Citrus Sinensis ID: 029810

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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-------
Protein Sequence
MVFRSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDRGRYRSGRDDYGYRRSPRRSPYRGGRDYSPRHSPPYGGRSRRERSRSVPRSPYGSPERKYARGSR
Secondary Structure (PSIPRED)
ccccccccccccccccccccEEEEccccccccHHHHHHHHHcccccEEEEEcccccccccccEEEEEEccHHHHHHHHHHHcccEEccEEEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHHHHcccEccccEEEEEccccccccccccccEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mvfrsrsrsrgrtetgnpgntlyVTGLSTRVTERDLekhfskegkvascflvveprtrisRGFAFVTMDGVEDAERCIKYLNQSVLegryitversrrkrprtptpghylglkssrdigrgdrgryrsgrddygyrrsprrspyrggrdysprhsppyggrsrrersrsvprspygsperkyargsr
Flexible Loop (DISEMBL)
mvfrsrsrsrgrtetgnpgntlyvtglstRVTERDLEkhfskegkvascflvveprtrisRGFAFVTMDGVEDAERCIKYlnqsvlegryitversrrkrprtptpghylglkssrdigrgdrgryrsgrddygyrrsprrspyrggrdysprhsppyggrsrrersrsvprspygsperkyargsr
Low Complexity Region (SEG)
MVFrsrsrsrgrTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYItversrrkrprtptpGHYLGLKssrdigrgdrgryrsgrddygyrrsprrspyrggrdysPRHsppyggrsrrersrsvprspyGSPERKYARGSR
Disordered region (IsUnstruct)
*********************LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV**********************************************************************************************
Disordered Region (DISOPRED)
**********************YVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV**********************************************************************************************
Disordered Region (DISEMBL)
***************GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDRGRYRSGRDDYGYRRSPRRSPYRGGRDYSP***********************************
Disordered Region (DISPRO)
*****************PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR****TP***********************************************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVFRSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDRGRYRSGRDDYGYRRSPRRSPYRGGRDYSPRHSPPYGGRSRRERSRSVPRSPYGSPERKYARGSR
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	187	2.2.26 [Sep-21-2011]
Q10422	297	Uncharacterized RNA-bindi	yes	no	0.711	0.447	0.393	6e-19
P62997	288	Transformer-2 protein hom	yes	no	0.695	0.451	0.440	3e-16
P62996	288	Transformer-2 protein hom	yes	no	0.695	0.451	0.440	3e-16
P62995	288	Transformer-2 protein hom	yes	no	0.695	0.451	0.440	3e-16
Q3ZBT6	288	Transformer-2 protein hom	yes	no	0.695	0.451	0.440	3e-16
Q6PFR5	281	Transformer-2 protein hom	no	no	0.572	0.380	0.411	3e-13
Q13595	282	Transformer-2 protein hom	no	no	0.572	0.379	0.411	3e-13
Q54Y98	326	Transformer-2 protein hom	no	no	0.529	0.303	0.373	1e-12
Q6IRQ4	370	RNA-binding motif protein	N/A	no	0.491	0.248	0.376	3e-11
Q7ZWA3	379	RNA-binding motif protein	no	no	0.465	0.229	0.363	4e-11

>sp|Q10422|YDC1_SCHPO Uncharacterized RNA-binding protein C25G10.01 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC25G10.01 PE=1 SV=1

 Score = 94.0 bits (232), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 57/145 (39%), Positives = 84/145 (57%), Gaps = 12/145 (8%)

Query: 17  NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
           N GN L+V+G+++R+ E +L++ FSK G V    ++ EP T+ SRGF F++   VE+A  
Sbjct: 98  NLGNDLFVSGIASRMQEDELQQIFSKFGTVTHVRIMREPVTKASRGFGFLSFSTVEEATS 157

Query: 77  CIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGL---KSSRDIGRGD------RGRYR 127
            I  LN     GR + V++++R RP +PTPG Y+G    ++SRD    +      R  YR
Sbjct: 158 AIDNLNSQEFYGRVLNVQKAKRSRPHSPTPGKYMGYDRRRNSRDFPSNNKDGGYRRNNYR 217

Query: 128 SGRDDYGYRRSPRRSPYRGGRDYSP 152
             RD   YR S R  P R  R++SP
Sbjct: 218 D-RDSNRYRNSYR--PSRPQREHSP 239

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

>sp|P62997|TRA2B_RAT Transformer-2 protein homolog beta OS=Rattus norvegicus GN=Tra2b PE=1 SV=1

 Score = 84.7 bits (208), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 59/134 (44%), Positives = 74/134 (55%), Gaps = 4/134 (2%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
           +R R  G     +P   L V GLS   TERDL + FSK G +A   +V + ++R SRGFA
Sbjct: 103 TRRRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 162

Query: 65  FVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLG---LKSSRDIGRG 121
           FV  + V+DA+   +  N   L+GR I V+ S  KRP TPTPG Y+G     SSR     
Sbjct: 163 FVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHTPTPGIYMGRPTYGSSRRRDYY 222

Query: 122 DRGRYRSGRDDYGY 135
           DRG Y  G DD  Y
Sbjct: 223 DRG-YDRGYDDRDY 235

Sequence-specific RNA-binding protein which participates in the control of pre-mRNA splicing. Can either activate or suppress exon inclusion. Acts additively with RBMX to promote exon 7 inclusion of the survival motor neuron SMN2. Activates the splicing of MAPT/Tau exon 10. Alters pre-mRNA splicing patterns by antagonizing the effects of splicing regulators, like RBMX. Binds to the AG-rich SE2 domain in the SMN exon 7 RNA. Binds to pre-mRNA.

Rattus norvegicus (taxid: 10116)

>sp|P62996|TRA2B_MOUSE Transformer-2 protein homolog beta OS=Mus musculus GN=Tra2b PE=1 SV=1

 Score = 84.7 bits (208), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 59/134 (44%), Positives = 74/134 (55%), Gaps = 4/134 (2%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
           +R R  G     +P   L V GLS   TERDL + FSK G +A   +V + ++R SRGFA
Sbjct: 103 TRRRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 162

Query: 65  FVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLG---LKSSRDIGRG 121
           FV  + V+DA+   +  N   L+GR I V+ S  KRP TPTPG Y+G     SSR     
Sbjct: 163 FVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHTPTPGIYMGRPTYGSSRRRDYY 222

Query: 122 DRGRYRSGRDDYGY 135
           DRG Y  G DD  Y
Sbjct: 223 DRG-YDRGYDDRDY 235

Sequence-specific RNA-binding protein which participates in the control of pre-mRNA splicing. Can either activate or suppress exon inclusion. Acts additively with RBMX to promote exon 7 inclusion of the survival motor neuron SMN2. Activates the splicing of MAPT/Tau exon 10. Alters pre-mRNA splicing patterns by antagonizing the effects of splicing regulators, like RBMX. Binds to the AG-rich SE2 domain in the SMN exon 7 RNA. Binds to pre-mRNA.

Mus musculus (taxid: 10090)

>sp|P62995|TRA2B_HUMAN Transformer-2 protein homolog beta OS=Homo sapiens GN=TRA2B PE=1 SV=1

 Score = 84.7 bits (208), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 59/134 (44%), Positives = 74/134 (55%), Gaps = 4/134 (2%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
           +R R  G     +P   L V GLS   TERDL + FSK G +A   +V + ++R SRGFA
Sbjct: 103 TRRRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 162

Query: 65  FVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLG---LKSSRDIGRG 121
           FV  + V+DA+   +  N   L+GR I V+ S  KRP TPTPG Y+G     SSR     
Sbjct: 163 FVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHTPTPGIYMGRPTYGSSRRRDYY 222

Query: 122 DRGRYRSGRDDYGY 135
           DRG Y  G DD  Y
Sbjct: 223 DRG-YDRGYDDRDY 235

Sequence-specific RNA-binding protein which participates in the control of pre-mRNA splicing. Can either activate or suppress exon inclusion. Acts additively with RBMX to promote exon 7 inclusion of the survival motor neuron SMN2. Activates the splicing of MAPT/Tau exon 10. Alters pre-mRNA splicing patterns by antagonizing the effects of splicing regulators, like RBMX. Binds to the AG-rich SE2 domain in the SMN exon 7 RNA. Binds to pre-mRNA.

Homo sapiens (taxid: 9606)

>sp|Q3ZBT6|TRA2B_BOVIN Transformer-2 protein homolog beta OS=Bos taurus GN=TRA2B PE=2 SV=1

 Score = 84.7 bits (208), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 59/134 (44%), Positives = 74/134 (55%), Gaps = 4/134 (2%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
           +R R  G     +P   L V GLS   TERDL + FSK G +A   +V + ++R SRGFA
Sbjct: 103 TRRRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 162

Query: 65  FVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLG---LKSSRDIGRG 121
           FV  + V+DA+   +  N   L+GR I V+ S  KRP TPTPG Y+G     SSR     
Sbjct: 163 FVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHTPTPGIYMGRPTYGSSRRRDYY 222

Query: 122 DRGRYRSGRDDYGY 135
           DRG Y  G DD  Y
Sbjct: 223 DRG-YDRGYDDRDY 235

Sequence-specific RNA-binding protein which participates in the control of pre-mRNA splicing. Can either activate or suppress exon inclusion. Acts additively with RBMX to promote exon 7 inclusion of the survival motor neuron SMN2. Activates the splicing of MAPT/Tau exon 10. Alters pre-mRNA splicing patterns by antagonizing the effects of splicing regulators, like RBMX. Binds to the AG-rich SE2 domain in the SMN exon 7 RNA. Binds to pre-mRNA.

Bos taurus (taxid: 9913)

>sp|Q6PFR5|TRA2A_MOUSE Transformer-2 protein homolog alpha OS=Mus musculus GN=Tra2a PE=1 SV=1

 Score = 74.7 bits (182), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 44/107 (41%), Positives = 62/107 (57%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
           +R R  G     +P   L V GLS   TERDL + FS+ G ++   +V + RT  SRGFA
Sbjct: 102 NRRRHTGSRANPDPNTCLGVFGLSLYTTERDLREVFSRYGPLSGVNVVYDQRTGRSRGFA 161

Query: 65  FVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLG 111
           FV  + ++D++  ++  N   L+GR I V+ S  KR  TPTPG Y+G
Sbjct: 162 FVYFERIDDSKEAMERANGMELDGRRIRVDYSITKRAHTPTPGIYMG 208

Sequence-specific RNA-binding protein which participates in the control of pre-mRNA splicing.

Mus musculus (taxid: 10090)

>sp|Q13595|TRA2A_HUMAN Transformer-2 protein homolog alpha OS=Homo sapiens GN=TRA2A PE=1 SV=1

 Score = 74.7 bits (182), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 44/107 (41%), Positives = 62/107 (57%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
           +R R  G     +P   L V GLS   TERDL + FS+ G ++   +V + RT  SRGFA
Sbjct: 104 NRRRHTGSRANPDPNTCLGVFGLSLYTTERDLREVFSRYGPLSGVNVVYDQRTGRSRGFA 163

Query: 65  FVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLG 111
           FV  + ++D++  ++  N   L+GR I V+ S  KR  TPTPG Y+G
Sbjct: 164 FVYFERIDDSKEAMERANGMELDGRRIRVDYSITKRAHTPTPGIYMG 210

Sequence-specific RNA-binding protein which participates in the control of pre-mRNA splicing.

Homo sapiens (taxid: 9606)

>sp|Q54Y98|TRA2_DICDI Transformer-2 protein homolog OS=Dictyostelium discoideum GN=tra2 PE=3 SV=1

 Score = 72.8 bits (177), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 37/99 (37%), Positives = 53/99 (53%)

Query: 13  TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVE 72
             T +P N L V GL+ +  ERDL+  FS+ GK+    L+++ +T  S+ F FV  +  E
Sbjct: 106 ANTASPSNVLGVFGLAPQTEERDLKDEFSRFGKIDHVDLIMDRKTGRSKCFGFVYFENKE 165

Query: 73  DAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLG 111
           DA R  +      L G+ I  + S  K+P  PTPG Y G
Sbjct: 166 DAVRAKEECQDLQLHGKSIRTDFSATKKPHEPTPGKYFG 204

Sequence-specific RNA-binding protein which participates in the control of pre-mRNA splicing.

Dictyostelium discoideum (taxid: 44689)

>sp|Q6IRQ4|RBMX_XENLA RNA-binding motif protein, X chromosome OS=Xenopus laevis GN=rbmx PE=2 SV=1

 Score = 68.2 bits (165), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 35/93 (37%), Positives = 51/93 (54%), Gaps = 1/93 (1%)

Query: 13  TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVE 72
            E   PG  L++ GL+T   E+ LE  F K G+V    L+ +  T  SRGFAFVT +   
Sbjct: 2   VEADRPGK-LFIGGLNTETNEKALEAVFCKYGRVVEVLLMKDRETNKSRGFAFVTFESPA 60

Query: 73  DAERCIKYLNQSVLEGRYITVERSRRKRPRTPT 105
           DA+   + LN   L+G+ I VE++ +    TP+
Sbjct: 61  DAKDAARELNGKALDGKPIKVEQATKPSFSTPS 93

RNA-binding protein that plays several role in the regulation of pre- and post-transcriptional processes. Implicated in tissue-specific regulation of gene transcription and alternative splicing of pre-mRNAs. Associates with chromatin. Associates with nascent mRNAs transcribed by RNA polymerase II. Component of the supraspliceosome complex that regulates pre-mRNA alternative splice site selection. Binds non-specifically to pre-mRNAs (By similarity). Required for embryonic development, in particular of the brain.

Xenopus laevis (taxid: 8355)

>sp|Q7ZWA3|RBMX_DANRE RNA-binding motif protein, X chromosome OS=Danio rerio GN=rbmx PE=2 SV=1

 Score = 67.8 bits (164), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 53/88 (60%), Gaps = 1/88 (1%)

Query: 13  TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVE 72
            E   PG  L++ GL+T  +E+ LE +FSK G+++   L+ +  T  SRGFAFVT +   
Sbjct: 2   AEADRPGK-LFIGGLNTETSEKVLEAYFSKFGRISEVLLMKDRETNKSRGFAFVTYENPG 60

Query: 73  DAERCIKYLNQSVLEGRYITVERSRRKR 100
           DA+   + +N   L+G+ I VE++ + +
Sbjct: 61  DAKDAAREMNGKPLDGKPIKVEQATKPQ 88

RNA-binding protein that plays several role in the regulation of pre- and post-transcriptional processes. Implicated in tissue-specific regulation of gene transcription and alternative splicing of pre-mRNAs. Associates with chromatin. Associates with nascent mRNAs transcribed by RNA polymerase II. Component of the supraspliceosome complex that regulates pre-mRNA alternative splice site selection. Binds non-specifically to pre-mRNAs (By similarity). Required for embryonic development, in particular of the brain.

Danio rerio (taxid: 7955)

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	187
255636876	246	unknown [Glycine max]	0.930	0.707	0.842	1e-69
357483947	303	Scaffold attachment factor B1 [Medicago	0.898	0.554	0.811	4e-69
449491291	244	PREDICTED: uncharacterized LOC101219220	0.898	0.688	0.723	3e-56
449434458	238	PREDICTED: uncharacterized RNA-binding p	0.898	0.705	0.723	3e-56
351726252	238	uncharacterized protein LOC100500170 [Gl	0.834	0.655	0.812	4e-56
388516667	268	unknown [Lotus japonicus]	0.930	0.649	0.777	1e-55
296084065	260	unnamed protein product [Vitis vinifera]	0.930	0.669	0.764	8e-55
359496147	228	PREDICTED: uncharacterized RNA-binding p	0.930	0.763	0.764	2e-54
1781299	235	transformer-SR ribonucleoprotein [Nicoti	0.770	0.612	0.815	6e-54
255579604	248	Arginine/serine-rich-splicing factor, pu	0.786	0.592	0.725	6e-51

>gi|255636876|gb|ACU18771.1| unknown [Glycine max]

 Score =  267 bits (683), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 155/184 (84%), Positives = 163/184 (88%), Gaps = 10/184 (5%)

Query: 14  ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
           E  N G TLYVTGLS+RVTERDLE+HFSKEGKVASCFLVVEPRTRISRGFAF+TMD VED
Sbjct: 63  EAKNAGTTLYVTGLSSRVTERDLEEHFSKEGKVASCFLVVEPRTRISRGFAFITMDTVED 122

Query: 74  AERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIG-RGDRGRYR---SG 129
           A RCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKS+RD G RGD GRYR   SG
Sbjct: 123 ANRCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSTRDYGHRGDHGRYRGGGSG 182

Query: 130 RDDYGYR----RSPRRS-PYRGGRDYSPRHS-PPYGGRSRRERSRSVPRSPYGSPERKYA 183
            DDYGYR    RSPR S PYRGGRDYSPRHS PPYGGRSRR+RSRS+P SPYGSP+R+YA
Sbjct: 183 HDDYGYRGDRGRSPRHSPPYRGGRDYSPRHSPPPYGGRSRRDRSRSLPYSPYGSPDRRYA 242

Query: 184 RGSR 187
           RGSR
Sbjct: 243 RGSR 246

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357483947|ref|XP_003612260.1| Scaffold attachment factor B1 [Medicago truncatula] gi|355513595|gb|AES95218.1| Scaffold attachment factor B1 [Medicago truncatula]

 Score =  266 bits (679), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 142/175 (81%), Positives = 155/175 (88%), Gaps = 7/175 (4%)

Query: 19  GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
           G+TLYVTGLS+RVTERDLE+HFSKEGKVASCFLVVEPRTRISRGFAFVTMD  EDA RCI
Sbjct: 130 GDTLYVTGLSSRVTERDLEEHFSKEGKVASCFLVVEPRTRISRGFAFVTMDTAEDANRCI 189

Query: 79  KYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGR--GDRGRYRS--GRDDYG 134
           KYLNQS+LEGRYITVERS+RKRPRTPTPGHYLGLK++RD G   GDRGR++   GRDDY 
Sbjct: 190 KYLNQSILEGRYITVERSKRKRPRTPTPGHYLGLKNTRDYGPRGGDRGRHQGGFGRDDYP 249

Query: 135 YRRSPRRSPYRGGRDYSPRHSPPYG--GRSRRERSRSVPRSPYGSPERKYARGSR 187
           Y RSPRRSPYRG RDYSPRHS PYG  GR RR+RSRS P +PYGSP+R+YARG R
Sbjct: 250 YHRSPRRSPYRGSRDYSPRHS-PYGGSGRYRRDRSRSPPYAPYGSPDRRYARGPR 303

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449491291|ref|XP_004158852.1| PREDICTED: uncharacterized LOC101219220 [Cucumis sativus]

 Score =  223 bits (568), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 139/192 (72%), Positives = 151/192 (78%), Gaps = 24/192 (12%)

Query: 14  ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
              NPGNTLYVTGLSTRVTERDLE+HFSKEGKVASCFLVVEPRTRISRGFAFVTMD V+D
Sbjct: 59  HANNPGNTLYVTGLSTRVTERDLEEHFSKEGKVASCFLVVEPRTRISRGFAFVTMDNVDD 118

Query: 74  AERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDRGRYRSG---- 129
           A RC+K+LNQS+LEGRYITVE+SRRKRPRTPTPGHYLGLKS+RD G      YR G    
Sbjct: 119 ANRCVKHLNQSILEGRYITVEKSRRKRPRTPTPGHYLGLKSTRDSG------YRGGDRGS 172

Query: 130 ----------RDDYGYRRSPRRSPYRGGRDYSPRHSPPY-GGRSRRERSR---SVPRSPY 175
                     R+DYGYRRSPRRSPYRG R+YSPRHSPPY GGRSRR+ SR          
Sbjct: 173 SRYRGGGGSFREDYGYRRSPRRSPYRGAREYSPRHSPPYGGGRSRRDHSRSPPPYSPPYG 232

Query: 176 GSPERKYARGSR 187
           GSP+R+Y RGSR
Sbjct: 233 GSPDRRYPRGSR 244

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434458|ref|XP_004135013.1| PREDICTED: uncharacterized RNA-binding protein C25G10.01-like, partial [Cucumis sativus]

 Score =  223 bits (567), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 139/192 (72%), Positives = 151/192 (78%), Gaps = 24/192 (12%)

