|+++|||||+|.+.++|.+|++.|||. .++|++|+|+++
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~-~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNR-WFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTC-EETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCC-EECCEEEEEEEC
Confidence            458888999999999999999999999999998774 7999999999999999999999999999 999999999985

>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=99.62  E-value=4.5e-16  Score=109.02  Aligned_cols=69  Identities=23%  Similarity=0.366  Sum_probs=60.1

Q ss_pred             CCCCCCeEEE--cCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCC
Q 038096           26 NSNSGCNVYI--GNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYN  100 (211)
Q Consensus        26 ~s~~~~~lfV--gnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~g  100 (211)
                      .+.++++|||  |||+.++++++|+++|++||.|..+.+..+      +|||||+|.+.++|++|++.|||+..+++
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~~~   84 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDD   84 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECT
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCCCC
Confidence            3456888999  559999999999999999999999998765      48999999999999999999999833344

>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=99.60  E-value=1.7e-15  Score=116.11  Aligned_cols=80  Identities=23%  Similarity=0.295  Sum_probs=72.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      .++|||||||+++++++|+++|++||.|.++.++++..++.++|||||+|.+.++|++|+..+++  .++++.+.+.+..
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~--~~~~~~~~~~~~~   83 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPH--KVDGRVVEPKRAV   83 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSC--EETTEECEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCC--cccccchhhhhhh
Confidence            47999999999999999999999999999999999999999999999999999999999997654  6889888887764


Q ss_pred             CC
Q 038096          110 QD  111 (211)
Q Consensus       110 ~~  111 (211)
                      ..
T Consensus        84 ~~   85 (183)
T d1u1qa_          84 SR   85 (183)
T ss_dssp             CT
T ss_pred             hc
Confidence            43

>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=99.60  E-value=9.4e-16  Score=109.44  Aligned_cols=73  Identities=15%  Similarity=0.173  Sum_probs=62.7

Q ss_pred             CCCeE-EEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCH-HHHHHHHHHcCCCeeeCCeEEEEE
Q 038096           29 SGCNV-YIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESE-EIGHYAIKLFSGIVTLYNRTLRFA  106 (211)
Q Consensus        29 ~~~~l-fVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~-~~A~~Ai~~lng~~~i~gr~l~v~  106 (211)
                      .++.| ||||||..+|+++|+++|++||+|..|.|+++      +|||||.|.+. ++|.+|+..+++. .+.++.+.|.
T Consensus         9 ~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~-~l~~~~~~v~   81 (113)
T d1owxa_           9 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNG-NLQLRNKEVT   81 (113)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTS-CBCTTSSSEE
T ss_pred             CCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCC-ceecCceEEE
Confidence            36665 99999999999999999999999999999864      59999999996 7899999999998 7777655555


Q ss_pred             ec
Q 038096          107 LS  108 (211)
Q Consensus       107 ~a  108 (211)
                      |+
T Consensus        82 ~~   83 (113)
T d1owxa_          82 WE   83 (113)
T ss_dssp             EE
T ss_pred             Ee
Confidence            54

>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=99.56  E-value=4.4e-15  Score=99.69  Aligned_cols=72  Identities=11%  Similarity=0.114  Sum_probs=61.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeE-EEEEec
Q 038096           30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRT-LRFALS  108 (211)
Q Consensus        30 ~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~-l~v~~a  108 (211)
                      .+.|+|+|+|++.+++.| ++|++||.|.++.+.      +.+|||||+|.++++|++||+ +||. .|+|+. |.|..+
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~-~~~g~~~vgV~~~   74 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGR-IFGESIMIGVKPC   74 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTC-EETTTEECEEEEC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCC-eECCcEEEEEEeC
Confidence            678999999999987655 579999999999874      456999999999999999996 8998 999984 568776


Q ss_pred             CC
Q 038096          109 GQ  110 (211)
Q Consensus       109 ~~  110 (211)
                      ..
T Consensus        75 ~~   76 (81)
T d1wwha1          75 ID   76 (81)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.52  E-value=3.7e-14  Score=98.69  Aligned_cols=78  Identities=19%  Similarity=0.205  Sum_probs=67.3

Q ss_pred             CCCeEEEcCC--CCCCc---------HHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCee
Q 038096           29 SGCNVYIGNL--DEKVN---------ERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVT   97 (211)
Q Consensus        29 ~~~~lfVgnL--p~~~~---------e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~   97 (211)
                      .+++|+|.||  +.++.         +++|++.|++||.|..|.+..+    ..+|||||+|.+.++|.+|+..|||. .
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~-~   81 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGR-W   81 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTC-E
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCc-E
Confidence            3789999999  54432         3688999999999999998764    46799999999999999999999999 9


Q ss_pred             eCCeEEEEEecCCC
Q 038096           98 LYNRTLRFALSGQD  111 (211)
Q Consensus        98 i~gr~l~v~~a~~~  111 (211)
                      ++|+.|.|.++.+.
T Consensus        82 ~~gr~i~v~~~~g~   95 (99)
T d2dita1          82 FGGRQITAQAWDGT   95 (99)
T ss_dssp             ETTEECEEEECCSC
T ss_pred             ECCEEEEEEEeCCc
Confidence            99999999997654