Query: 14  ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
              NPGNTLYVTGLSTRVTERDLE+HFSKEGKVASCFLVVEPRTRISRGFAFVTMD V+D
Sbjct: 53  HANNPGNTLYVTGLSTRVTERDLEEHFSKEGKVASCFLVVEPRTRISRGFAFVTMDNVDD 112

Query: 74  AERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDRGRYRSG---- 129
           A RC+K+LNQS+LEGRYITVE+SRRKRPRTPTPGHYLGLKS+RD G      YR G    
Sbjct: 113 ANRCVKHLNQSILEGRYITVEKSRRKRPRTPTPGHYLGLKSTRDSG------YRGGDRGS 166

Query: 130 ----------RDDYGYRRSPRRSPYRGGRDYSPRHSPPY-GGRSRRERSR---SVPRSPY 175
                     R+DYGYRRSPRRSPYRG R+YSPRHSPPY GGRSRR+ SR          
Sbjct: 167 SRYRGGGGSFREDYGYRRSPRRSPYRGAREYSPRHSPPYGGGRSRRDHSRSPPPYSPPYG 226

Query: 176 GSPERKYARGSR 187
           GSP+R+Y RGSR
Sbjct: 227 GSPDRRYPRGSR 238

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351726252|ref|NP_001237888.1| uncharacterized protein LOC100500170 [Glycine max] gi|255629542|gb|ACU15118.1| unknown [Glycine max]

 Score =  223 bits (567), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 130/160 (81%), Positives = 143/160 (89%), Gaps = 4/160 (2%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
           RSRS   GR+E  NPG+TLYVTGLS+RVTERDLE+HFSKEGKV+SCFLVVEPRTRISRGF
Sbjct: 55  RSRSPIHGRSEPSNPGDTLYVTGLSSRVTERDLEEHFSKEGKVSSCFLVVEPRTRISRGF 114

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIG-RGD 122
           AFVTM+  EDAERCIKYLNQSVLEGRYIT+ERSRRKR RTPTPGHYLGLK++R+ G RG+
Sbjct: 115 AFVTMESAEDAERCIKYLNQSVLEGRYITIERSRRKRARTPTPGHYLGLKNTREYGFRGE 174

Query: 123 RGRYRSG--RDDYGYRRSPRRSPYRGGRDYSPRHSPPYGG 160
           RGRYR G  RD+Y  RRSPRRSPYRGG+DYSPR S PYGG
Sbjct: 175 RGRYRDGPDRDNYSRRRSPRRSPYRGGQDYSPRRS-PYGG 213

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388516667|gb|AFK46395.1| unknown [Lotus japonicus]

 Score =  221 bits (562), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 143/184 (77%), Positives = 153/184 (83%), Gaps = 10/184 (5%)

Query: 14  ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
           E  N GNTLYVTGLS+RVTERDLE+HF+KEGKVASCFLVVEPRTRISRGFAF+TMD VED
Sbjct: 85  EDRNGGNTLYVTGLSSRVTERDLEEHFAKEGKVASCFLVVEPRTRISRGFAFITMDTVED 144

Query: 74  AERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRD----------IGRGDR 123
           A RC+KYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKS+RD                
Sbjct: 145 ANRCVKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSTRDRDYGHRGGDRGRYRGG 204

Query: 124 GRYRSGRDDYGYRRSPRRSPYRGGRDYSPRHSPPYGGRSRRERSRSVPRSPYGSPERKYA 183
           G   SGRDDY +RRSPRRSPYRGGRDYSPR S PY G SRRERSRS+P SPY SP+R+YA
Sbjct: 205 GGGGSGRDDYQHRRSPRRSPYRGGRDYSPRRSSPYAGSSRRERSRSLPYSPYASPDRRYA 264

Query: 184 RGSR 187
           RGSR
Sbjct: 265 RGSR 268

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296084065|emb|CBI24453.3| unnamed protein product [Vitis vinifera]

 Score =  218 bits (555), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 136/178 (76%), Positives = 147/178 (82%), Gaps = 4/178 (2%)

Query: 13  TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVE 72
           T+T NPGNTLYVTGLSTRVTER LE HFS+EGKVASCFLV+EPRTRISRGFAFVTM+ VE
Sbjct: 84  TDTSNPGNTLYVTGLSTRVTERALEDHFSREGKVASCFLVMEPRTRISRGFAFVTMETVE 143

Query: 73  DAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRD---IGRGDRGRYRSG 129
           DA RCIK+LNQSVLEGRYITVE+SRRKR RTPTPGHYLGLK++RD    G   R R  SG
Sbjct: 144 DANRCIKHLNQSVLEGRYITVEKSRRKRARTPTPGHYLGLKNTRDSGYRGDRGRYRGGSG 203

Query: 130 RDDYGYRRSPRRSPYRGGRDYSPRHSPPYGGRSRRERSRSVPRSPYGSPERKYARGSR 187
           RDDYG RRSPR SPYRGGRDYS     P  GRSRR+RSRS+P SPY SPER Y   +R
Sbjct: 204 RDDYGSRRSPRPSPYRGGRDYS-PRRSPPRGRSRRDRSRSIPYSPYASPERGYGHRAR 260

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359496147|ref|XP_003635162.1| PREDICTED: uncharacterized RNA-binding protein C25G10.01-like [Vitis vinifera]

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 136/178 (76%), Positives = 147/178 (82%), Gaps = 4/178 (2%)

Query: 13  TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVE 72
           T+T NPGNTLYVTGLSTRVTER LE HFS+EGKVASCFLV+EPRTRISRGFAFVTM+ VE
Sbjct: 52  TDTSNPGNTLYVTGLSTRVTERALEDHFSREGKVASCFLVMEPRTRISRGFAFVTMETVE 111

Query: 73  DAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRD---IGRGDRGRYRSG 129
           DA RCIK+LNQSVLEGRYITVE+SRRKR RTPTPGHYLGLK++RD    G   R R  SG
Sbjct: 112 DANRCIKHLNQSVLEGRYITVEKSRRKRARTPTPGHYLGLKNTRDSGYRGDRGRYRGGSG 171

Query: 130 RDDYGYRRSPRRSPYRGGRDYSPRHSPPYGGRSRRERSRSVPRSPYGSPERKYARGSR 187
           RDDYG RRSPR SPYRGGRDYS     P  GRSRR+RSRS+P SPY SPER Y   +R
Sbjct: 172 RDDYGSRRSPRPSPYRGGRDYS-PRRSPPRGRSRRDRSRSIPYSPYASPERGYGHRAR 228

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|1781299|emb|CAA70700.1| transformer-SR ribonucleoprotein [Nicotiana tabacum]

 Score =  215 bits (548), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 119/146 (81%), Positives = 128/146 (87%), Gaps = 2/146 (1%)

Query: 14  ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
           E  NPGNTLYVTGLSTRVTERDLE+HFSKEGKV S FLVVEPR+RISRGFAF+TMD +ED
Sbjct: 60  EVSNPGNTLYVTGLSTRVTERDLEEHFSKEGKVKSVFLVVEPRSRISRGFAFITMDSLED 119

Query: 74  AERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDRGRYRSGRDDY 133
           A RCIK+LNQSVLEGRYITVE+SRRKR RTPTPGHYLGLK++R  GRGDRGR    R+DY
Sbjct: 120 ANRCIKHLNQSVLEGRYITVEKSRRKRARTPTPGHYLGLKNARGEGRGDRGR-YRDREDY 178

Query: 134 GYRRSPRRSPYRGGRDYSPRHSPPYG 159
           GYRRSPR SPYR  RDYSPR S PYG
Sbjct: 179 GYRRSPRHSPYRSRRDYSPRRS-PYG 203

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255579604|ref|XP_002530643.1| Arginine/serine-rich-splicing factor, putative [Ricinus communis] gi|223529816|gb|EEF31751.1| Arginine/serine-rich-splicing factor, putative [Ricinus communis]

 Score =  205 bits (522), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 119/164 (72%), Positives = 125/164 (76%), Gaps = 17/164 (10%)

Query: 13  TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVE 72
           TE  NPGNTLYVTGLSTRVTER LE+HF+KEGKVASCFLVVEPRTRISRGFAFVTMD VE
Sbjct: 67  TEAVNPGNTLYVTGLSTRVTERGLEEHFAKEGKVASCFLVVEPRTRISRGFAFVTMDNVE 126

Query: 73  DAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDRGRYRS---- 128
           DA RC+KYLNQSVLEGRYITVE+SRRKRPRTPTPGHYLGLKS+RD G       R     
Sbjct: 127 DANRCVKYLNQSVLEGRYITVEKSRRKRPRTPTPGHYLGLKSNRDYGHRGDRGDRGRYRG 186

Query: 129 -----GRDDYGYRRSPRRSPY-------RGGRDYSPRHSPPYGG 160
                GRDDY  R   RRSP        R GR+YSPR S PYGG
Sbjct: 187 RDDYHGRDDYRGRDDYRRSPRRSPYRGERAGREYSPRRS-PYGG 229

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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	187
TAIR|locus:2025092	382	SR45a "serine/arginine rich-li	0.540	0.264	0.544	1.8e-23
ASPGD|ASPL0000005578	307	AN6676 [Emericella nidulans (t	0.508	0.309	0.378	2.1e-12
DICTYBASE|DDB_G0292698	306	DDB_G0292698 "RNA-binding regi	0.508	0.310	0.347	2.8e-11
UNIPROTKB|Q9DDU8	289	TRA2B "Uncharacterized protein	0.508	0.328	0.389	5.2e-10
POMBASE|SPAC25G10.01	297	SPAC25G10.01 "RNA-binding prot	0.508	0.319	0.347	7.4e-10
UNIPROTKB|E1C875	182	TRA2A "Uncharacterized protein	0.508	0.521	0.347	8.4e-10
UNIPROTKB|Q3ZBT6	288	TRA2B "Transformer-2 protein h	0.508	0.329	0.378	1.1e-09
UNIPROTKB|E2RD37	288	TRA2B "Uncharacterized protein	0.508	0.329	0.378	1.1e-09
UNIPROTKB|P62995	288	TRA2B "Transformer-2 protein h	0.508	0.329	0.378	1.1e-09
MGI|MGI:106016	288	Tra2b "transformer 2 beta homo	0.508	0.329	0.378	1.1e-09

TAIR|locus:2025092 SR45a "serine/arginine rich-like protein 45a" [Arabidopsis thaliana (taxid:3702)]

 Score = 270 (100.1 bits), Expect = 1.8e-23, P = 1.8e-23
 Identities = 55/101 (54%), Positives = 67/101 (66%)

Query:    13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVE 72
             ++  NPGN+LYVTGLS RVTERDLE HF+KEGKV    LV++P TR SRGF F++M  V 
Sbjct:    68 SDAENPGNSLYVTGLSHRVTERDLEDHFAKEGKVTDVHLVLDPWTRESRGFGFISMKSVG 127

Query:    73 DAERCIKYLNQSVLEGRYIXXXXXXXXXXXXXXXGHYLGLK 113
             DA RCI+ L+ SVL+GR I               G YLGL+
Sbjct:   128 DANRCIRSLDHSVLQGRVITVEKARRRRGRTPTPGKYLGLR 168

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008380 "RNA splicing" evidence=NAS

GO:0009644 "response to high light intensity" evidence=IMP

GO:0043484 "regulation of RNA splicing" evidence=IMP

ASPGD|ASPL0000005578 AN6676 [Emericella nidulans (taxid:162425)]

 Score = 169 (64.5 bits), Expect = 2.1e-12, P = 2.1e-12
 Identities = 36/95 (37%), Positives = 50/95 (52%)

Query:    17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
             N G+ L+VTG+  R+TE D+ + F K G V SC ++V+P T+ SRGF FV M   E A+ 
Sbjct:    64 NTGSNLFVTGIHPRLTESDISRLFEKYGDVESCSIMVDPHTKESRGFGFVNMVTAEQADA 123

Query:    77 CIKYLNQSVLEGRYIXXXXXXXXXXXXXXXGHYLG 111
               + L   V+EGR +               G Y G
Sbjct:   124 AKEGLQGEVIEGRTLSIEKARRSRPRTPTPGKYFG 158

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

DICTYBASE|DDB_G0292698 DDB_G0292698 "RNA-binding region RNP-1 domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 159 (61.0 bits), Expect = 2.8e-11, P = 2.8e-11
 Identities = 33/95 (34%), Positives = 51/95 (53%)

Query:    17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
             N GNTL+V+ L+ R  E DL   F+  GKV  C ++++P T+ SRGF FVT    ++A+ 
Sbjct:    68 NNGNTLHVSNLNPRTRESDLRDTFASIGKVIDCTILLDPNTKESRGFGFVTYSSGDEAQD 127

Query:    77 CIKYLNQSVLEGRYIXXXXXXXXXXXXXXXGHYLG 111
              I+ L+ + ++G  I               G Y+G
Sbjct:   128 AIQRLDSTKIDGNTIRVEKSKRSKARDPTPGFYMG 162

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0044351 "macropinocytosis" evidence=RCA

UNIPROTKB|Q9DDU8 TRA2B "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 147 (56.8 bits), Expect = 5.2e-10, P = 5.2e-10
 Identities = 37/95 (38%), Positives = 49/95 (51%)

Query:    17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
             +P   L V GLS   TERDL + FSK G +A   +V + ++R SRGFAFV  + VEDA+ 
Sbjct:   115 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVEDAKE 174

Query:    77 CIKYLNQSVLEGRYIXXXXXXXXXXXXXXXGHYLG 111
               +  N   L+GR I               G Y+G
Sbjct:   175 AKERANGMELDGRRIRVDFSITKRPHTPTPGIYMG 209

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IEA

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

GO:0003729 "mRNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=IEA

POMBASE|SPAC25G10.01 SPAC25G10.01 "RNA-binding protein" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 146 (56.5 bits), Expect = 7.4e-10, P = 7.4e-10
 Identities = 33/95 (34%), Positives = 50/95 (52%)

Query:    17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
             N GN L+V+G+++R+ E +L++ FSK G V    ++ EP T+ SRGF F++   VE+A  
Sbjct:    98 NLGNDLFVSGIASRMQEDELQQIFSKFGTVTHVRIMREPVTKASRGFGFLSFSTVEEATS 157

Query:    77 CIKYLNQSVLEGRYIXXXXXXXXXXXXXXXGHYLG 111
              I  LN     GR +               G Y+G
Sbjct:   158 AIDNLNSQEFYGRVLNVQKAKRSRPHSPTPGKYMG 192

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|E1C875 TRA2A "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 141 (54.7 bits), Expect = 8.4e-10, P = 8.4e-10
 Identities = 33/95 (34%), Positives = 49/95 (51%)

Query:    17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
             +P   L V GLS   TERDL + FS+ G +    +V + RT  SRGFAFV  + ++D++ 
Sbjct:    15 DPNTCLGVFGLSLYTTERDLREVFSRYGPLTGVNVVYDQRTGRSRGFAFVYFERIDDSKE 74

Query:    77 CIKYLNQSVLEGRYIXXXXXXXXXXXXXXXGHYLG 111
              +++ N   L+GR I               G Y+G
Sbjct:    75 AMEHANGMELDGRRIRVDYSITKRAHTPTPGIYMG 109

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q3ZBT6 TRA2B "Transformer-2 protein homolog beta" [Bos taurus (taxid:9913)]

 Score = 144 (55.7 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 36/95 (37%), Positives = 49/95 (51%)

Query:    17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
             +P   L V GLS   TERDL + FSK G +A   +V + ++R SRGFAFV  + V+DA+ 
Sbjct:   115 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 174

Query:    77 CIKYLNQSVLEGRYIXXXXXXXXXXXXXXXGHYLG 111
               +  N   L+GR I               G Y+G
Sbjct:   175 AKERANGMELDGRRIRVDFSITKRPHTPTPGIYMG 209

GO:0003729 "mRNA binding" evidence=ISS

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=ISS

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

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

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2RD37 TRA2B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 144 (55.7 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 36/95 (37%), Positives = 49/95 (51%)

Query:    17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
             +P   L V GLS   TERDL + FSK G +A   +V + ++R SRGFAFV  + V+DA+ 
Sbjct:   115 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 174

Query:    77 CIKYLNQSVLEGRYIXXXXXXXXXXXXXXXGHYLG 111
               +  N   L+GR I               G Y+G
Sbjct:   175 AKERANGMELDGRRIRVDFSITKRPHTPTPGIYMG 209

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|P62995 TRA2B "Transformer-2 protein homolog beta" [Homo sapiens (taxid:9606)]

 Score = 144 (55.7 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 36/95 (37%), Positives = 49/95 (51%)

Query:    17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
             +P   L V GLS   TERDL + FSK G +A   +V + ++R SRGFAFV  + V+DA+ 
Sbjct:   115 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 174

Query:    77 CIKYLNQSVLEGRYIXXXXXXXXXXXXXXXGHYLG 111
               +  N   L+GR I               G Y+G
Sbjct:   175 AKERANGMELDGRRIRVDFSITKRPHTPTPGIYMG 209

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

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

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IDA

GO:0003729 "mRNA binding" evidence=IDA

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=IDA

MGI|MGI:106016 Tra2b "transformer 2 beta homolog (Drosophila)" [Mus musculus (taxid:10090)]

 Score = 144 (55.7 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 36/95 (37%), Positives = 49/95 (51%)

Query:    17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
             +P   L V GLS   TERDL + FSK G +A   +V + ++R SRGFAFV  + V+DA+ 
Sbjct:   115 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 174

Query:    77 CIKYLNQSVLEGRYIXXXXXXXXXXXXXXXGHYLG 111
               +  N   L+GR I               G Y+G
Sbjct:   175 AKERANGMELDGRRIRVDFSITKRPHTPTPGIYMG 209

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=ISO

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00012366001	SubName- Full=Chromosome chr4 scaffold_373, whole genome shotgun sequence; (227 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00015172001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (294 aa)			•						0.501
	GSVIVG00020349001	SubName- Full=Chromosome chr5 scaffold_2, whole genome shotgun sequence; (283 aa)			•						0.495
	GSVIVG00008860001	SubName- Full=Chromosome chr13 scaffold_210, whole genome shotgun sequence; (247 aa)			•						0.495
	GSVIVG00026169001	SubName- Full=Chromosome chr15 scaffold_37, whole genome shotgun sequence; (269 aa)			•						0.491
	GSVIVG00025933001	SubName- Full=Chromosome chr12 scaffold_36, whole genome shotgun sequence; (103 aa)			•						0.488
	GSVIVG00008544001	SubName- Full=Chromosome undetermined scaffold_1542, whole genome shotgun sequence; (133 aa)			•						0.479
	GSVIVG00030123001	SubName- Full=Chromosome chr1 scaffold_5, whole genome shotgun sequence; (140 aa)			•						0.471
	GSVIVG00018272001	SubName- Full=Chromosome chr13 scaffold_17, whole genome shotgun sequence; (287 aa)			•						0.464
	GSVIVG00002935001	SubName- Full=Chromosome chr18 scaffold_137, whole genome shotgun sequence; (258 aa)			•						0.445
	GSVIVG00031983001	SubName- Full=Chromosome chr18 scaffold_61, whole genome shotgun sequence; (264 aa)			•						0.442

---

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	187
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-37
smart00360	73	smart00360, RRM, RNA recognition motif	5e-24
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	5e-20
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	8e-19
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-17
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	7e-16
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-15
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	8e-15
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-14
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-14
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-14
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	7e-14
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-13
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	2e-13
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-13
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	5e-13
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	8e-13
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	8e-13
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-12
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	2e-12
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	5e-12
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	9e-12
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-11
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	1e-11
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	5e-11
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	7e-11
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	8e-11
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	8e-11
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	8e-11
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	9e-11
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-10
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-10
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	3e-10
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	3e-10
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	9e-10
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-09
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	1e-09
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-09
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-09
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	1e-09
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	1e-09
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-09
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-09
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-09
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-09
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-09
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	3e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-09
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	4e-09
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	4e-09
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	5e-09
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	8e-09
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-08
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	1e-08
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	1e-08
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	2e-08
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-08
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-08
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	3e-08
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	3e-08
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	3e-08
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	3e-08
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	4e-08
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-08
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	6e-08
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	6e-08
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	6e-08
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	7e-08
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	8e-08
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	9e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-07
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	1e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-07
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	1e-07
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-07
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-07
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-07
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	2e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-07
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	2e-07
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	3e-07
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	3e-07
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	4e-07
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	4e-07
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	4e-07
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	4e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	5e-07
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	5e-07
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	5e-07
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	5e-07
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	5e-07
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	6e-07
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	6e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	7e-07
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	7e-07
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	8e-07
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	9e-07
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	9e-07
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	9e-07
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	9e-07
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	1e-06
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	1e-06
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	1e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-06
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-06
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	2e-06
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	2e-06
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-06
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	2e-06
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-06
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	4e-06
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	4e-06
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	5e-06
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	5e-06
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	5e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	5e-06
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	6e-06
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	9e-06
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	1e-05
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	1e-05
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	2e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	2e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-05
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	2e-05
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	2e-05
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	2e-05
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	3e-05
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	3e-05
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	3e-05
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	4e-05
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	4e-05
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	5e-05
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	5e-05
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	6e-05
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	6e-05
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	7e-05
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	8e-05
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	8e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	8e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-04
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	1e-04
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	1e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	1e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	1e-04
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	1e-04
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	1e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	1e-04
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	1e-04
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	1e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-04
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	2e-04
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	2e-04
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	2e-04
cd12282	91	cd12282, RRM2_TatSF1_like, RNA recognition motif 2	2e-04
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	2e-04
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-04
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-04
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	2e-04
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-04
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	2e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	2e-04
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	3e-04
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	3e-04
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	3e-04
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	3e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-04
cd12438	98	cd12438, RRM_CNOT4, RNA recognition motif in Eukar	4e-04
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	4e-04
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	4e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-04
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	5e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	5e-04
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	5e-04
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	5e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	5e-04
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	6e-04
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	6e-04
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	6e-04
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	6e-04
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	7e-04
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	7e-04
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	7e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	8e-04
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	8e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	8e-04
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	9e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.001
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	0.001
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	0.001
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	0.001
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	0.001
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	0.001
cd12689	80	cd12689, RRM1_hnRNPL_like, RNA recognition motif 1	0.001
cd12627	77	cd12627, RRM1_IGF2BP3, RNA recognition motif 1 in	0.001
cd12248	74	cd12248, RRM_RBM44, RNA recognition motif in RNA-b	0.001
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	0.001
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	0.001
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	0.001
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	0.002
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	0.002
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	0.002
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	0.002
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	0.002
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	0.002
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.002
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	0.002
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	0.002
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	0.002
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	0.002
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	0.003
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	0.003
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	0.004
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	0.004

>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 =  123 bits (311), Expect = 2e-37
 Identities = 43/80 (53%), Positives = 56/80 (70%)

Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          GN L+V+GLSTR TE++LE  FSK G+V    L+ +P T  SRGF FVT + VEDA+  I
Sbjct: 1  GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60

Query: 79 KYLNQSVLEGRYITVERSRR 98
          + LN   LEGR I VE+++R
Sbjct: 61 RDLNGKELEGRVIKVEKAKR 80

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|214636 smart00360, RRM, RNA recognition motif

 Score = 89.2 bits (222), Expect = 5e-24
 Identities = 33/73 (45%), Positives = 44/73 (60%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          TL+V  L    TE +L + FSK GKV S  LV +  T  S+GFAFV  +  EDAE+ ++ 
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 81 LNQSVLEGRYITV 93
          LN   L+GR + V
Sbjct: 61 LNGKELDGRPLKV 73

Length = 73

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

 Score = 79.3 bits (196), Expect = 5e-20
 Identities = 29/73 (39%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V  L    TE DL + FSK G++ S  +V +   + S+GFAFV  +  EDAE+ ++ L
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGK-SKGFAFVEFESPEDAEKALEAL 59

Query: 82 NQSVLEGRYITVE 94
          N   L+GR + V 
Sbjct: 60 NGKELDGRKLKVS 72

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 76.2 bits (188), Expect = 8e-19
 Identities = 33/73 (45%), Positives = 49/73 (67%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V+GLS+     DL++ FSK GKV    +V   R+  +R F FVTM  VE+A +CI++L
Sbjct: 2  LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 82 NQSVLEGRYITVE 94
          +++ L GR I+VE
Sbjct: 62 HRTELHGRVISVE 74

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

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

 Score = 72.6 bits (179), Expect = 1e-17
 Identities = 29/71 (40%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V  L    TE DL+  FSK G + S  +V +   R S+GFAFV  +  EDAE+ ++ L
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGR-SKGFAFVEFEDEEDAEKALEAL 59

Query: 82 NQSVLEGRYIT 92
          N   L GR + 
Sbjct: 60 NGKELGGRELR 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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 68.3 bits (168), Expect = 7e-16
 Identities = 33/70 (47%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LYV  L   VTE DL + FS  GKV    LV        RGFAFV     EDAE  +K L
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLV--RNKDRPRGFAFVEFASPEDAEAALKKL 58

Query: 82 NQSVLEGRYI 91
          N  VL+GR +
Sbjct: 59 NGLVLDGRTL 68

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

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

 Score = 67.6 bits (166), Expect = 1e-15
 Identities = 30/73 (41%), Positives = 41/73 (56%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           LYV  L   VTE DL+  F + G+V S  ++ +  T  SRGF FV M+  E+A   I+ 
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 81 LNQSVLEGRYITV 93
          LN +   GR +TV
Sbjct: 61 LNGTDFGGRTLTV 73

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

 Score = 65.7 bits (161), Expect = 8e-15
 Identities = 32/75 (42%), Positives = 44/75 (58%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L V GLS   TERDL + FS+ G +    +V + +T  SRGF FV  + VEDA+   + L
Sbjct: 2  LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 82 NQSVLEGRYITVERS 96
          N   ++GR I V+ S
Sbjct: 62 NGMEIDGRRIRVDYS 76

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

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

 Score = 64.9 bits (159), Expect = 2e-14
 Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 5/81 (6%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVV-----EPRTRISRGFAFVTMDGVEDAE 75
          TL+V  L+ + TE  L+KHF K G V S  +        P   +S G+ FV     E A+
Sbjct: 2  TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 76 RCIKYLNQSVLEGRYITVERS 96
          + +K L  +VL+G  + ++ S
Sbjct: 62 KALKRLQGTVLDGHALELKLS 82

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

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

 Score = 64.6 bits (158), Expect = 2e-14
 Identities = 28/79 (35%), Positives = 46/79 (58%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          TL+V  L    T+  LE+ FS+ G +  CF+V +  ++  RGF +VT    EDA+R ++ 
Sbjct: 1  TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 81 LNQSVLEGRYITVERSRRK 99
            ++   GR I VE +++K
Sbjct: 61 KKKTKFGGRKIHVEFAKKK 79

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|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 = 63.9 bits (156), Expect = 4e-14
 Identities = 23/72 (31%), Positives = 39/72 (54%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V  L    TE +L + F   G+++   L ++  T+ S+GFAFV+    E A +    L
Sbjct: 2  LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 82 NQSVLEGRYITV 93
          + S+ +GR + V
Sbjct: 62 DGSIFQGRLLHV 73

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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 63.3 bits (154), Expect = 7e-14
 Identities = 23/78 (29%), Positives = 47/78 (60%), Gaps = 1/78 (1%)

Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
             L+V GL+ + ++  L +HF++ GK+  C ++V+P T+ SRGF F+T    ++A+  +
Sbjct: 2  LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61

Query: 79 KYLNQSVLEGRYITVERS 96
          +      ++G  I ++R+
Sbjct: 62 E-AQPHSIDGNQIELKRA 78

This subfamily corresponds to the RRM1 of hnRNP A0 which 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 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 = 79

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

 Score = 66.9 bits (162), Expect = 2e-13
 Identities = 46/168 (27%), Positives = 69/168 (41%), Gaps = 6/168 (3%)

Query: 2   VFRSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISR 61
           +FRS    + R ++    NTL+V  L   VTE DL + F K G V    LV +  T  SR
Sbjct: 98  LFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSR 157

Query: 62  GFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR-RKRPRTPTPGHYLGLKSSRDIGR 120
           GFAFV  +  E AE+ I+ LN   LEGR + V++++   +PR+    +     + +    
Sbjct: 158 GFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRG 217

Query: 121 GDRGRYRS-----GRDDYGYRRSPRRSPYRGGRDYSPRHSPPYGGRSR 163
                 +S     G              ++   D      PP      
Sbjct: 218 KALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKI 265

Length = 306

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

 Score = 62.6 bits (153), Expect = 2e-13
 Identities = 28/82 (34%), Positives = 40/82 (48%), Gaps = 5/82 (6%)

Query: 18 PGNTLYVTGLSTRVTERDLEKHFSKEGK--VASCFLVVEPRTRISRGFAFVTMDGVEDAE 75
          P NTL + GL    TE D+ +  S      +    L+ +  T  SRGFAFV    +EDA 
Sbjct: 1  PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDAT 60

Query: 76 RCIKYLNQS---VLEGRYITVE 94
          + +  LN     V++GR + V 
Sbjct: 61 QWMDALNNLDPFVIDGRVVRVS 82

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

 Score = 61.5 bits (150), Expect = 3e-13
 Identities = 23/81 (28%), Positives = 43/81 (53%), Gaps = 5/81 (6%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          T+++  L    TE +L++ FS+ G+V    +V +  T  S+G AFV     E A++C++ 
Sbjct: 2  TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEA 61

Query: 81 LNQSV-----LEGRYITVERS 96
           + +      L+GR + V  +
Sbjct: 62 ADNAEDSGLSLDGRRLIVTLA 82

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

 Score = 61.0 bits (149), Expect = 5e-13
 Identities = 28/62 (45%), Positives = 35/62 (56%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          T+ VT LS    E DL + F   G ++  +L  +  T  SRGFAFVT    EDAER I+ 
Sbjct: 1  TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 81 LN 82
          LN
Sbjct: 61 LN 62

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|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 60.5 bits (146), Expect = 8e-13
 Identities = 32/76 (42%), Positives = 47/76 (61%)

Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          G  L+V+GLS+     DL+  FSK GKV    +V   R+  +R + FVTM   E+A +CI
Sbjct: 1  GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCI 60

Query: 79 KYLNQSVLEGRYITVE 94
           +L+++ L GR I+VE
Sbjct: 61 NHLHRTELHGRMISVE 76

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1. Length = 76

>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 = 60.4 bits (147), Expect = 8e-13
 Identities = 31/73 (42%), Positives = 41/73 (56%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          T+YV+ L   +T  DL K FSK GKV    +V +  TR S+G AF+     EDA +C+K 
Sbjct: 3  TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 81 LNQSVLEGRYITV 93
          LN   L GR +  
Sbjct: 63 LNNKELFGRTLKC 75

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

 Score = 59.9 bits (146), Expect = 1e-12
 Identities = 24/73 (32%), Positives = 43/73 (58%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V  L+  V +  L++ FS  G V    L ++    + RG+A+V  +  EDAE+ IK++
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 82 NQSVLEGRYITVE 94
          +   ++G+ +TVE
Sbjct: 61 DGGQIDGQEVTVE 73

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

 Score = 59.2 bits (144), Expect = 2e-12
 Identities = 26/73 (35%), Positives = 33/73 (45%), Gaps = 8/73 (10%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V  L    T  +L   F K G V  C +V        + + FV M+  EDAE  IK L
Sbjct: 2  LFVGNLPDATTSEELRALFEKYGTVTECDVV--------KNYGFVHMEEEEDAEDAIKAL 53

Query: 82 NQSVLEGRYITVE 94
          N     G+ I VE
Sbjct: 54 NGYEFMGKRINVE 66

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

>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 58.7 bits (142), Expect = 5e-12
 Identities = 27/79 (34%), Positives = 42/79 (53%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          TL+V  L+  VT+ DL   FS    +    +V +P T  SRG+ FVT   +EDA+  +  
Sbjct: 1  TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 81 LNQSVLEGRYITVERSRRK 99
          L    L GR + ++ + R+
Sbjct: 61 LKNKKLHGRILRLDIAERR 79

This subgroup corresponds to the RRM1 of Nop4p (also known as 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 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 57.6 bits (140), Expect = 9e-12
 Identities = 28/72 (38%), Positives = 38/72 (52%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LYV GL+  V E+ L   F   G +    + ++  T+  RGFAFV  +  EDA   I  +
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 82 NQSVLEGRYITV 93
          N+S L GR I V
Sbjct: 61 NESELFGRTIRV 72

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

 Score = 57.7 bits (140), Expect = 1e-11
 Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 3/76 (3%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVAS---CFLVVEPRTRISRGFAFVTMDGVEDAERC 77
           L++  L +R+TE  L K FSK GK+      F    P     RG+ FVT +  E+AE+ 
Sbjct: 1  RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 78 IKYLNQSVLEGRYITV 93
          +K LN     G+ + V
Sbjct: 61 LKSLNGKTALGKKLVV 76

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

 Score = 57.6 bits (140), Expect = 1e-11
 Identities = 29/80 (36%), Positives = 41/80 (51%), Gaps = 10/80 (12%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRT------RISRGFAFVTMDGVEDAE 75
          +YV  L  ++ E DL   FSK G+V S   +  P+       R++ GFAFVT      AE
Sbjct: 3  IYVRNLDFKLDEDDLRGIFSKFGEVES---IRIPKKQDEKQGRLNNGFAFVTFKDASSAE 59

Query: 76 RCIKYLNQSVLEGRYITVER 95
            ++ LN + L GR I+V  
Sbjct: 60 NALQ-LNGTELGGRKISVSL 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|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 = 56.0 bits (135), Expect = 5e-11
 Identities = 27/75 (36%), Positives = 47/75 (62%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L++ GLS    E+ LE+ FSK G+++   +V +  T+ SRGF FVT +  +DA+  +  +
Sbjct: 3  LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 82 NQSVLEGRYITVERS 96
          N   ++GR I V+++
Sbjct: 63 NGKSVDGRQIRVDQA 77

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

 Score = 55.5 bits (134), Expect = 7e-11
 Identities = 29/80 (36%), Positives = 44/80 (55%), Gaps = 4/80 (5%)

Query: 14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
          ETG     L+V  L     E DLEK FSK G+++   + ++ ++  S+GFA+V     ED
Sbjct: 1  ETGR----LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPED 56

Query: 74 AERCIKYLNQSVLEGRYITV 93
          A +  K L+  V +GR I +
Sbjct: 57 AVKAYKELDGKVFQGRLIHI 76

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

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

 Score = 55.3 bits (134), Expect = 8e-11
 Identities = 29/74 (39%), Positives = 38/74 (51%), Gaps = 5/74 (6%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTR--ISRGFAFVTMDGVEDAERCIK 79
          L V  L  + TE DL+K FS  G V   + V  PR      +GFAFV      DAE+ IK
Sbjct: 2  LIVRNLPFKCTEADLKKLFSPFGFV---WEVTIPRKPDGKKKGFAFVQFTSKADAEKAIK 58

Query: 80 YLNQSVLEGRYITV 93
           +N   ++GR + V
Sbjct: 59 GVNGKKIKGRPVAV 72

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

 Score = 55.0 bits (133), Expect = 8e-11
 Identities = 24/57 (42%), Positives = 34/57 (59%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          L+V GL   VTE DL ++FS+ G V S  +V +  T   RGFAFVT D  +  ++ +
Sbjct: 2  LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIV 58

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

 Score = 54.9 bits (133), Expect = 8e-11
 Identities = 27/77 (35%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          +YV  L  R T+R+LE  F K G + S ++   P      GFAFV  +   DAE  ++ L
Sbjct: 2  VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPP-----GFAFVEFEDPRDAEDAVRAL 56

Query: 82 NQSVLEGRYITVERSRR 98
          +   + G  + VE SR 
Sbjct: 57 DGRRICGNRVRVELSRG 73

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

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

 Score = 55.2 bits (134), Expect = 9e-11
 Identities = 31/80 (38%), Positives = 42/80 (52%), Gaps = 6/80 (7%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVAS---CFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          LYV  L   VTE  L + FS  G V S   C  ++   TR S G+A+V      DAER +
Sbjct: 2  LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLI---TRRSLGYAYVNFQNPADAERAL 58

Query: 79 KYLNQSVLEGRYITVERSRR 98
            LN  V++G+ I +  S+R
Sbjct: 59 DTLNFDVIKGKPIRIMWSQR 78

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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 55.0 bits (133), Expect = 1e-10
 Identities = 28/74 (37%), Positives = 44/74 (59%), Gaps = 2/74 (2%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LYV+GL   +T+++LE  FS  G++ +  ++ +  T +SRG  F+  D   +AER IK L
Sbjct: 3  LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 82 NQSVLEG--RYITV 93
          N ++  G    ITV
Sbjct: 63 NGTIPPGATEPITV 76

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

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

 Score = 54.2 bits (131), Expect = 2e-10
 Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           ++V GL    T+  L K+FS+ G++    ++ + +T  SRG+ FVT    E AER  K 
Sbjct: 2  KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 81 LNQSVLEGRYITVE 94
           N  +++GR   V 
Sbjct: 62 PNP-IIDGRKANVN 74

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

 Score = 53.7 bits (130), Expect = 3e-10
 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
           GN +++  L   +  + L   FS  G + SC +  +     S+G+ FV  +  E A R 
Sbjct: 2  VGN-IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDE-NGGSKGYGFVHFETEEAAVRA 59

Query: 78 IKYLNQSVLEGRYITV 93
          I+ +N  +L  + + V
Sbjct: 60 IEKVNGMLLNDKKVFV 75

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|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins

 Score = 53.5 bits (128), Expect = 3e-10
 Identities = 27/73 (36%), Positives = 43/73 (58%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V+GLS+     DL+  F K GKV S  +V   R+  ++ +  VTM    +  RCI +L
Sbjct: 2  LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61

Query: 82 NQSVLEGRYITVE 94
          +++ L G+ I+VE
Sbjct: 62 HRTELHGQQISVE 74

This subgroup corresponds to the RRM domain of SLTM, also termed modulator of estrogen-induced transcription, which shares high sequence similarity with scaffold attachment factor B1 (SAFB1). It contains a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. To a large extent, SLTM co-localizes with SAFB1 in the nucleus, which suggests that they share similar functions, such as the inhibition of an oestrogen reporter gene. However, rather than mediating a specific inhibitory effect on oestrogen action, SLTM is shown to exert a generalized inhibitory effect on gene expression associated with induction of apoptosis in a wide range of cell lines. . Length = 74

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

 Score = 52.7 bits (127), Expect = 9e-10
 Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 2/80 (2%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
          N ++V G+    TE +L   FS+ G V    ++ + R  +S+G+ FVT +  EDAE  I 
Sbjct: 3  NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAE-KIL 60

Query: 80 YLNQSVLEGRYITVERSRRK 99
           +      G+ + +  + RK
Sbjct: 61 AMGNLNFRGKKLNIGPAIRK 80

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

 Score = 52.2 bits (126), Expect = 1e-09
 Identities = 30/72 (41%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L++ GLS   TE  L ++FSK G+V  C ++ +P T  SRGF FVT     D     K L
Sbjct: 1  LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTF---ADPSSVDKVL 57

Query: 82 NQS--VLEGRYI 91
               VL+GR I
Sbjct: 58 AAKPHVLDGREI 69

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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 52.7 bits (126), Expect = 1e-09
 Identities = 37/89 (41%), Positives = 50/89 (56%)

Query: 11 GRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDG 70
          G     +P   L V GLS   TERDL + FSK G +A   +V + ++R SRGFAFV  + 
Sbjct: 1  GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

Query: 71 VEDAERCIKYLNQSVLEGRYITVERSRRK 99
          V+DA+   +  N   L+GR I V+ S  K
Sbjct: 61 VDDAKEAKERANGMELDGRRIRVDFSITK 89

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). 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. It 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. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

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

 Score = 52.6 bits (127), Expect = 1e-09
 Identities = 22/80 (27%), Positives = 44/80 (55%), Gaps = 1/80 (1%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
            +YV  L   + +  L++ F K GK+ S  ++ +   + S+GF FV  +  E A++ ++
Sbjct: 2  TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGK-SKGFGFVNFENHEAAQKAVE 60