>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=99.44  E-value=8.6e-14  Score=97.61  Aligned_cols=81  Identities=21%  Similarity=0.161  Sum_probs=69.1

Q ss_pred             CCCeEEEcCC--CCCCc--------HHHHHHHHhcCCCeEEEEEccCCCC--CCCccEEEEEeCCHHHHHHHHHHcCCCe
Q 038096           29 SGCNVYIGNL--DEKVN--------ERVLYDILIQAGRVVDLYIPRDKET--DKPKGFAFVEYESEEIGHYAIKLFSGIV   96 (211)
Q Consensus        29 ~~~~lfVgnL--p~~~~--------e~~L~~~F~~~G~i~~v~i~~d~~t--g~~rg~aFV~f~~~~~A~~Ai~~lng~~   96 (211)
                      +++.|.+.||  +.++.        .+||++.|++||.|.+|.|.++..+  ....|++||+|.+.++|.+|+..|||. 
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr-   81 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR-   81 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC-
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC-
Confidence            4788999999  44432        3578999999999999999987654  345699999999999999999999999 


Q ss_pred             eeCCeEEEEEecCC
Q 038096           97 TLYNRTLRFALSGQ  110 (211)
Q Consensus        97 ~i~gr~l~v~~a~~  110 (211)
                      .++||.|.|.++..
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999753

>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=97.51  E-value=0.00051  Score=45.39  Aligned_cols=78  Identities=15%  Similarity=0.101  Sum_probs=62.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCC--CccEEEEEeCCHHHHHHHHHHcCCCeeeCCe----EEE
Q 038096           31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDK--PKGFAFVEYESEEIGHYAIKLFSGIVTLYNR----TLR  104 (211)
Q Consensus        31 ~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~--~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr----~l~  104 (211)
                      ++|.|..||+.++|+++.+.++..|.+........+.+.+  .-.-|+|.|.+.++...-.+.++|.+-++.+    .-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            6899999999999999999999999988877776665433  3367899999999999999999998444432    334


Q ss_pred             EEec
Q 038096          105 FALS  108 (211)
Q Consensus       105 v~~a  108 (211)
                      |++|
T Consensus        82 VE~A   85 (91)
T d1uw4a_          82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            5555

>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=97.40  E-value=0.00066  Score=42.36  Aligned_cols=61  Identities=13%  Similarity=0.169  Sum_probs=51.6

Q ss_pred             HHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeeeCCeEEEEEecC
Q 038096           45 RVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSG  109 (211)
Q Consensus        45 ~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i~gr~l~v~~a~  109 (211)
                      +.|.+.|.++|.|.++.|....+ |.  -.|-|...+.++|.-|+..|+.. .|++++|.|+++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~d-g~--~~A~V~v~~~q~A~~~v~~LhR~-KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTD-YQ--LKAVVQMENLQDAIGAVNSLHRY-KIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCS-TT--CCEEEEESSHHHHHHHHHHHTTE-EETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccC-Cc--EEEEEEcCCHHHHHHHHHHHHHH-hcCCeEEEEEEec
Confidence            34567789999999998876543 33  57899999999999999999998 9999999999874

>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=97.37  E-value=0.00027  Score=46.42  Aligned_cols=71  Identities=14%  Similarity=0.204  Sum_probs=55.3

Q ss_pred             CCCCeEEEcCCCCCC------cH---HHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcCCCeee
Q 038096           28 NSGCNVYIGNLDEKV------NE---RVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTL   98 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~------~e---~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~lng~~~i   98 (211)
                      ++.-+|.|.=.....      +|   ++|.+.|..||+|.-+++..|        --.|+|.+-+.|.+|+.. +|. ++
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l-~g~-~v   82 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDV-DGM-KV   82 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHG-GGS-EE
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhcc-CCe-EE
Confidence            456677775443222      22   377888999999999999874        589999999999999984 887 99


Q ss_pred             CCeEEEEEec
Q 038096           99 YNRTLRFALS  108 (211)
Q Consensus        99 ~gr~l~v~~a  108 (211)
                      .|+.|+|...
T Consensus        83 ~G~~l~It~~   92 (95)
T d1ufwa_          83 KGRAVKISGP   92 (95)
T ss_dssp             TTEEEEEECC
T ss_pred             cceEEEEecC
Confidence            9999998753

>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=94.44  E-value=0.072  Score=35.00  Aligned_cols=58  Identities=17%  Similarity=0.113  Sum_probs=46.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcCCCeEEEEEccCCCCCCCccEEEEEeCCHHHHHHHHHHcC
Q 038096           28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFS   93 (211)
Q Consensus        28 ~~~~~lfVgnLp~~~~e~~L~~~F~~~G~i~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~Ai~~ln   93 (211)
                      +...-||.-..|..+...||.++|+.||.|.-- ++.|       --|||...+.++|+.++..+.
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~Vs-wIdd-------TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQIS-WIDD-------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCE-EEET-------TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCcceeEEEeCCcccchhHHHHHhcCCCceEEE-EecC-------ceEEEEecCHHHHHHHHHHhc
Confidence            445568888999999999999999999987433 3343       269999999999999887653