Query: 80 YLNQSVLEGRYITVERSRRK 99
           LN   + G+ + V R+++K
Sbjct: 61 ELNGKEVNGKKLYVGRAQKK 80

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

 Score = 52.3 bits (126), Expect = 1e-09
 Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          +++V  LS  VT+ +L + FS+ GK+    L+   R   +  FAF+  +  + A R ++ 
Sbjct: 5  SIFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVES 62

Query: 81 LNQSVLEGRYITVER 95
           N S+L+ + + V+ 
Sbjct: 63 ENHSMLKNKTMHVQY 77

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

 Score = 52.1 bits (125), Expect = 1e-09
 Identities = 21/55 (38%), Positives = 34/55 (61%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
          ++V GLS   TE D++K+FS+ GKV    L+ + +T   RGF FVT +  +  ++
Sbjct: 2  IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDK 56

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

 Score = 51.9 bits (125), Expect = 1e-09
 Identities = 25/76 (32%), Positives = 44/76 (57%), Gaps = 7/76 (9%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV---TMDGVEDAERC 77
           L+V  L   V  ++L+++FS+ GKV SC +  +  T +S+G+ FV   + DG+E+A + 
Sbjct: 1  KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQ- 59

Query: 78 IKYLNQSVLEGRYITV 93
               + +LEG  + V
Sbjct: 60 ---KQKHILEGNKLQV 72

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

 Score = 51.8 bits (125), Expect = 1e-09
 Identities = 23/66 (34%), Positives = 35/66 (53%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          T++V  LS +V ERDL + FSK GKV    ++ +  +R S+G A+V     E     +  
Sbjct: 1  TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGL 60

Query: 81 LNQSVL 86
            Q +L
Sbjct: 61 TGQRLL 66

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

 Score = 52.3 bits (126), Expect = 2e-09
 Identities = 28/84 (33%), Positives = 45/84 (53%)

Query: 17  NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
           +P  TL+V  LS + TE  L + FS+ G +    LV +  T  S+G+AFV  +   DA R
Sbjct: 1   DPYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALR 60

Query: 77  CIKYLNQSVLEGRYITVERSRRKR 100
             +  ++ V++G  I V+  R + 
Sbjct: 61  AYRDAHKLVIDGSEIFVDFERERT 84

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

 Score = 51.8 bits (125), Expect = 2e-09
 Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 9/81 (11%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRIS----RGFAFVTMDGVEDA-ER 76
          L+V GLS  VTE DLE+ FS+ G V+     VE   +      RGFA++ +   E   ++
Sbjct: 2  LFVGGLSPSVTESDLEERFSRFGTVSD----VEIIKKKDAGPDRGFAYIDLRTSEAQLKK 57

Query: 77 CIKYLNQSVLEGRYITVERSR 97
          C   LN +  +G  + +E ++
Sbjct: 58 CKSTLNGTKWKGSVLKIEEAK 78

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|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 = 51.9 bits (125), Expect = 2e-09
 Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 6/69 (8%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          T+YV  L   +TE +L++ FS  G +       E R    +G+AFV  D  E A   I  
Sbjct: 2  TVYVGNLPHGLTEEELQRTFSPFGAIE------EVRVFKDKGYAFVRFDTHEAAATAIVA 55

Query: 81 LNQSVLEGR 89
          +N + + G+
Sbjct: 56 VNGTSINGQ 64

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

 Score = 51.5 bits (124), Expect = 2e-09
 Identities = 26/72 (36%), Positives = 37/72 (51%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LYV  L   +TE DL   F   G++    L  +P T  S+G+ F+     EDA++ ++ L
Sbjct: 1  LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 82 NQSVLEGRYITV 93
          N   L GR I V
Sbjct: 61 NGFELAGRPIKV 72

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|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 = 51.5 bits (124), Expect = 2e-09
 Identities = 23/73 (31%), Positives = 39/73 (53%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L++  L    T++DL + F+  G V S  + V+  T  S+ F FV+ D  E A+  IK +
Sbjct: 1  LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 82 NQSVLEGRYITVE 94
          N   + G+ + V+
Sbjct: 61 NGFQVGGKRLKVQ 73

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

 Score = 51.0 bits (123), Expect = 3e-09
 Identities = 27/73 (36%), Positives = 39/73 (53%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LYV  LS   TE  + + FS+ G +    + ++  T+   GF FV     EDAE  +KYL
Sbjct: 1  LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 82 NQSVLEGRYITVE 94
          N + L+ R I V+
Sbjct: 61 NGTKLDDRIIRVD 73

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

 Score = 54.8 bits (132), Expect = 4e-09
 Identities = 27/84 (32%), Positives = 46/84 (54%), Gaps = 1/84 (1%)

Query: 19  GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
           G  LYV  L   VT+  L + FS+ G++ S  ++++    +SRGF FV     E+A R +
Sbjct: 285 GVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAV 343

Query: 79  KYLNQSVLEGRYITVERSRRKRPR 102
             ++  +L G+ + V  ++RK  R
Sbjct: 344 TEMHGRMLGGKPLYVALAQRKEQR 367

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

 Score = 50.8 bits (122), Expect = 4e-09
 Identities = 27/76 (35%), Positives = 42/76 (55%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          TL+V  LS  V +  L+  F K G V    ++ +  T  SRGF +V  +  EDA++ I+ 
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 81 LNQSVLEGRYITVERS 96
          ++   L+GR I V+ S
Sbjct: 61 MDGKELDGRPINVDFS 76

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

 Score = 50.7 bits (122), Expect = 4e-09
 Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          + V  L   VTE  L +HF  +G+V     V+  R   SR F FV     EDA++ +KY 
Sbjct: 3  IIVKNLPKYVTEDRLREHFESKGEVTDV-KVMRTRDGKSRRFGFVGFKSEEDAQQAVKYF 61

Query: 82 NQSVLEGRYITVE 94
          N++ ++   I+VE
Sbjct: 62 NKTFIDTSKISVE 74

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

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 50.7 bits (122), Expect = 5e-09
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 22 LYVTGLSTRVTERDLEKHFSK-EGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          L V  L   +TE +L++HFSK  G++    L+     + SR  AF+     E+A++   Y
Sbjct: 3  LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGK-SRRIAFIGYKTEEEAQKAKDY 61

Query: 81 LNQSVLEGRYITVE 94
           N + +    I+VE
Sbjct: 62 FNNTYINTSKISVE 75

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

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

 Score = 50.0 bits (120), Expect = 8e-09
 Identities = 24/75 (32%), Positives = 35/75 (46%)

Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          G  ++V  L     E  L + FS  G V +  ++ +  T   +G+ FVTM   E+A   I
Sbjct: 1  GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60

Query: 79 KYLNQSVLEGRYITV 93
            LN   L GR + V
Sbjct: 61 ASLNGYRLGGRVLQV 75

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

 Score = 50.0 bits (120), Expect = 1e-08
 Identities = 26/79 (32%), Positives = 44/79 (55%)

Query: 18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
          P N L+V  L+   T+ DLE  FS+ GK+ SC ++ + +T  S  +AF+  +  ED E  
Sbjct: 2  PENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61

Query: 78 IKYLNQSVLEGRYITVERS 96
             ++  +++ R I V+ S
Sbjct: 62 YFKMDNVLIDDRRIHVDFS 80

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

>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 49.3 bits (118), Expect = 1e-08
 Identities = 25/72 (34%), Positives = 37/72 (51%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L V  L   +T+ ++   FS  G++ SC L+ +  T  S G+ FV     EDAE+ I  L
Sbjct: 4  LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63

Query: 82 NQSVLEGRYITV 93
          N   L+ + I V
Sbjct: 64 NGLRLQNKTIKV 75

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 49.2 bits (117), Expect = 1e-08
 Identities = 26/75 (34%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          +++ GLS   T++DL+ +FSK G+V  C L ++P T  SRGF FV     E  ++ +   
Sbjct: 1  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ- 59

Query: 82 NQSVLEGRYITVERS 96
           +  L G+ I  +R+
Sbjct: 60 KEHKLNGKVIDPKRA 74

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 49.3 bits (118), Expect = 2e-08
 Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
            L+V+ +  R  + DL + F + G +    ++   R   S+GF FVT     DA+R  +
Sbjct: 1  KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERG--SKGFGFVTFANSADADRARE 58

Query: 80 YLNQSVLEGRYITVERS 96
           L+ +V+EGR I V  +
Sbjct: 59 KLHGTVVEGRKIEVNNA 75

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

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

 Score = 48.8 bits (117), Expect = 2e-08
 Identities = 21/67 (31%), Positives = 35/67 (52%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          +Y+ GL    T+ DLEK     GK+ S   +++ +T   +G+ FV  D  E A + I+ L
Sbjct: 3  VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62

Query: 82 NQSVLEG 88
          N   ++ 
Sbjct: 63 NGRGVQA 69

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

 Score = 49.2 bits (118), Expect = 2e-08
 Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGK-VASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
          G  L++  L   V E+ L   FS  G  + +  ++ +P T  S+GFAF++ D  E ++  
Sbjct: 1  GANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAA 60

Query: 78 IKYLNQSVLEGRYITVERSRRK 99
          I+ +N   L  R ITV  + +K
Sbjct: 61 IEAMNGQYLCNRPITVSYAFKK 82

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

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

 Score = 48.4 bits (116), Expect = 3e-08
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRIS---RGFAFVTMDGVEDAERCI 78
          +YV  L  +VTE  L + F + G V +  +   P+ R++   +G+ FV     EDA+  I
Sbjct: 1  VYVGNLDEKVTEELLWELFIQAGPVVNVHI---PKDRVTQAHQGYGFVEFLSEEDADYAI 57

Query: 79 KYLNQSVLEGRYITVER 95
          K +N   L G+ I V +
Sbjct: 58 KIMNMIKLYGKPIRVNK 74

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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 48.7 bits (116), Expect = 3e-08
 Identities = 27/75 (36%), Positives = 44/75 (58%), Gaps = 1/75 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V GLS   T++DL+++FSK G+V  C + ++P T  SRGF FV        E+ +   
Sbjct: 1  MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLD-Q 59

Query: 82 NQSVLEGRYITVERS 96
           +  L+GR I  +R+
Sbjct: 60 KEHKLDGRVIDPKRA 74

This subfamily corresponds to the RRM1 in 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 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 = 74

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

 Score = 48.5 bits (116), Expect = 3e-08
 Identities = 19/58 (32%), Positives = 34/58 (58%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
          L++ GLS   T+  L+ +FS+ G++  C ++ +P T+ SRGF FVT     + +  + 
Sbjct: 2  LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMN 59

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

 Score = 48.1 bits (115), Expect = 3e-08
 Identities = 22/70 (31%), Positives = 37/70 (52%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V  LS  +    L   F+  G+++   +V + +T  S+G+ FV+    EDAE  I+ +
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 82 NQSVLEGRYI 91
          N   L GR I
Sbjct: 62 NGQWLGGRAI 71

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

 Score = 48.4 bits (115), Expect = 4e-08
 Identities = 25/67 (37%), Positives = 41/67 (61%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LYV+GL   +T+++LE+ FS+ G++ +  ++ +  T +SRG  F+  D   +AE  IK L
Sbjct: 3  LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 82 NQSVLEG 88
          N    EG
Sbjct: 63 NGQKPEG 69

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|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 = 48.3 bits (116), Expect = 4e-08
 Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V  L    TE D+   F + G +    ++ +  T  S+G AFV     E+A++ I+ L
Sbjct: 2  LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 82 NQSV-LEG 88
          +  V + G
Sbjct: 62 HGKVTMPG 69

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

 Score = 47.6 bits (114), Expect = 6e-08
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          G  LYV  L   + +  L + FS  G + S  ++ + + R S+GF FV     E+A + +
Sbjct: 1  GVNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGR-SKGFGFVCFSSPEEATKAV 59

Query: 79 KYLNQSVLEGRYITV 93
            +N  ++ G+ + V
Sbjct: 60 TEMNGRIIGGKPLYV 74

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

 Score = 47.6 bits (113), Expect = 6e-08
 Identities = 26/68 (38%), Positives = 37/68 (54%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LYVT L  ++TE +L K F   G +  C L+ +  T + RG AFV  D  E+A+  I  L
Sbjct: 3  LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 82 NQSVLEGR 89
          N ++  G 
Sbjct: 63 NGTIPPGS 70

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

 Score = 47.6 bits (114), Expect = 6e-08
 Identities = 18/72 (25%), Positives = 33/72 (45%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          TL++  L   + E  +   F++ G+V S  ++   +T  S G+ FV     E AE+ ++ 
Sbjct: 1  TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 81 LNQSVLEGRYIT 92
          LN   +      
Sbjct: 61 LNGKPIPNTQQR 72

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|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 47.6 bits (113), Expect = 7e-08
 Identities = 32/76 (42%), Positives = 47/76 (61%)

Query: 24 VTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQ 83
          V GLS   TERDL + FS+ G +A   +V + RT  SRGFAFV  + ++D++  +++ N 
Sbjct: 4  VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 84 SVLEGRYITVERSRRK 99
            L+GR I V+ S  K
Sbjct: 64 MELDGRRIRVDYSITK 79

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) 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-alpha 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 = 79

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

 Score = 47.3 bits (113), Expect = 8e-08
 Identities = 21/72 (29%), Positives = 33/72 (45%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L V  L   +T+ +L   F   G + SC +V +  T  S G+ FV      DA++ I  L
Sbjct: 3  LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62

Query: 82 NQSVLEGRYITV 93
          N   +  + + V
Sbjct: 63 NGFEIRNKRLKV 74

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

 Score = 47.0 bits (112), Expect = 9e-08
 Identities = 26/75 (34%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
            L+V  L    T  DL  HF   G   S  L+ + +T  S+G AFV  D  E   + +K
Sbjct: 1  FILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK 60

Query: 80 YLNQSVLEGRYITVE 94
            + ++L+GR I VE
Sbjct: 61 L-HHTLLKGRKINVE 74

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

 Score = 50.2 bits (120), Expect = 1e-07
 Identities = 27/78 (34%), Positives = 38/78 (48%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          +LYV  L   VTE  L   F   G V S  +  +  TR S G+ +V      DAER ++ 
Sbjct: 2  SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 81 LNQSVLEGRYITVERSRR 98
          +N   L G+ I +  S+R
Sbjct: 62 MNFKRLGGKPIRIMWSQR 79

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|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 46.9 bits (112), Expect = 1e-07
 Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 8/80 (10%)

Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          GNTLYV G    +TE  L+K FS  G + +  +  E      +   FVT + +E A+R I
Sbjct: 4  GNTLYVHGYG--LTEEILKKAFSPFGNIINISMEKE------KNCGFVTFEKMESADRAI 55

Query: 79 KYLNQSVLEGRYITVERSRR 98
            LN + ++G  + V  +R+
Sbjct: 56 AELNGTTVQGVQLKVSLARK 75

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

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

 Score = 49.9 bits (119), Expect = 1e-07
 Identities = 24/70 (34%), Positives = 41/70 (58%)

Query: 19  GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
           G  LYV+GL   +T+ +LE  FS  G++ +  ++ +  T +S+G  F+  D  ++A+R I
Sbjct: 89  GANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAI 148

Query: 79  KYLNQSVLEG 88
           K LN +   G
Sbjct: 149 KTLNGTTPSG 158

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

 Score = 46.7 bits (111), Expect = 1e-07
 Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 9/75 (12%)

Query: 21 TLYVTGLSTRVT-ERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
          TL+V G     T E D+EK F   G +  C         I + FAFV  +  EDA + ++
Sbjct: 1  TLFVVGFDPGTTREEDIEKLFEPFGPLVRC--------DIRKTFAFVEFEDSEDATKALE 52

Query: 80 YLNQSVLEGRYITVE 94
           L+ S ++G  +TVE
Sbjct: 53 ALHGSRIDGSVLTVE 67

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

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

 Score = 46.6 bits (111), Expect = 2e-07
 Identities = 23/57 (40%), Positives = 32/57 (56%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          ++V GL   VTE + +++FS+ GKV    L+ +  T  SRGF FVT D     ER  
Sbjct: 2  IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVF 58

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

 Score = 46.1 bits (110), Expect = 2e-07
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 6/72 (8%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V  L   +TE + ++ FSK G+V+  FL  E      +GF F+ +D   +AE+    L
Sbjct: 4  LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAEL 57

Query: 82 NQSVLEGRYITV 93
          +  + +GR + V
Sbjct: 58 DGIMRKGRQLRV 69

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

 Score = 46.1 bits (110), Expect = 2e-07
 Identities = 27/72 (37%), Positives = 38/72 (52%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L V  L+ R T  DL + F K G+V   ++  +  TR SRGFAFV      DAE  +  +
Sbjct: 1  LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 82 NQSVLEGRYITV 93
          +   L+GR + V
Sbjct: 61 DGKELDGRELRV 72

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

 Score = 45.8 bits (109), Expect = 2e-07
 Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 6/79 (7%)

Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
           LY+  LS+ V E DL + F +     S  LV +       G+AFV       A++ I+ L
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKK------GGYAFVDCPDQSWADKAIEKL 54

Query: 82  NQSVLEGRYITVERSRRKR 100
           N  +L+G+ I VE S  K+
Sbjct: 55  NGKILQGKVIEVEHSVPKK 73

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 45.6 bits (109), Expect = 2e-07
 Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 5/59 (8%)

Query: 38 KHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS 96
          K FS  G V    L+ +       GFAFV     E AE+ ++YLN  +  GR + V+ S
Sbjct: 3  KLFSPFGNVEKIKLLKK-----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 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|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 46.2 bits (110), Expect = 2e-07
 Identities = 26/68 (38%), Positives = 39/68 (57%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L++  L+   TE DLEK FSK G ++   L ++  T+  +GFAFVT    E A +    L
Sbjct: 5  LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 82 NQSVLEGR 89
          + +V +GR
Sbjct: 65 DGTVFQGR 72

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|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 46.3 bits (109), Expect = 3e-07
 Identities = 24/61 (39%), Positives = 40/61 (65%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LYV+GL   +T+++LE+ FS+ G++ +  ++V+  T +SRG  F+  D   +AE  IK L
Sbjct: 8  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67

Query: 82 N 82
          N
Sbjct: 68 N 68

This subgroup corresponds to the RRM2 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 = 90

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

 Score = 45.7 bits (109), Expect = 3e-07
 Identities = 21/77 (27%), Positives = 40/77 (51%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
          N +YV  +   ++E D++  F   GK+ SC L  +P T   +G+ F+  +  + A+  I 
Sbjct: 1  NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 80 YLNQSVLEGRYITVERS 96
           +N   L G+ + V ++
Sbjct: 61 SMNLFDLGGQQLRVGKA 77

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

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

 Score = 45.4 bits (108), Expect = 4e-07
 Identities = 24/74 (32%), Positives = 31/74 (41%), Gaps = 15/74 (20%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRI-------SRGFAFVTMDGVEDA 74
          LY++ L   + E+DLE      G+V S        TRI       SRG  F  M+  E  
Sbjct: 3  LYISNLPLHMDEQDLETMLKPYGQVIS--------TRILRDSKGQSRGVGFARMESREKC 54

Query: 75 ERCIKYLNQSVLEG 88
          E  I   N   L+G
Sbjct: 55 EDIISKFNGKYLKG 68

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|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 45.2 bits (107), Expect = 4e-07
 Identities = 27/75 (36%), Positives = 36/75 (48%), Gaps = 9/75 (12%)

Query: 21 TLYVTGLST-RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
          TL+V          RDLE+HF   GK+           RI R FAFV  +  EDA + ++
Sbjct: 1  TLFVINFDPINTRTRDLERHFEPYGKLV--------NVRIRRNFAFVQYETQEDATKALE 52

Query: 80 YLNQSVLEGRYITVE 94
            N S +  R I+VE
Sbjct: 53 STNMSKVLDRVISVE 67

This subgroup corresponds to the RRM2 in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 70

>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 45.5 bits (107), Expect = 4e-07
 Identities = 24/61 (39%), Positives = 40/61 (65%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LYV+GL   +T+++LE+ FS+ G++ +  ++V+  T +SRG  F+  D   +AE  IK L
Sbjct: 5  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 82 N 82
          N
Sbjct: 65 N 65

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD 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 = 81

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 45.4 bits (107), Expect = 4e-07
 Identities = 23/61 (37%), Positives = 40/61 (65%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LYV+GL   ++++++E+ FS+ G++ +  ++V+  T ISRG  F+  D   +AE  IK L
Sbjct: 4  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 82 N 82
          N
Sbjct: 64 N 64

This subgroup corresponds to the RRM2 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 = 81

>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 = 45.3 bits (108), Expect = 5e-07
 Identities = 22/72 (30%), Positives = 34/72 (47%)

Query: 23 YVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLN 82
          +V  +    TE  L + FS+ G V S  LV +  T   +G+ F   + +E A   I+ LN
Sbjct: 2  FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 83 QSVLEGRYITVE 94
               GR + V+
Sbjct: 62 GYEFNGRALRVD 73

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

 Score = 45.3 bits (108), Expect = 5e-07
 Identities = 29/74 (39%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           L V+ L   VTE DLE+ F + G+V    +  +   R S G A V  +  EDAER IK 
Sbjct: 2  RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGR-SEGTADVVFEKREDAERAIKQ 60

Query: 81 LNQSVLEGRYITVE 94
           N  +L+G+ + VE
Sbjct: 61 FNGVLLDGQPMQVE 74

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

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 45.1 bits (107), Expect = 5e-07
 Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L V GL  + TE+DL+ +FS  G++    +  +P+T  S+GF FV     ED  + +   
Sbjct: 2  LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLS-- 59

Query: 82 NQSVLEGRYITVERSRRK 99
           + +++GR+  V+    K
Sbjct: 60 QRHMIDGRWCDVKIPNSK 77

This subfamily corresponds to the RRM1 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 = 77

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 45.0 bits (106), Expect = 5e-07
 Identities = 22/76 (28%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          +++ GLS   +++DL ++ S+ G+V  C +  +P T  SRGF FV        ++ ++ L
Sbjct: 2  MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLE-L 60

Query: 82 NQSVLEGRYITVERSR 97
           +  L+G+ I  +R++
Sbjct: 61 KEHKLDGKLIDPKRAK 76

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which 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. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

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

 Score = 45.0 bits (107), Expect = 5e-07
 Identities = 22/64 (34%), Positives = 31/64 (48%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          T+YV  L    T   L+  FSK G V    L     T   +GFAF+  +  E+A++  K+
Sbjct: 1  TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKH 60

Query: 81 LNQS 84
          LN  
Sbjct: 61 LNNP 64

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

 Score = 45.1 bits (107), Expect = 6e-07
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
          + L+V+GL   VT+ +LEK F K G V S  LV   R+   +G A+V  +    A + + 
Sbjct: 3  HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTN-RSGKPKGLAYVEYENESSASQAVL 61

Query: 80 YLNQSVLEGRYITVERS 96
           ++ + ++ + I+V  S
Sbjct: 62 KMDGTEIKEKTISVAIS 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|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 45.0 bits (106), Expect = 6e-07
 Identities = 22/61 (36%), Positives = 38/61 (62%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LY++GL   +T++D+E  FS+ G++ +  ++V+  T +SRG AF+  D   +AE  I   
Sbjct: 3  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 82 N 82
          N
Sbjct: 63 N 63

This subgroup corresponds to the RRM2 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|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 45.1 bits (107), Expect = 7e-07
 Identities = 27/83 (32%), Positives = 46/83 (55%), Gaps = 2/83 (2%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           +LYV  ++      DL + F K G +   ++ ++  TR  RGFA+V  + V DAE  + Y
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 81  LNQSVLEGRYITVERSR--RKRP 101
           L+++   GR I ++ ++  RK P
Sbjct: 62  LDRTRFLGREIEIQFAQGDRKTP 84

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

 Score = 44.6 bits (106), Expect = 7e-07
 Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 6/73 (8%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          TL++  LS +VTE DL+  F + G++ S  ++        RG A+V M+  +DA R ++ 
Sbjct: 4  TLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP------PRGCAYVCMETRQDAHRALQK 57

Query: 81 LNQSVLEGRYITV 93
          L    L G+ I V
Sbjct: 58 LRNVKLAGKKIKV 70

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

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 44.7 bits (105), Expect = 8e-07
 Identities = 24/60 (40%), Positives = 35/60 (58%), Gaps = 2/60 (3%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVE--DAERCIK 79
          L++ GLS   T+  L +HF K G +  C ++ +P+T+ SRGF FVT   VE  DA    +
Sbjct: 5  LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSAR 64

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It 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 = 81

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 44.6 bits (105), Expect = 9e-07
 Identities = 23/70 (32%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V GLS   +++DL+ +F+K G+V  C + ++P T  SRGF F+        E+ ++  
Sbjct: 2  MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ- 60

Query: 82 NQSVLEGRYI 91
           +  L+GR I
Sbjct: 61 KEHRLDGRLI 70

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which 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 A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 44.3 bits (105), Expect = 9e-07
 Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 3/63 (4%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          +++ GLS + T   L ++FSK G++  C ++ +P T+ SRGF FVT     D     K L
Sbjct: 1  MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFS---DPASVDKVL 57

Query: 82 NQS 84
           Q 
Sbjct: 58 AQG 60

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is 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 = 75

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

 Score = 44.7 bits (106), Expect = 9e-07
 Identities = 26/77 (33%), Positives = 38/77 (49%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           L +  L   +T+ +    F   G V +C +V + RT  S GF FV     EDA+R I+ 
Sbjct: 2  NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 81 LNQSVLEGRYITVERSR 97
          LN   L+ + I V  +R
Sbjct: 62 LNGLQLQNKRIKVAYAR 78

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

 Score = 44.2 bits (105), Expect = 9e-07
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V  L   VT +DL+  F + G V    +  +   R S+GF  V  +  EDA+R I+  
Sbjct: 1  IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGR-SKGFGTVLFESPEDAQRAIEMF 59

Query: 82 NQSVLEGRYITV 93
          N   LEGR + V
Sbjct: 60 NGYDLEGRELEV 71

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|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 44.1 bits (104), Expect = 1e-06
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 8/73 (10%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V  +S   T  +L   F + G+V  C  V          +AFV M+  E+A   I+ L
Sbjct: 3  IFVGNVSATCTSDELRGLFEEFGRVVECDKVK--------DYAFVHMEREEEALAAIEAL 54

Query: 82 NQSVLEGRYITVE 94
          N   ++GR I VE
Sbjct: 55 NGKEVKGRRINVE 67

This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 68

>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 44.4 bits (105), Expect = 1e-06
 Identities = 19/46 (41%), Positives = 28/46 (60%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVT 67
          L+V GLS   T+  L ++FS+ G+V  C ++ +  T  SRGF FV 
Sbjct: 2  LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVK 47

This subfamily corresponds to the RRM1 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 form is predominantly nuclear and the nonacetylated form is in cytoplasm. It 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 = 82

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 44.0 bits (104), Expect = 1e-06
 Identities = 24/80 (30%), Positives = 45/80 (56%), Gaps = 1/80 (1%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
          N ++V G+  +  E DL K FS+ G V    +V + R  +S+G+ FVT +  EDA++ ++
Sbjct: 3  NRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQKILQ 61

Query: 80 YLNQSVLEGRYITVERSRRK 99
            N+     + + + ++ RK
Sbjct: 62 EANRLCFRDKKLNIGQAIRK 81

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

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

 Score = 43.8 bits (104), Expect = 2e-06
 Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 8/72 (11%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LYV  L    TE  L + FS+ G+V         R +  + +AFV  +  +DA + ++ +
Sbjct: 4  LYVRNLPLSTTEEQLRELFSEYGEVE--------RVKKIKDYAFVHFEERDDAVKAMEEM 55

Query: 82 NQSVLEGRYITV 93
          N   LEG  I V
Sbjct: 56 NGKELEGSPIEV 67

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

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 43.7 bits (104), Expect = 2e-06
 Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 2/79 (2%)

Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          G  ++V  +   + E +L   F K G +    L+++    ++RG+AFVT    E A+R +
Sbjct: 1  GCEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSG-LNRGYAFVTYTNKEAAQRAV 59

Query: 79 KYLNQSVLE-GRYITVERS 96
          K L+   +  G+ + V  S
Sbjct: 60 KQLHNYEIRPGKRLGVCIS 78

This subfamily corresponds to the RRM1 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 binds 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); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 43.8 bits (103), Expect = 2e-06
 Identities = 18/46 (39%), Positives = 31/46 (67%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVT 67
          +++ GLS + T+  L ++F + G+V  C ++ +P T+ SRGF FVT
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVT 48

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is 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. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 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, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains 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 = 77

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

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 28/74 (37%), Positives = 41/74 (55%), Gaps = 7/74 (9%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          TLYV GL  RVTE+DL  HF + G++ S  +V        +  AFVT    E AE+  + 
Sbjct: 3  TLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPR------QQCAFVTFTTREAAEKAAER 56

Query: 81 L-NQSVLEGRYITV 93
          L N+ ++ GR + +
Sbjct: 57 LFNKLIINGRRLKL 70

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

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

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 8/73 (10%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V  L    TE+++   F + GKV  C ++        + + FV MD    A+  I+ L
Sbjct: 3  LFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRNL 54

Query: 82 NQSVLEGRYITVE 94
          +   L G  I VE
Sbjct: 55 HHYKLHGVAINVE 67

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

>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 43.3 bits (103), Expect = 2e-06
 Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 12/81 (14%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF--AFVTMDGVEDAERCIK 79
          L++  L   VTE DL    S  GKV +          + RG   A V MD VE A+  + 
Sbjct: 2  LHLRNLPPDVTESDLIALVSPFGKVTN--------VLLLRGKNQALVEMDSVESAKSMVD 53

Query: 80 YL--NQSVLEGRYITVERSRR 98
          Y     +++ GR + ++ S  
Sbjct: 54 YYLTVPALIRGRRVYIQYSNH 74

This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM. . Length = 74

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

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 21/76 (27%), Positives = 31/76 (40%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           L V  L    T+    +  S  G V  CFLV    T  S+G+ FV       A +    
Sbjct: 1  LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQ 60

Query: 81 LNQSVLEGRYITVERS 96
          L+   + GR + V+ +
Sbjct: 61 LDGKQIGGRKLQVDWA 76

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

 Score = 43.1 bits (102), Expect = 4e-06
 Identities = 18/59 (30%), Positives = 31/59 (52%)

Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
             ++V GL   VTE DL K+FS+ G V    ++ +   +  RGF F+T +  +  ++ 
Sbjct: 2  TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60

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

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

 Score = 42.7 bits (101), Expect = 4e-06
 Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          TL+V  LS    + DLE+ F + G+V    +  +   R S+GF  V     E A++ ++ 
Sbjct: 1  TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGR-SKGFGHVEFATEEGAQKALEK 59

Query: 81 LNQSVLEGRYITVERSRRK 99
            +  L GR I V+ +  +
Sbjct: 60 SGEE-LLGREIRVDLATER 77

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

 Score = 42.5 bits (100), Expect = 5e-06
 Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 8/75 (10%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V  +    ++ +L   F   G V SC ++        R FAFV + G   A+R I+ L
Sbjct: 3  IFVGNVDEDTSQEELRALFEAYGAVLSCAVM--------RQFAFVHLRGEAAADRAIEEL 54

Query: 82 NQSVLEGRYITVERS 96
          N   L GR + VE S
Sbjct: 55 NGRELHGRKLVVEHS 69

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

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

 Score = 42.4 bits (100), Expect = 5e-06
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 4/75 (5%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          T+Y     T     D+++ F   G V    ++    +R  +  AF+T + +E A+  I+ 
Sbjct: 1  TVYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIET 56

Query: 81 LNQSVLEGRYITVER 95
          LN + ++G  I V+R
Sbjct: 57 LNGASVDGNCIKVQR 71

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

>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 42.3 bits (99), Expect = 5e-06
 Identities = 19/55 (34%), Positives = 31/55 (56%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
          ++V GLS   T  D++++F + GKV    L+ +  T   RGF FVT +  +  E+
Sbjct: 2  IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK 56

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is 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. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and 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. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains 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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 42.6 bits (101), Expect = 5e-06
 Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 2/80 (2%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
           TL+V  L+   TE  L + F + G +    LV + +T   RG+AF+  +   D +   K
Sbjct: 2  KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 80 YLNQSVLEGRYITV--ERSR 97
          Y +   ++GR + V  ER R
Sbjct: 62 YADGKKIDGRRVLVDVERGR 81

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

 Score = 42.4 bits (100), Expect = 6e-06
 Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 11/81 (13%)

Query: 21 TLYVTGLSTRVTE----RDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTM---DGVED 73
          T++V G  + + E    R L +HFS  G++    +  +  T  S+GFA++     DGVE 
Sbjct: 1  TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 74 AERCIKYLNQSVLEGRYITVE 94
          A      L+ S L G  + V+
Sbjct: 61 A----LELDGSDLGGGNLVVD 77

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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 42.0 bits (98), Expect = 9e-06
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L++ GLS   T+  L  HF + G +  C ++ +P T+ SRGF FVT   VE+ +  +   
Sbjct: 5  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNAR 64

Query: 82 NQSVLEGRYITVERS 96
             V +GR +  +R+
Sbjct: 65 PHKV-DGRVVEPKRA 78

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 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. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

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

 Score = 44.2 bits (104), Expect = 1e-05
 Identities = 48/169 (28%), Positives = 61/169 (36%), Gaps = 15/169 (8%)

Query: 22  LYVTGLSTRVTERDLEKHFS--KEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
           LYV  L T  TE  +EK FS  K GKV         R +  R +AFV  +  EDA + + 
Sbjct: 236 LYVRNLMTTTTEEIIEKSFSEFKPGKVE--------RVKKIRDYAFVHFEDREDAVKAMD 287

Query: 80  YLNQSVLEGRYITVERSR---RKRPRTPTPGHYLGLKSSRDIGRGDRGRYRSGRDDYGYR 136
            LN   LEG  I V  ++   +K     T G     K  +   +     Y        Y 
Sbjct: 288 ELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYE 347

Query: 137 RSPRRSPYRGGRDYSPRHSPPYGGRSRRERSRSVPRSPYGSPERKYARG 185
                 PY     + PR   P  GR  R  + S      G P   Y   
Sbjct: 348 DYYYHPPYAPSLHF-PRMPGPIRGRG-RGGAPSRAAGGRGYPPYGYEAY 394

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

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 41.4 bits (97), Expect = 1e-05
 Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 5/61 (8%)

Query: 36 LEKHFSKEGKVASCFLVVEPRTRISR--GFAFVTMDGVEDAERCIKYLNQSVLEGRYITV 93
          L+K F + GKV    +   PR R  +  GFAFVTM   ++AE  ++  N   ++GR + V
Sbjct: 18 LKKIFGRYGKVREATI---PRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAV 74

Query: 94 E 94
          +
Sbjct: 75 D 75

This subgroup corresponds to the RRM2 of Nop4p (also known as 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 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

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

 Score = 41.1 bits (96), Expect = 2e-05
 Identities = 20/67 (29%), Positives = 35/67 (52%)

Query: 16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAE 75
          G  G  L++  L    T+ DL + F   G V S  + ++ +T +S+ F FV+ D  + A+
Sbjct: 1  GPEGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQ 60

Query: 76 RCIKYLN 82
            I+ +N
Sbjct: 61 AAIQAMN 67

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

 Score = 40.8 bits (96), Expect = 2e-05
 Identities = 23/76 (30%), Positives = 34/76 (44%), Gaps = 8/76 (10%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          +Y+  L  R  ERD+E+ F   G++    L          GF FV  +   DA+  +  L
Sbjct: 2  VYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAVYEL 53

Query: 82 NQSVLEGRYITVERSR 97
          N   L G  + VE +R
Sbjct: 54 NGKELCGERVIVEHAR 69

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

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

 Score = 40.8 bits (96), Expect = 2e-05
 Identities = 19/68 (27%), Positives = 33/68 (48%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V  LS    E  + + F + G+++S  L  +P +   +GF +V     E A+  +  L
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 82 NQSVLEGR 89
            + L GR
Sbjct: 61 GGTDLLGR 68

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

 Score = 40.5 bits (95), Expect = 2e-05
 Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 8/72 (11%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LYV       +E  + + FS  G V    ++          FAFV  + +E A R    +
Sbjct: 2  LYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIRAKDSV 53

Query: 82 NQSVLEGRYITV 93
          +  VL    + V
Sbjct: 54 HGKVLNNNPLYV 65

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

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

 Score = 40.4 bits (94), Expect = 2e-05
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 8/73 (10%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V  +S+  T ++L   F + G V  C +V        + +AFV M+  EDA   I+ L
Sbjct: 3  LHVGNISSSCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGL 54

Query: 82 NQSVLEGRYITVE 94
          + +  +G+ + V+
Sbjct: 55 DNTEFQGKRMHVQ 67

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

>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 23/77 (29%), Positives = 38/77 (49%)

Query: 18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
          P   +  + L+  + E  L+    K G+V    +   P+T    G A V  D V+ A+RC
Sbjct: 1  PPREVTFSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRC 60

Query: 78 IKYLNQSVLEGRYITVE 94
          ++ LNQ+ + G+ I V 
Sbjct: 61 VEKLNQTSVMGKIIKVF 77

This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. . Length = 93

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 40.4 bits (94), Expect = 3e-05
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          G  ++V  +   + E +L   F K G +    L+++P T ++RG+AFVT    E A+  +
Sbjct: 1  GTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAV 60

Query: 79 K-YLNQSVLEGRYITV 93
          K Y N  +  G++I V
Sbjct: 61 KLYNNHEIRPGKHIGV 76

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

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

 Score = 40.2 bits (94), Expect = 3e-05
 Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 6/71 (8%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          T+YV  +    T+ DL   F   G       ++E R +  RGFAFV +D  E A   I  
Sbjct: 2  TVYVGNIPPYTTQADLIPLFQNFG------YILEFRHQPDRGFAFVKLDTHEQAAMAIVQ 55

Query: 81 LNQSVLEGRYI 91
          L    + GR +
Sbjct: 56 LQGFPVHGRPL 66

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

>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 40.4 bits (94), Expect = 3e-05
 Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
          ++V GLS      D++++F + GKV    L+ +  T   RGF FVT +  ED
Sbjct: 6  IFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFE-NED 56

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which 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. Musashi-2 contains 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 = 79

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

 Score = 39.8 bits (94), Expect = 4e-05
 Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 7/81 (8%)

Query: 21 TLYVTGLSTRVTERDLEKH----FSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
          TLY+  L+ ++ + +L++     FS+ G V     +V  +T   RG AFV    VE A  
Sbjct: 1  TLYINNLNEKIKKDELKRSLYALFSQFGPVLD---IVASKTLKMRGQAFVVFKDVESATN 57

Query: 77 CIKYLNQSVLEGRYITVERSR 97
           ++ L       + + ++ ++
Sbjct: 58 ALRALQGFPFYDKPMRIQYAK 78

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|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 40.3 bits (95), Expect = 4e-05
 Identities = 28/74 (37%), Positives = 34/74 (45%), Gaps = 2/74 (2%)

Query: 21 TLYVTGLSTRVTERD-LEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
           L+V  L     +   L K FS+ GK   C L + P     RGFAFV     EDAE   +
Sbjct: 4  CLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNG-QPRGFAFVEYATAEDAEEAQQ 62

Query: 80 YLNQSVLEGRYITV 93
           LN   L+G  I V
Sbjct: 63 ALNGHSLQGSPIRV 76

This subfamily corresponds to the RRM3 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 = 92

>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 39.7 bits (92), Expect = 5e-05
 Identities = 18/47 (38%), Positives = 30/47 (63%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTM 68
          +++ GLS + +   L  +FSK G++  C ++ +P T+ SRGF FVT 
Sbjct: 2  MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTF 48

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which 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. Musashi-2 contains 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 = 76

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

 Score = 39.5 bits (93), Expect = 5e-05
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 31 VTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY 90
          + E +L KHF   G V +  +V + +T I +GF +V     +     +K LN   L+GR 
Sbjct: 11 IEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALK-LNGIKLKGRK 69

Query: 91 ITVE 94
          I V+
Sbjct: 70 IRVK 73

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

 Score = 39.6 bits (93), Expect = 6e-05
 Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 5/76 (6%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRT----RISRGFAFVTMDGVEDAERC 77
          LYV  L+ +VTE  L + F + G +AS   ++ PRT    R +R   FV      DAER 
Sbjct: 4  LYVGNLNPKVTEEVLCQEFGRFGPLAS-VKIMWPRTEEERRRNRNCGFVAFMNRADAERA 62

Query: 78 IKYLNQSVLEGRYITV 93
          +  L+   + G  + +
Sbjct: 63 LDELDGKDVMGYELKL 78

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|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 39.7 bits (92), Expect = 6e-05
 Identities = 21/75 (28%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L++ GLS   TE  L  ++ + GK+  C ++ +P ++ SRGF FVT   + + +  +   
Sbjct: 5  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAAR 64

Query: 82 NQSVLEGRYITVERS 96
            ++ +GR +  +R+
Sbjct: 65 PHTI-DGRVVEPKRA 78

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which 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 A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 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 = 81

>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 39.7 bits (92), Expect = 7e-05
 Identities = 26/76 (34%), Positives = 39/76 (51%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L V  L   +T+ +L+  F   G++ SC LV +  T  S G+ FV     +DAE+ I  L
Sbjct: 7  LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66

Query: 82 NQSVLEGRYITVERSR 97
          N   L+ + I V  +R
Sbjct: 67 NGLRLQTKTIKVSYAR 82

This subgroup corresponds to the RRM1 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 and 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 = 83

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

 Score = 39.1 bits (92), Expect = 8e-05
 Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 3/74 (4%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASC-FLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
           + + GL    TE D+   FS          +V +   R + G A+V     EDA R ++
Sbjct: 1  VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPT-GEAYVEFASPEDARRALR 59

Query: 80 YLNQSVLEGRYITV 93
            N   + GRYI V
Sbjct: 60 KHNNK-MGGRYIEV 72

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

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 39.1 bits (92), Expect = 8e-05
 Identities = 25/86 (29%), Positives = 37/86 (43%), Gaps = 18/86 (20%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFL--VVEPRTRIS---------RGFAFVTM 68
            LYV  LS RVTE DL   F +       F+    E +             +G AFVT 
Sbjct: 2  KRLYVKNLSKRVTEEDLVYIFGR-------FVDSSSEEKNMFDIRLMTEGRMKGQAFVTF 54

Query: 69 DGVEDAERCIKYLNQSVLEGRYITVE 94
             E A + +  +N  VL+G+ + ++
Sbjct: 55 PSEEIATKALNLVNGYVLKGKPMVIQ 80

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

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

 Score = 39.1 bits (91), Expect = 8e-05
 Identities = 20/55 (36%), Positives = 30/55 (54%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
          L+V GL   V E DL +HFS+ G V    ++ + +T   RGF FV     + A++
Sbjct: 2  LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADK 56

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

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 5/85 (5%)

Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
           LYV  L   V E  L + F+K G++ S   V++  +  SRGFAFV  +  EDA + ++ +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSA-AVMKDGSGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 82  NQ----SVLEGRYITVERSRRKRPR 102
           N        EG+ + V R++++  R
Sbjct: 240 NGKKIGLAKEGKKLYVGRAQKRAER 264

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

 Score = 38.7 bits (90), Expect = 1e-04
 Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 1/72 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LYV  L  RVTE  L++ F   G V +  ++ + +      + FV      DAE  ++ L
Sbjct: 1  LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPD-KNNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 82 NQSVLEGRYITV 93
          N   +E   I V
Sbjct: 60 NGRQIENNEIRV 71

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

 Score = 38.9 bits (91), Expect = 1e-04
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
          P + L++      VTE DL + F+  G++   ++V + +T+ S+G A+V       A R 
Sbjct: 2  PNSRLFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARA 60

Query: 78 IKYLNQSVLEGR 89
          ++ +N   L G 
Sbjct: 61 MEEMNGKCLGGD 72

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

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

 Score = 38.8 bits (90), Expect = 1e-04
 Identities = 24/85 (28%), Positives = 47/85 (55%), Gaps = 1/85 (1%)

Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
           ++L+V  ++      DL + F + G +   ++ ++  TR  RGFA+V  + V DAE  + 
Sbjct: 1   SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 80  YLNQSVLEGRYITVERSRRKRPRTP 104
            L++  + GR I ++ ++  R +TP
Sbjct: 61  NLDRKWICGRQIEIQFAQGDR-KTP 84

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

 Score = 41.6 bits (97), Expect = 1e-04
 Identities = 19/77 (24%), Positives = 37/77 (48%)

Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
           N +YV  +   ++E D++  F   G++  C L   P  R  +G+ F+  + ++     I 
Sbjct: 205 NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA 264

Query: 80  YLNQSVLEGRYITVERS 96
            +N   L G+Y+ V + 
Sbjct: 265 SMNLFDLGGQYLRVGKC 281

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|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 38.4 bits (90), Expect = 1e-04
 Identities = 22/74 (29%), Positives = 31/74 (41%), Gaps = 1/74 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L V  L   + E  L K F   G +    L         R F FV     E+A++ +K+ 
Sbjct: 3  LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTK-DGKFRKFGFVGYKTEEEAQKALKHF 61

Query: 82 NQSVLEGRYITVER 95
          N S ++   ITVE 
Sbjct: 62 NNSFIDTSKITVEI 75

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), 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 = 76

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

 Score = 38.5 bits (89), Expect = 1e-04
 Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 8/72 (11%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V  L+T VTE  LEK FS+ GK+         R +  + +AFV  +  + A R +  +
Sbjct: 4  LFVRNLATTVTEEILEKSFSEFGKLE--------RVKKLKDYAFVHFEERDAAVRAMDEM 55

Query: 82 NQSVLEGRYITV 93
          N   +EG  I +
Sbjct: 56 NGKEIEGEEIEI 67

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

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

 Score = 38.5 bits (90), Expect = 1e-04
 Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V GLS   TE  + ++F K G +    L ++ +T   RGF F+T D  E  ++ ++  
Sbjct: 2  IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILETQ 61

Query: 82 NQSVLEGRYITVERS 96
             V+ G+ + V+++
Sbjct: 62 FH-VIGGKKVEVKKA 75

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|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 38.4 bits (89), Expect = 1e-04
 Identities = 25/79 (31%), Positives = 44/79 (55%), Gaps = 3/79 (3%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          TL+V GLS   TE  L++ F  +G +A+  +V +  T  S+GF FV     EDA+   + 
Sbjct: 2  TLFVKGLSEDTTEETLKESF--DGSIAA-RIVTDRDTGSSKGFGFVDFSSEEDAKAAKEA 58

Query: 81 LNQSVLEGRYITVERSRRK 99
          +    ++G  +T++ ++ K
Sbjct: 59 MEDGEIDGNKVTLDFAKPK 77

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

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

 Score = 38.6 bits (90), Expect = 1e-04
 Identities = 24/74 (32%), Positives = 39/74 (52%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          +YV  +S  + E  + + FS  G + S  +  +P T   +GFAFV  +  E A+  ++ +
Sbjct: 3  VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 82 NQSVLEGRYITVER 95
          N  +L GR I V R
Sbjct: 63 NGVMLGGRNIKVGR 76

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

 Score = 40.9 bits (96), Expect = 2e-04
 Identities = 30/101 (29%), Positives = 47/101 (46%), Gaps = 5/101 (4%)

Query: 6   RSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAF 65
           R  S  R+  GN    ++V  L   V  + L   FSK G + SC +  +   + SRG+ F
Sbjct: 79  RDPSLRRSGVGN----IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGK-SRGYGF 133

Query: 66  VTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTP 106
           V  +  E A+  I+ +N  +L  + + V R  +K  R   P
Sbjct: 134 VHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAP 174

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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 40.6 bits (95), Expect = 2e-04
 Identities = 37/118 (31%), Positives = 54/118 (45%), Gaps = 12/118 (10%)

Query: 2   VFRSRSRSRGR------TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEP 55
            +R   R  GR      TE      T++V  L+ +  ERDL + FSK GKV     + + 
Sbjct: 66  SYRRDDRRSGRNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDR 125

Query: 56  RTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV-----ERSRRKRPRTPTPGH 108
            +R S+G A+V    VE   + +    Q +L GR I V     E++R  +  T  PG 
Sbjct: 126 NSRRSKGVAYVEFYDVESVIKALALTGQMLL-GRPIIVQSSQAEKNRAAKAATHQPGD 182

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

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          TL+V  L  RVTE  L + F + G +    +  +P  +  + FAFVT          I+ 
Sbjct: 3  TLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGK-PKSFAFVTFKHEVSVPYAIQL 61

Query: 81 LNQSVLEGRYITVE 94
          LN   L GR + ++
Sbjct: 62 LNGIRLFGRELRIK 75

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

 Score = 38.5 bits (89), Expect = 2e-04
 Identities = 24/84 (28%), Positives = 46/84 (54%), Gaps = 1/84 (1%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           +L+V  ++      DL + F + G +   ++ ++  TR  RGFA++  + V DAE  +  
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 81  LNQSVLEGRYITVERSRRKRPRTP 104
           LN+  + GR I ++ ++  R +TP
Sbjct: 62  LNRKWVCGRQIEIQFAQGDR-KTP 84

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

 Score = 38.3 bits (89), Expect = 2e-04
 Identities = 20/75 (26%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          +++ GL+   T+  L ++F + G+V  C ++ +  T  SRGF F+T    +     +K  
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMK-- 58

Query: 82 NQSVLEGRYITVERS 96
           + +L+G+ I  +R+
Sbjct: 59 KEHILDGKIIDPKRA 73

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

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 31/103 (30%), Positives = 43/103 (41%), Gaps = 1/103 (0%)

Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
           L++ GLS    +  L   F+  G V    ++V+  T  SRGF FV  +    A   I  +
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 82  NQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDRG 124
           +   L GR+I V  +   RP  P      G  S    G G  G
Sbjct: 97  DGKELNGRHIRVNPA-NDRPSAPRAYGGGGGYSGGGGGYGGGG 138

Length = 144

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 21/62 (33%), Positives = 27/62 (43%), Gaps = 4/62 (6%)

Query: 34 RDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV 93
           DL +   K G+V      V    R   G A V     E+A+RCI+ LN     GR +  
Sbjct: 27 DDLREECEKFGQVKK----VVVFDRHPDGVASVKFKEPEEADRCIEALNGRWFAGRQLEA 82

Query: 94 ER 95
          ER
Sbjct: 83 ER 84

This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. . Length = 91

>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 38.3 bits (89), Expect = 2e-04
 Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 2/68 (2%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V  LS +  E D+   F+  G +  C  V+  +   SRG AFVT    + A   IK +
Sbjct: 4  LFVGMLSKKCNENDVRIMFAPFGSIEEC-TVLRDQNGQSRGCAFVTFASRQCALNAIKAM 62

Query: 82 NQSV-LEG 88
          + S  +EG
Sbjct: 63 HHSQTMEG 70

This subgroup corresponds to the RRM2 of Bruno, 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 = 81

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

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LYV  L   VTE  L + FS+ G + SC L+ E     +  +AFV       A   ++ +
Sbjct: 1  LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHG---NDPYAFVEYYDHRSAAAALQTM 57

Query: 82 NQSVLEGRYITV 93
          N  ++ G+ I V
Sbjct: 58 NGRLILGQEIKV 69

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

>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 38.5 bits (89), Expect = 2e-04
 Identities = 23/89 (25%), Positives = 42/89 (47%)

Query: 16  GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAE 75
           G  G  L++  L     ++DL + F   G V S  + ++ +T +S+ F FV+ D    A+
Sbjct: 4   GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQ 63

Query: 76  RCIKYLNQSVLEGRYITVERSRRKRPRTP 104
             I+ +N   +  + + V+  R K    P
Sbjct: 64  AAIQAMNGFQIGMKRLKVQLKRSKNDSKP 92

This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 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 two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 92

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 38.0 bits (88), Expect = 2e-04
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 5/74 (6%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           L V  LS   +E  L++ F K     +  + +       +G+AFV  +  EDA+  +  
Sbjct: 3  VLVVNNLSYSASEDSLQEVFEK-----ATSIRIPQNNGRPKGYAFVEFESAEDAKEALNS 57

Query: 81 LNQSVLEGRYITVE 94
           N + +EGR I +E
Sbjct: 58 CNNTEIEGRSIRLE 71

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

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

 Score = 38.0 bits (89), Expect = 2e-04
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 5/79 (6%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRI--SRGFAFVTMDGVEDAERC 77
            L V  +    T+++L + FS  G+V S  L   P+      RGFAFV     ++A+  
Sbjct: 1  TKLIVRNVPFEATKKELRELFSPFGQVKSVRL---PKKFDGSHRGFAFVEFVTKQEAQNA 57

Query: 78 IKYLNQSVLEGRYITVERS 96
          ++ L  + L GR++ +E +
Sbjct: 58 MEALKSTHLYGRHLVLEYA 76

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

>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          +YV G+    TE ++  +FS  G++    L+  P T   RG AF+T    E A+R +  L
Sbjct: 1  VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALA-L 59

Query: 82 NQSVLEGRYITVE 94
          +   + GR++ VE
Sbjct: 60 DGEDMGGRFLKVE 72

This subfamily corresponds to the RRM1 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|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 37.7 bits (87), Expect = 2e-04
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 8/72 (11%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V  L+  VTE  LEK F + GK+         R +  + +AF+  D  + A + ++ +
Sbjct: 4  LFVRNLANTVTEEILEKAFGQFGKLE--------RVKKLKDYAFIHFDERDGAVKAMEEM 55

Query: 82 NQSVLEGRYITV 93
          N   LEG  I +
Sbjct: 56 NGKELEGENIEI 67

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

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

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 20/72 (27%), Positives = 41/72 (56%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++VTG+     E D+   F++ G++ +  L ++ RT   +G+A +  +  ++A+  I+ L
Sbjct: 9  IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 82 NQSVLEGRYITV 93
          N   L G+ I+V
Sbjct: 69 NGKELLGQTISV 80

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

 Score = 37.9 bits (88), Expect = 3e-04
 Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 1/61 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V  L+ + TE+++E+ FS  G+V   +++ +   + SRG AFV     E A+  IK L
Sbjct: 2  LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKAL 60

Query: 82 N 82
          N
Sbjct: 61 N 61

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|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins

 Score = 37.5 bits (87), Expect = 3e-04
 Identities = 24/69 (34%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          TLYVTG       RDL   F + G++  C +   PRT  SR FAFV  +   DAE   + 
Sbjct: 1  TLYVTGFGAETRARDLAYEFERYGRLVRCDIPP-PRTFQSRPFAFVEYESHRDAEDAYEE 59

Query: 81 LNQSVLEGR 89
          ++       
Sbjct: 60 MHGRRFPDT 68

This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but not essential for growth. Srp1p is closely related to the SR protein family found in metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. Some family members also contain another RRM domain. Length = 78

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

 Score = 37.6 bits (88), Expect = 3e-04
 Identities = 21/75 (28%), Positives = 36/75 (48%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V  L   VT+  L + FSK        +V + RT  S+G+ FV+     D  + +K +
Sbjct: 9  IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 82 NQSVLEGRYITVERS 96
          N   +  R I + +S
Sbjct: 69 NGKYVGNRPIKLRKS 83

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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 39.5 bits (92), Expect = 4e-04
 Identities = 21/75 (28%), Positives = 34/75 (45%)

Query: 19  GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
           G  ++V  LS    E  L + F   G V +  ++ +  T   +G+ FV+M   ++A   I
Sbjct: 269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAI 328

Query: 79  KYLNQSVLEGRYITV 93
             LN   L  R + V
Sbjct: 329 LSLNGYTLGNRVLQV 343

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|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins

 Score = 37.9 bits (89), Expect = 4e-04
 Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 10/78 (12%)

Query: 20 NTLYVTGLSTRV-TERDLEKH--FSKEGKVASCFLVVEPRTRISR-----GFAFVTMDGV 71
          N +YV GL  R+  E  L+K   F + GK+    +V+   T  +        A+VT    
Sbjct: 6  NLVYVVGLPPRLADEEVLKKPEYFGQYGKIKK--IVINRNTSYNGSQGPSASAYVTYSRK 63

Query: 72 EDAERCIKYLNQSVLEGR 89
          EDA RCI+ ++   L+GR
Sbjct: 64 EDALRCIQAVDGFYLDGR 81

This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T. Length = 98

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 37.5 bits (86), Expect = 4e-04
 Identities = 19/68 (27%), Positives = 34/68 (50%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LY+ GL    T++DL K     GK+ S   +++  T   +G+ FV  D    A++ +  L
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69

Query: 82 NQSVLEGR 89
            S ++ +
Sbjct: 70 KASGVQAQ 77

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has 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. MSSP-1 contains 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 as well as induction of apoptosis. . Length = 86

>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 = 4e-04
 Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 6/80 (7%)

Query: 20 NTLYVTGLSTRVTE---RDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
          N +++ GL   ++E   ++L + F   GK+ +  LV +  T +S+G+AF         ++
Sbjct: 1  NKIFIGGLPNYLSEDQVKELLESF---GKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQ 57

Query: 77 CIKYLNQSVLEGRYITVERS 96
           I  LN   L  + +TV+R+
Sbjct: 58 AIAGLNGMQLGDKKLTVQRA 77

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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 39.5 bits (92), Expect = 5e-04
 Identities = 25/81 (30%), Positives = 39/81 (48%)

Query: 17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
               L V  L   +T+ ++   F+  G++ SC LV +  T  S G+ FV     EDAE+
Sbjct: 1  ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60

Query: 77 CIKYLNQSVLEGRYITVERSR 97
           +  LN   L+ + I V  +R
Sbjct: 61 AVNSLNGLRLQNKTIKVSYAR 81

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|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 37.0 bits (86), Expect = 5e-04
 Identities = 25/70 (35%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPR-TRISRGFAFVTMDGVEDAER 76
          P NT+ + GL   VTE D+       G       ++  + T  SRGFAFV    +E+A R
Sbjct: 1  PNNTIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATR 60

Query: 77 CIKYLNQSVL 86
           ++ LNQ  L
Sbjct: 61 WME-LNQGKL 69

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, 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. Both, RBM5 and RBM10, 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 = 81

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

 Score = 36.8 bits (86), Expect = 5e-04
 Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 9/55 (16%)

Query: 22 LYVTGLST-RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAE 75
          ++V  L+T +V++ DLE+ FSK GK+            + +G+ FV  D  EDA 
Sbjct: 3  VFVGNLNTDKVSKEDLEEIFSKYGKILGI--------SLHKGYGFVQFDNEEDAR 49

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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 37.4 bits (86), Expect = 5e-04
 Identities = 24/76 (31%), Positives = 37/76 (48%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L V  L   +T+ + +  F   G++ SC LV +  T  S G+ FV      DA++ I  L
Sbjct: 6  LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTL 65

Query: 82 NQSVLEGRYITVERSR 97
          N   L+ + I V  +R
Sbjct: 66 NGLKLQTKTIKVSYAR 81

This subgroup corresponds to the RRM1 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 = 84

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 37.2 bits (87), Expect = 5e-04
 Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 6/76 (7%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI--- 78
          +Y+ GL   +TE D+   FS+ G++    LV + +T  S+GFAF+     ED    I   
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFL---AYEDQRSTILAV 68

Query: 79 KYLNQSVLEGRYITVE 94
            LN   L GR I V+
Sbjct: 69 DNLNGIKLLGRTIRVD 84

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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 37.0 bits (85), Expect = 5e-04
 Identities = 25/76 (32%), Positives = 37/76 (48%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L V  L   +T+ +    F   G++ SC LV +  T  S G+ FV     +DAE+ I  L
Sbjct: 5  LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 82 NQSVLEGRYITVERSR 97
          N   L+ + I V  +R
Sbjct: 65 NGLRLQTKTIKVSYAR 80

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD 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 = 83

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

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 23/80 (28%), Positives = 38/80 (47%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           T++V  +   V++  + K   K GKV S   V +P T   + F F   +  E A R ++ 
Sbjct: 2   TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61

Query: 81  LNQSVLEGRYITVERSRRKR 100
           LN   L G+ + V+   + R
Sbjct: 62  LNGLELGGKKLLVKVDAKTR 81

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

 Score = 36.7 bits (85), Expect = 6e-04
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          T+YV  L   + ER++E  F K G +    L + PR     G+AF+  +   DAE  I+ 
Sbjct: 1  TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPR---PPGYAFIEFEDARDAEDAIRG 57

Query: 81 LNQSVLEGRYITVER 95
           +    +G+ + VE 
Sbjct: 58 RDGYDFDGQRLRVEL 72

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

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

 Score = 36.9 bits (85), Expect = 6e-04
 Identities = 26/74 (35%), Positives = 33/74 (44%), Gaps = 10/74 (13%)

Query: 22 LYVTGLSTRVTERDLEKHFS--KEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
          LYV  L    TE  +EK F+  K G V         R +  R +AFV     EDA   + 
Sbjct: 11 LYVRNLMLSTTEETIEKEFNSIKPGAVE--------RVKKIRDYAFVHFSNREDAVDAMN 62

Query: 80 YLNQSVLEGRYITV 93
           LN  V++G  I V
Sbjct: 63 ALNGKVIDGSPIEV 76

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

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 36.7 bits (84), Expect = 6e-04
 Identities = 19/68 (27%), Positives = 34/68 (50%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LY+ GL    T++DL K     GK+ S   +++  T   +G+ FV  D    A++ +  L
Sbjct: 4  LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 63

Query: 82 NQSVLEGR 89
            S ++ +
Sbjct: 64 KASGVQAQ 71

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has 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. MSSP-2 contains 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 as well as induction of apoptosis. . Length = 75

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

 Score = 36.6 bits (85), Expect = 7e-04
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          T+Y+  L+  +TE D+ + F K  ++ S  L  +  T   +GF  V     E  +  +K 
Sbjct: 1  TVYIGNLAWDITEDDVREFF-KGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALK- 58

Query: 81 LNQSVLEGRYITV 93
          L+ +VL GR I +
Sbjct: 59 LDGTVLCGRPIRI 71

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

 Score = 36.6 bits (84), Expect = 7e-04
 Identities = 23/77 (29%), Positives = 39/77 (50%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V  LS  +T  D++  F+  GK++   +V +  T  S+G+ FV+     DAE  I ++
Sbjct: 4  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 82 NQSVLEGRYITVERSRR 98
              L GR I    + R
Sbjct: 64 GGQWLGGRQIRTNWATR 80

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

>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins

 Score = 37.0 bits (86), Expect = 7e-04
 Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 8/85 (9%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGV--------ED 73
          + +TGLS   T + +  HF   G++    L ++PRT  S G   VT  G         E 
Sbjct: 1  ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEA 60

Query: 74 AERCIKYLNQSVLEGRYITVERSRR 98
          A+  +  LN   + G+ + VE  R 
Sbjct: 61 AKAAVDGLNGRRIGGKRVRVELDRD 85

This subfamily corresponds to the RRM of spSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, or Set1 complex component, is encoded by SET1 from the fission yeast S. pombe. It is essential for the H3 lysine-4 methylation. in vivo, and plays an important role in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway. spSet1p is the homology counterpart of Saccharomyces cerevisiae Set1p (scSet1p). However, it is more closely related to Set1 found in mammalian. Moreover, unlike scSet1p, spSet1p is not required for heterochromatin assembly in fission yeast. spSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 86

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 38.8 bits (90), Expect = 8e-04
 Identities = 27/91 (29%), Positives = 44/91 (48%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S      +T N G  L V  L   +T+R+L   F   G + +C ++ + +T  S G+AFV
Sbjct: 95  SGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFV 154

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVERSR 97
                 D++R IK LN   +  + + V  +R
Sbjct: 155 DFGSEADSQRAIKNLNGITVRNKRLKVSYAR 185

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|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 36.6 bits (84), Expect = 8e-04
 Identities = 15/57 (26%), Positives = 30/57 (52%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          L+V G+     E  L  +F + GK+ +  ++ + ++   RGF FVT D  +  ++ +
Sbjct: 3  LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIV 59

This subgroup corresponds to the RRM2 of hnRNP A2/B1, 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 A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 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|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 36.7 bits (84), Expect = 8e-04
 Identities = 18/68 (26%), Positives = 34/68 (50%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LY+ GL    T++DL K     GK+ S   +++  T   +G+ FV  D    A++ +  L
Sbjct: 7  LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66

Query: 82 NQSVLEGR 89
            + ++ +
Sbjct: 67 KANGVQAQ 74

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It 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. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 36.4 bits (85), Expect = 9e-04
 Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 3/72 (4%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LYV  L  +++  +L   F K G +    +     TR   G AFV  + + DA+    +L
Sbjct: 5  LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETR---GTAFVVYEDIYDAKNACDHL 61

Query: 82 NQSVLEGRYITV 93
          +   +  RY+ V
Sbjct: 62 SGFNVANRYLVV 73

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is 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 has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

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

 Score = 38.3 bits (89), Expect = 0.001
 Identities = 26/107 (24%), Positives = 46/107 (42%)

Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
           LYV  L   +TE++L + F   G +    L  +P T  S+GF F+     E+A+  ++ +
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248

Query: 82  NQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDRGRYRS 128
           N   L GR I V  ++           +  +   + +G+      R 
Sbjct: 249 NGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEERE 295

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|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 36.1 bits (84), Expect = 0.001
 Identities = 28/76 (36%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
          P N +++ GL   VTE+ L +HFS+ G V     VV  R    RG A V  D VE A+  
Sbjct: 6  PTNCVWLDGLDESVTEQYLTRHFSRYGPVVH---VVIDR---QRGQALVFFDKVEAAQAA 59

Query: 78 IKYLNQSVLEGRYITV 93
          +  +    L GR + V
Sbjct: 60 VNEMKGRKLGGRKLQV 75

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 77

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

 Score = 35.9 bits (83), Expect = 0.001
 Identities = 21/70 (30%), Positives = 34/70 (48%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V  LS  VT+  L   FS     +   ++ + ++  SRG+ FV+    +DAE  I  +
Sbjct: 2  IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 82 NQSVLEGRYI 91
          N   L  R I
Sbjct: 62 NGKWLGSRPI 71

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

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 19/69 (27%), Positives = 27/69 (39%), Gaps = 7/69 (10%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           L V+ L   VTE D+ + FS  G +            +  G A V     +DA   I  
Sbjct: 2  RLVVSNLHPSVTEDDIVELFSAIGALKRA-------RLVRPGVAEVVYVRKDDALTAIDK 54

Query: 81 LNQSVLEGR 89
           N   L+G+
Sbjct: 55 YNNRELDGQ 63

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

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

 Score = 36.0 bits (84), Expect = 0.001
 Identities = 23/72 (31%), Positives = 32/72 (44%), Gaps = 9/72 (12%)

Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPR--------TRISRGFAFVTMDG 70
           N + V GL   V E  LEK      K+ S F V +          T  ++G+AFV    
Sbjct: 1  DNVVVVDGLP-VVGEEKLEKLKKVLRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFAT 59

Query: 71 VEDAERCIKYLN 82
           E+A+  +K LN
Sbjct: 60 PEEAKEAVKALN 71

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|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 35.9 bits (83), Expect = 0.001
 Identities = 17/60 (28%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
          NT++V G+  R+ E ++   F+K G V    ++ + RT +S+G+ FV+     D ++ ++
Sbjct: 6  NTVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFYDDVDVQKIVE 64

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. 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 = 82

>gnl|CDD|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 8/85 (9%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
           P   ++V GL   VTE DL +  S+ G +   ++ + P+ R     A V  + + DA+ C
Sbjct: 1   PSPVVHVRGLPDGVTEADLVEALSEFGPI--SYVTMMPKKRQ----ALVEFEDISDAKAC 54

Query: 78  IKY--LNQSVLEGRYITVERSRRKR 100
           + +   N   + GR      S  + 
Sbjct: 55  VNHAQQNPVYIAGRQAYFNYSTSQE 79

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 80

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

 Score = 35.7 bits (82), Expect = 0.001
 Identities = 30/84 (35%), Positives = 39/84 (46%), Gaps = 11/84 (13%)

Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKV--ASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
           N LY+  LS   +  DLE  F K+ K+  +  FLV         G+AFV       A + 
Sbjct: 2   NKLYIGNLSENASPLDLESIF-KDSKIPFSGPFLV-------KSGYAFVDCPDESWAMKA 53

Query: 78  IKYLNQSV-LEGRYITVERSRRKR 100
           I  L+  V L G+ I VE S  KR
Sbjct: 54  IDTLSGKVELHGKVIEVEHSVPKR 77

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

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

 Score = 35.7 bits (82), Expect = 0.001
 Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 5/72 (6%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V GLS  V+E DL  HF K  +V+   L      R    +A +  D   DA   +K +
Sbjct: 2  VHVGGLSPSVSEGDLRSHFQKY-QVSVISLCKLSNYR----YASLHFDRASDALLAVKKM 56

Query: 82 NQSVLEGRYITV 93
          N  VL G  I V
Sbjct: 57 NGGVLSGLSIKV 68

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

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

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 7/74 (9%)

Query: 23 YVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA---FVTMDGVEDAERCIK 79
          +V  +    T  +L++HF   G +    ++ +  T   +GFA   F+    VE+A     
Sbjct: 3  FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENA----L 58

Query: 80 YLNQSVLEGRYITV 93
           LN+S   GR I V
Sbjct: 59 LLNESEFRGRQIKV 72

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

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVV-EPRTRISR-----GFAFVTMDGVEDA 74
           +Y++ LS   +E DLE+ F K+ +  S  +     R   SR     G A+      E A
Sbjct: 1  RVYISNLSYSSSEEDLEE-FLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59

Query: 75 ERCIKYLNQSVLEGRYITV 93
          E+ +K LN  V + R + V
Sbjct: 60 EKVVKDLNGKVFKNRKLFV 78

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

>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 35.7 bits (82), Expect = 0.001
 Identities = 21/81 (25%), Positives = 42/81 (51%), Gaps = 8/81 (9%)

Query: 17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
          +P   ++V GL+   TE  + ++F + G++ +  L ++P+T   RGF F+T    +  ++
Sbjct: 2  DPVKKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKK 61

Query: 77 CIKYLNQSVLEGRYITVERSR 97
                  VLE ++  V  S+
Sbjct: 62 --------VLEKKFHNVSGSK 74

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), 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 A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 38.1 bits (88), Expect = 0.002
 Identities = 23/67 (34%), Positives = 35/67 (52%)

Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
           LYVT L   +T+  L+  F K G++    ++ +  T   RG AFV  +  E+A+  I  L
Sbjct: 196 LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISAL 255

Query: 82  NQSVLEG 88
           N  + EG
Sbjct: 256 NNVIPEG 262

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|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 35.7 bits (82), Expect = 0.002
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          G  ++V  +   + E +L   F K G +    L+++P +  +RG+AF+T  G E A+  +
Sbjct: 1  GTEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAV 60

Query: 79 KYL-NQSVLEGRYITV 93
          K   N  +  G+++ V
Sbjct: 61 KLCDNYEIRPGKHLGV 76

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 8/69 (11%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V GLS   TE  ++++F   G++ +  L ++ +T   RGF FVT    E         
Sbjct: 2  VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPV------- 54

Query: 82 NQSVLEGRY 90
           Q +LE RY
Sbjct: 55 -QKLLESRY 62

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), 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. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two 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|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 26/76 (34%), Positives = 37/76 (48%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L V  L   +T+ +L   FS  G+V S  L+ +     S G+ FV     +DAER I  L
Sbjct: 4  LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 82 NQSVLEGRYITVERSR 97
          N   L+ + I V  +R
Sbjct: 64 NGLRLQSKTIKVSYAR 79

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a 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. Meanwhile, 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 = 81

>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 = 0.002
 Identities = 22/81 (27%), Positives = 33/81 (40%), Gaps = 8/81 (9%)

Query: 22 LYVTGLSTRVTERDLEKHF--------SKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
          ++V+ L    TE+DL +HF         K+      +L  +  T   +G A VT D    
Sbjct: 1  VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 74 AERCIKYLNQSVLEGRYITVE 94
          A   I++ N     G  I V 
Sbjct: 61 ASAAIEWFNNKDFMGNTIKVS 81

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|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 2/68 (2%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L++  +S +  E D+   FS  G++  C ++  P   +SRG AFVT      A+  IK +
Sbjct: 4  LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDG-LSRGCAFVTFTTRAMAQTAIKAM 62

Query: 82 NQS-VLEG 88
          +Q+  +EG
Sbjct: 63 HQAQTMEG 70

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 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 two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

>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 = 35.2 bits (82), Expect = 0.002
 Identities = 21/74 (28%), Positives = 36/74 (48%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           +Y+  L     E +L K+FS+ G V    L    +T  S+G+AFV  +  E A+   + 
Sbjct: 1  VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAET 60

Query: 81 LNQSVLEGRYITVE 94
          +N  +L  R +  +
Sbjct: 61 MNNYLLFERLLKCK 74

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

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 22/77 (28%), Positives = 39/77 (50%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V  LS  +T  D++  F+  G+++   +V +  T  S+G+ FV+     DAE  I+ +
Sbjct: 4  VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 82 NQSVLEGRYITVERSRR 98
              L GR I    + R
Sbjct: 64 GGQWLGGRQIRTNWATR 80

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

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

 Score = 34.9 bits (81), Expect = 0.002
 Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 5/72 (6%)

Query: 24 VTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQ 83
          V+GL    + +DL+    + G V   +  V+       G   V     ED ER ++ L+ 
Sbjct: 5  VSGLPEGASWQDLKDFGRQAGDV--TYADVDRD---QEGEGVVEFTSQEDMERALRKLDG 59

Query: 84 SVLEGRYITVER 95
          +   GR + VE 
Sbjct: 60 TEFRGRRVRVEE 71

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

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 24/91 (26%), Positives = 38/91 (41%), Gaps = 20/91 (21%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVAS----------CFLVVEPRTRISRGF------- 63
          T++V  L     ++DL+K F + G + S            L  +    I + F       
Sbjct: 2  TVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAA-IKKKFHDKKDNV 60

Query: 64 -AFVTMDGVEDAERCIKYLNQSVLEGRYITV 93
           A+V     E AE+ +K LN +  EG +I V
Sbjct: 61 NAYVVFKEEESAEKALK-LNGTEFEGHHIRV 90

This subfamily corresponds to the RRM1 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 = 91

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

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 19/73 (26%), Positives = 36/73 (49%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           +Y+  L     E++L+K+FS+ G V +  +    +T  S+ + F+     E A    K 
Sbjct: 1  VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 81 LNQSVLEGRYITV 93
          +N  +L G+ + V
Sbjct: 61 MNNYLLMGKVLQV 73

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|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 35.2 bits (82), Expect = 0.003
 Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRI--SRGFAFVTMDGVEDAERC 77
          +TL+VT       + D+   F + G++ S   +  P  R   +R F +V     E A   
Sbjct: 1  STLWVTNFPPSFDQSDIRDLFEQYGEILS---IRFPSLRFNKTRRFCYVQFTSPESAAAA 57

Query: 78 IKYLNQSVLEGRYITVERSR 97
          +  LN  + EG  + V+ S 
Sbjct: 58 VALLNGKLGEGYKLVVKISD 77

This subfamily corresponds to the RRM2 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|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 20/61 (32%), Positives = 26/61 (42%)

Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
            TL+V  L    TE  L  HFSK G V     V++  T  ++G  FV          C+
Sbjct: 1  DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

Query: 79 K 79
          K
Sbjct: 61 K 61

This subgroup corresponds to the RRM3 of Nop4p (also known as 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 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 107

>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 34.7 bits (79), Expect = 0.004
 Identities = 19/71 (26%), Positives = 38/71 (53%), Gaps = 6/71 (8%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          T+Y  G+++ +TE+ + + FS  G++      +E R    +G++FV  +  E A   I  
Sbjct: 2  TVYCGGVTSGLTEQLMRQTFSPFGQI------MEVRVFPDKGYSFVRFNSHESAAHAIVS 55

Query: 81 LNQSVLEGRYI 91
          +N + +EG  +
Sbjct: 56 VNGTTIEGHVV 66

This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 34.7 bits (80), Expect = 0.004
 Identities = 26/87 (29%), Positives = 44/87 (50%), Gaps = 7/87 (8%)

Query: 18  PGNTLYVTGLSTRVTERDLE----KHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
           P   ++V  L    ++ +LE    +HFSK G +   F+ V    R  R +AFV     +D
Sbjct: 1   PSACVFVASLPASKSDDELEAAVTEHFSKYGTLV--FVKVLRDWR-QRPYAFVQFTNDDD 57

Query: 74  AERCIKYLNQSVLEGRYITVERSRRKR 100
           A+  +     ++L+GR+I  ER++  R
Sbjct: 58  AKNALAKGQGTILDGRHIRCERAKVNR 84

This subfamily corresponds to the RRM1 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 = 86

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	187
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.92
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.91
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.85
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.84
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.83
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.81
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.81
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.8
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.78
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.77
KOG0122	270	consensus Translation initiation factor 3, subunit	99.77
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.74
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.74
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.72
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.71
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.7
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.69
PLN03120	260	nucleic acid binding protein; Provisional	99.68
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.68
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.66
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.66
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.66
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.65
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.65
PLN03213	759	repressor of silencing 3; Provisional	99.65
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.65
smart00362	72	RRM_2 RNA recognition motif.	99.65
PLN03121	243	nucleic acid binding protein; Provisional	99.64
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.64
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.64
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.63
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.63
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.63
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.63
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.62
smart00360	71	RRM RNA recognition motif.	99.61
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.6
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.59
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.59
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.58
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.58
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.58
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.57
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.57
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.57
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.56
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.55
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.54
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.54
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.53
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.52
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.49
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.49
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.49
smart00361	70	RRM_1 RNA recognition motif.	99.48
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.47
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.43
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.4
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.4
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.39
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.36
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.32
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.3
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.3
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.29
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.28
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.27
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.26
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.24
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.21
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.2
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	99.19
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.18
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.17
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.17
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.15
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.14
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.13
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.12
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.09
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	99.04
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.01
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.95
KOG0151	877	consensus Predicted splicing regulator, contains R	98.9
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.87
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.87
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.83
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.82
KOG0226	290	consensus RNA-binding proteins [General function p	98.76
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.73
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.7
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.66
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.66
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.62
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.61
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.55
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.45
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.43
KOG4210	285	consensus Nuclear localization sequence binding pr	98.4
KOG2314	698	consensus Translation initiation factor 3, subunit	98.32
KOG3152	278	consensus TBP-binding protein, activator of basal	98.23
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.23
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.19
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.19
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.18
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.15
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.13
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	98.1
KOG1855	484	consensus Predicted RNA-binding protein [General f	98.08
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.06
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.05
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	98.04
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	98.0
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.95
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.93
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.85
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.81
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.67
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.63
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.63
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.55
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.42
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.41
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.41
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.39
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.33
KOG4660	549	consensus Protein Mei2, essential for commitment t	97.33
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.18
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	97.14
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	97.04
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.01
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	96.99
KOG2591	684	consensus c-Mpl binding protein, contains La domai	96.99
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.91
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.91
KOG2068	327	consensus MOT2 transcription factor [Transcription	96.85
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	96.82
KOG2135	526	consensus Proteins containing the RNA recognition	96.36
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	96.36
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	96.08
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	95.96
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.91
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	95.85
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	95.79
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	95.72
KOG4210	285	consensus Nuclear localization sequence binding pr	95.44
KOG2318	650	consensus Uncharacterized conserved protein [Funct	94.36
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	93.86
smart00596	69	PRE_C2HC PRE_C2HC domain.	93.33
PF07530	68	PRE_C2HC: Associated with zinc fingers; InterPro:	93.13
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	92.6
KOG4483	528	consensus Uncharacterized conserved protein [Funct	92.24
KOG2891	445	consensus Surface glycoprotein [General function p	91.15
KOG4207	256	consensus Predicted splicing factor, SR protein su	90.37
KOG4019	193	consensus Calcineurin-mediated signaling pathway i	89.55
KOG2295	648	consensus C2H2 Zn-finger protein [General function	84.78
PF03468	116	XS: XS domain; InterPro: IPR005380 The XS (rice ge	84.12
COG5638	622	Uncharacterized conserved protein [Function unknow	80.15

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

Probab=99.92  E-value=7.3e-24  Score=151.70  Aligned_cols=81  Identities=37%  Similarity=0.606  Sum_probs=75.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      +.+++|||+||+..+++.||+.+|..||.|..|+|..++     .|||||||++..+|+.|+..|+|..|+|..|.|+++
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S   82 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELS   82 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEee
Confidence            457999999999999999999999999999999998754     789999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 029810           97 RRKRPR  102 (187)
Q Consensus        97 ~~~~~~  102 (187)
                      +.+...
T Consensus        83 ~G~~r~   88 (195)
T KOG0107|consen   83 TGRPRG   88 (195)
T ss_pred             cCCccc
Confidence            877653

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

Probab=99.91  E-value=5.5e-23  Score=147.68  Aligned_cols=87  Identities=26%  Similarity=0.404  Sum_probs=81.6

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      .....++|||+|||+++++++|+++|.+||.|..|.|+.+..|+++++||||+|++.++|++||+.|++..|+|+.|.|+
T Consensus        30 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~  109 (144)
T PLN03134         30 LRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVN  109 (144)
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            35667899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 029810           95 RSRRKRP  101 (187)
Q Consensus        95 ~a~~~~~  101 (187)
                      ++..+..
T Consensus       110 ~a~~~~~  116 (144)
T PLN03134        110 PANDRPS  116 (144)
T ss_pred             eCCcCCC
Confidence            9986543

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

Probab=99.85  E-value=5.9e-20  Score=141.48  Aligned_cols=100  Identities=27%  Similarity=0.402  Sum_probs=90.1

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      .....++-+||||+-|+.+|+|.+|+.+|+.||+|+.|.|+.++.|++++|||||+|+++.++.+|.+..+|..|+|+.|
T Consensus        94 p~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri  173 (335)
T KOG0113|consen   94 PNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRI  173 (335)
T ss_pred             CcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEE
Confidence            34445788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeccCCCCCCCCCCCCCC
Q 029810           92 TVERSRRKRPRTPTPGHYLG  111 (187)
Q Consensus        92 ~v~~a~~~~~~~~~~~~~~g  111 (187)
                      .|.+-.....+...|..-+|
T Consensus       174 ~VDvERgRTvkgW~PRRLGG  193 (335)
T KOG0113|consen  174 LVDVERGRTVKGWLPRRLGG  193 (335)
T ss_pred             EEEecccccccccccccccC
Confidence            99998887777665544333

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

Probab=99.84  E-value=9.3e-20  Score=133.96  Aligned_cols=89  Identities=34%  Similarity=0.526  Sum_probs=82.8

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .++.+.-++|.|-||..-|+.++|..+|++||.|.+|.|+.|..|.+++|||||.|....+|+.|+++|+|..|+|+.|.
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            45566678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeccCCCC
Q 029810           93 VERSRRKRP  101 (187)
Q Consensus        93 v~~a~~~~~  101 (187)
                      |++|+-...
T Consensus        87 Vq~arygr~   95 (256)
T KOG4207|consen   87 VQMARYGRP   95 (256)
T ss_pred             ehhhhcCCC
Confidence            999885433

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

Probab=99.83  E-value=2.7e-20  Score=127.10  Aligned_cols=98  Identities=29%  Similarity=0.473  Sum_probs=88.5

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ....+++|||+||+..++|++|.++|+++|+|..|.|-.|+.+..++|||||+|.+.++|+.||+.+++..++.+.|.|.
T Consensus        32 a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D  111 (153)
T KOG0121|consen   32 ALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRID  111 (153)
T ss_pred             HHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeee
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 029810           95 RSRRKRPRTPTPGHYLGLKSSRDIGRGDRGR  125 (187)
Q Consensus        95 ~a~~~~~~~~~~~~~~g~~~~r~~g~g~~g~  125 (187)
                      |.-             |.-.++.+|+|..|+
T Consensus       112 ~D~-------------GF~eGRQyGRG~sGG  129 (153)
T KOG0121|consen  112 WDA-------------GFVEGRQYGRGKSGG  129 (153)
T ss_pred             ccc-------------cchhhhhhcCCCCCC
Confidence            854             455567777776654

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.81  E-value=6.9e-19  Score=142.96  Aligned_cols=84  Identities=30%  Similarity=0.461  Sum_probs=77.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--eEEEEEe
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG--RYITVER   95 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g--~~l~v~~   95 (187)
                      ..++|||+|||+.+++++|+++|++||+|+.|.|+.+..++++++||||+|++.++|++||+.|++..|.+  +.|.|.+
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            46789999999999999999999999999999999999999999999999999999999999999998866  6899999


Q ss_pred             ccCCCC
Q 029810           96 SRRKRP  101 (187)
Q Consensus        96 a~~~~~  101 (187)
                      ++....
T Consensus       272 a~~~~~  277 (346)
T TIGR01659       272 AEEHGK  277 (346)
T ss_pred             CCcccc
Confidence            886543

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).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.81  E-value=3.1e-19  Score=144.96  Aligned_cols=85  Identities=31%  Similarity=0.497  Sum_probs=80.7

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      .+....++|||+|||+++|+++|+++|+.||+|+.|+|+.+..++++++||||+|+++++|++||+.|++..|.+++|+|
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence            45667899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeccC
Q 029810           94 ERSRR   98 (187)
Q Consensus        94 ~~a~~   98 (187)
                      .++++
T Consensus       182 ~~a~p  186 (346)
T TIGR01659       182 SYARP  186 (346)
T ss_pred             ecccc
Confidence            98765

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).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.80  E-value=6.6e-19  Score=143.85  Aligned_cols=84  Identities=26%  Similarity=0.349  Sum_probs=79.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      .+.+|||+|||+.+++++|+++|++||.|..|.|+.+..|+.++|||||+|.+.++|.+||..|||..|.|+.|.|.|+.
T Consensus       268 ~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~  347 (352)
T TIGR01661       268 AGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKT  347 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcc
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 029810           98 RKRP  101 (187)
Q Consensus        98 ~~~~  101 (187)
                      .+..
T Consensus       348 ~~~~  351 (352)
T TIGR01661       348 NKAY  351 (352)
T ss_pred             CCCC
Confidence            7643

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.78  E-value=1.7e-18  Score=141.50  Aligned_cols=83  Identities=30%  Similarity=0.432  Sum_probs=79.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      +.++|||+|||..+++++|+++|+.||+|..|.|+.++.+++++|||||+|.+.++|++||+.|++..|.|+.|.|++++
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~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 029810           98 RKR  100 (187)
Q Consensus        98 ~~~  100 (187)
                      +..
T Consensus        82 ~~~   84 (352)
T TIGR01661        82 PSS   84 (352)
T ss_pred             ccc
Confidence            654

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.77  E-value=2.8e-18  Score=107.98  Aligned_cols=70  Identities=39%  Similarity=0.605  Sum_probs=66.6

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        22 l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      |||+|||+++++++|+++|.+||.|..+.+..+ .++..+++|||+|++.++|++|++.|++..|+|+.|+
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-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999987 6788899999999999999999999999999999885

(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=99.77  E-value=3e-18  Score=128.90  Aligned_cols=84  Identities=35%  Similarity=0.486  Sum_probs=80.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ....++|-|.||+.++++++|.++|.+||.|..|.|..++.||.++|||||+|.+.++|++||+.|||.-++.-.|.|+|
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEw  265 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEW  265 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEe
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 029810           96 SRRK   99 (187)
Q Consensus        96 a~~~   99 (187)
                      ++|+
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9975

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

Probab=99.74  E-value=6.4e-18  Score=116.52  Aligned_cols=84  Identities=27%  Similarity=0.480  Sum_probs=80.2

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ...+..|||.++...+++++|.+.|..||+|++|++.++..||..+|||+|+|++.++|++||..|||..|.++.|.|.|
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw  148 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDW  148 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEE
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 029810           96 SRRK   99 (187)
Q Consensus        96 a~~~   99 (187)
                      +..+
T Consensus       149 ~Fv~  152 (170)
T KOG0130|consen  149 CFVK  152 (170)
T ss_pred             EEec
Confidence            8755

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

Probab=99.74  E-value=6.2e-18  Score=126.63  Aligned_cols=80  Identities=23%  Similarity=0.414  Sum_probs=74.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      .-++|||++|+|++..++|+++|++||+|++..|+.|+.|++++||+||+|.+.+.|+.|++ -....|+|++..|++|-
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~-dp~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACK-DPNPIIDGRKANCNLAS   89 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhc-CCCCcccccccccchhh
Confidence            45799999999999999999999999999999999999999999999999999999999999 34568999999988875


Q ss_pred             C
Q 029810           98 R   98 (187)
Q Consensus        98 ~   98 (187)
                      -
T Consensus        90 l   90 (247)
T KOG0149|consen   90 L   90 (247)
T ss_pred             h
Confidence            4

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

Probab=99.72  E-value=4.3e-17  Score=118.17  Aligned_cols=81  Identities=28%  Similarity=0.381  Sum_probs=72.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ...++|||+|||.++.+.+|+++|.+||.|..|.|....   ...+||||+|+++.+|+.||..-+|..++|..|.|+++
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            456899999999999999999999999999999986543   23579999999999999999999999999999999998


Q ss_pred             cCCC
Q 029810           97 RRKR  100 (187)
Q Consensus        97 ~~~~  100 (187)
                      ..-.
T Consensus        81 rggr   84 (241)
T KOG0105|consen   81 RGGR   84 (241)
T ss_pred             cCCC
Confidence            7543

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.71  E-value=1.2e-16  Score=100.96  Aligned_cols=70  Identities=37%  Similarity=0.616  Sum_probs=64.4

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        22 l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      |||+|||+++++++|.++|..||.|..+.+..++. +..+++|||+|.++++|++|+..+++..|+|+.|.
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-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999876 88899999999999999999999998999999874

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 ....

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

Probab=99.70  E-value=5.9e-16  Score=132.38  Aligned_cols=77  Identities=36%  Similarity=0.453  Sum_probs=70.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcC--CceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKE--GKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~--G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ...++|||+||++++++++|+++|++|  |+|+.|.++        ++||||+|++.++|++||+.||+.+|+|+.|+|.
T Consensus       231 ~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~  302 (578)
T TIGR01648       231 AKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVT  302 (578)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            446789999999999999999999999  999999876        4599999999999999999999999999999999


Q ss_pred             eccCCCC
Q 029810           95 RSRRKRP  101 (187)
Q Consensus        95 ~a~~~~~  101 (187)
                      |+++...
T Consensus       303 ~Akp~~~  309 (578)
T TIGR01648       303 LAKPVDK  309 (578)
T ss_pred             EccCCCc
Confidence            9987543

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

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

Probab=99.69  E-value=2.9e-16  Score=134.56  Aligned_cols=85  Identities=22%  Similarity=0.455  Sum_probs=79.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ...++|||+||+.++++++|+++|+.||.|..+.|..+..++.++|||||+|.+.++|++||+.||+..|+|+.|.|.++
T Consensus       202 ~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kA  281 (612)
T TIGR01645       202 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  281 (612)
T ss_pred             cccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEec
Confidence            34579999999999999999999999999999999999989999999999999999999999999999999999999998


Q ss_pred             cCCCC
Q 029810           97 RRKRP  101 (187)
Q Consensus        97 ~~~~~  101 (187)
                      ...+.
T Consensus       282 i~pP~  286 (612)
T TIGR01645       282 VTPPD  286 (612)
T ss_pred             CCCcc
Confidence            86543

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.

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.68  E-value=2.7e-16  Score=121.20  Aligned_cols=76  Identities=24%  Similarity=0.357  Sum_probs=70.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccC
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR   98 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   98 (187)
                      .++|||+||++.+++++|+++|+.||+|..|.|+.+..   ..+||||+|.++++|+.||. |+|..|.|+.|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            57999999999999999999999999999999998764   36899999999999999996 999999999999999864

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

Probab=99.68  E-value=4.5e-16  Score=132.99  Aligned_cols=83  Identities=18%  Similarity=0.293  Sum_probs=78.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ...++|||+|||..+++++|+++|+.||.|..+.|+.+..++.++|||||+|.+.++|+.||+.|+|..|.|+.|.|+++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            44679999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             cCC
Q 029810           97 RRK   99 (187)
Q Consensus        97 ~~~   99 (187)
                      ...
T Consensus       373 ~~~  375 (509)
T TIGR01642       373 CVG  375 (509)
T ss_pred             ccC
Confidence            654

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

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

Probab=99.66  E-value=3e-16  Score=134.51  Aligned_cols=83  Identities=28%  Similarity=0.393  Sum_probs=77.9

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      .....++|||+||++.+++++|+++|.+||.|..|.|+.+..+++++|||||+|.+.++|+.||+.|||..|.|+.|.|.
T Consensus       103 a~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~  182 (612)
T TIGR01645       103 ALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG  182 (612)
T ss_pred             hhcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeec
Confidence            34566899999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ecc
Q 029810           95 RSR   97 (187)
Q Consensus        95 ~a~   97 (187)
                      +..
T Consensus       183 rp~  185 (612)
T TIGR01645       183 RPS  185 (612)
T ss_pred             ccc
Confidence            644

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.

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

Probab=99.66  E-value=3.4e-16  Score=122.24  Aligned_cols=86  Identities=33%  Similarity=0.503  Sum_probs=77.6

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ..+.....+.|+|.|||+...+.||+.+|.+||.|.+|.|+.+.  .-+|||+||+|++.++|++|-++|||..|.|++|
T Consensus        89 ~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkI  166 (376)
T KOG0125|consen   89 NSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKI  166 (376)
T ss_pred             cCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEE
Confidence            34455667899999999999999999999999999999999875  3369999999999999999999999999999999


Q ss_pred             EEEeccCC
Q 029810           92 TVERSRRK   99 (187)
Q Consensus        92 ~v~~a~~~   99 (187)
                      +|..++..
T Consensus       167 EVn~ATar  174 (376)
T KOG0125|consen  167 EVNNATAR  174 (376)
T ss_pred             EEeccchh
Confidence            99998754

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

Probab=99.66  E-value=5.6e-16  Score=130.81  Aligned_cols=81  Identities=30%  Similarity=0.455  Sum_probs=77.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ..++|||+|||..+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+.|+|..|.|+.|.|.++.
T Consensus       185 ~~~~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       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            36899999999999999999999999999999999999888999999999999999999999999999999999999987


Q ss_pred             C
Q 029810           98 R   98 (187)
Q Consensus        98 ~   98 (187)
                      .
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.

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

Probab=99.65  E-value=8.6e-16  Score=129.68  Aligned_cols=83  Identities=33%  Similarity=0.472  Sum_probs=77.2

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ..+..+|||+|||..+++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|++||. |++..|.|..|.|++
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            3457899999999999999999999999999999999999999999999999999999999998 999999999999988


Q ss_pred             ccCC
Q 029810           96 SRRK   99 (187)
Q Consensus        96 a~~~   99 (187)
                      +...
T Consensus       165 ~~~~  168 (457)
T TIGR01622       165 SQAE  168 (457)
T ss_pred             cchh
Confidence            7543

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.

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

Probab=99.65  E-value=7.3e-16  Score=133.28  Aligned_cols=79  Identities=34%  Similarity=0.457  Sum_probs=75.7

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccC
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR   98 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   98 (187)
                      .+|||+|||.++|+++|.++|.+||.|..|.|+.+..|++++|||||+|.+.++|++||+.|++..|.|+.|.|.|+..
T Consensus         1 ~sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628         1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            3799999999999999999999999999999999999999999999999999999999999999999999999999764

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

>PLN03213 repressor of silencing 3; Provisional

Probab=99.65  E-value=6.5e-16  Score=126.56  Aligned_cols=81  Identities=27%  Similarity=0.415  Sum_probs=74.2

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCH--HHHHHHHHHhCCCccCCeEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGV--EDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~--~~a~~ai~~l~g~~i~g~~l   91 (187)
                      +....+.+|||+||++.+++++|..+|..||.|..|.|+  ..||  +|||||+|.+.  +++++||..|||..|.|..|
T Consensus         5 es~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~L   80 (759)
T PLN03213          5 SSGGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRL   80 (759)
T ss_pred             ccCCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCcee
Confidence            345567899999999999999999999999999999998  5566  89999999987  78999999999999999999


Q ss_pred             EEEeccC
Q 029810           92 TVERSRR   98 (187)
Q Consensus        92 ~v~~a~~   98 (187)
                      +|+.|++
T Consensus        81 KVNKAKP   87 (759)
T PLN03213         81 RLEKAKE   87 (759)
T ss_pred             EEeeccH
Confidence            9999886

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

Probab=99.65  E-value=2e-16  Score=117.61  Aligned_cols=89  Identities=33%  Similarity=0.502  Sum_probs=83.0

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      .....-.+|||++|..++++.-|...|-+||.|+.|.++.|.++++.++|+||+|+..|+|.+||..||+.+|.|+.|.|
T Consensus         5 ~~a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirV   84 (298)
T KOG0111|consen    5 QMANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRV   84 (298)
T ss_pred             cccccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEE
Confidence            34556689999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeccCCCCC
Q 029810           94 ERSRRKRPR  102 (187)
Q Consensus        94 ~~a~~~~~~  102 (187)
                      .+|+|.+..
T Consensus        85 N~AkP~kik   93 (298)
T KOG0111|consen   85 NLAKPEKIK   93 (298)
T ss_pred             eecCCcccc
Confidence            999986543

>smart00362 RRM_2 RNA recognition motif

Probab=99.65  E-value=1.6e-15  Score=94.84  Aligned_cols=72  Identities=44%  Similarity=0.626  Sum_probs=66.5

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        21 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      +|||.|||..+++++|+++|.+||.|..+.+..+.  +.+.++|||+|.+.++|++|++.+++..|.++.|.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999888765  5678999999999999999999999999999998873

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.64  E-value=1.5e-15  Score=115.38  Aligned_cols=77  Identities=23%  Similarity=0.287  Sum_probs=70.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ..+.+|||+||++.+|+++|++||+.||+|..|.|+.+..+   .+||||+|+++++|+.||. |+|..|.++.|.|..+
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et---~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~   78 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEY---ACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRW   78 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCc---ceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeC
Confidence            35689999999999999999999999999999999988543   4799999999999999997 9999999999999876


Q ss_pred             c
Q 029810           97 R   97 (187)
Q Consensus        97 ~   97 (187)
                      .
T Consensus        79 ~   79 (243)
T PLN03121         79 G   79 (243)
T ss_pred             c
Confidence            5

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

Probab=99.64  E-value=8.8e-16  Score=131.30  Aligned_cols=78  Identities=29%  Similarity=0.477  Sum_probs=70.6

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-CeEEEEE
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE-GRYITVE   94 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~-g~~l~v~   94 (187)
                      ...+++|||+|||+++++++|.++|++||.|..|.|+.+ .++++++||||+|.+.++|++||+.||+..|. ++.|.|.
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~  133 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVC  133 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccc
Confidence            445799999999999999999999999999999999999 78999999999999999999999999998774 5555554

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.

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

Probab=99.64  E-value=5.1e-16  Score=112.22  Aligned_cols=84  Identities=32%  Similarity=0.431  Sum_probs=79.9

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      .+.+...+|||+||+..++++.|+++|-+.|+|..++|+.+..+...+|||||+|.++++|+-||+.|+...|.|++|.|
T Consensus         4 ~~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv   83 (203)
T KOG0131|consen    4 IERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRV   83 (203)
T ss_pred             cccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEE
Confidence            35667899999999999999999999999999999999999999999999999999999999999999988999999999


Q ss_pred             Eecc
Q 029810           94 ERSR   97 (187)
Q Consensus        94 ~~a~   97 (187)
                      ..+.
T Consensus        84 ~kas   87 (203)
T KOG0131|consen   84 NKAS   87 (203)
T ss_pred             Eecc
Confidence            9877

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

Probab=99.63  E-value=1.8e-15  Score=130.87  Aligned_cols=84  Identities=31%  Similarity=0.552  Sum_probs=78.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ...+++|||+||+.++++++|+++|++||.|..|.|+.+ .++.++|||||+|.+.++|++||..||+..|.|+.|.|.+
T Consensus       282 ~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~  360 (562)
T TIGR01628       282 KAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVAL  360 (562)
T ss_pred             ccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEe
Confidence            456788999999999999999999999999999999988 5788999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 029810           96 SRRKR  100 (187)
Q Consensus        96 a~~~~  100 (187)
                      +..+.
T Consensus       361 a~~k~  365 (562)
T TIGR01628       361 AQRKE  365 (562)
T ss_pred             ccCcH
Confidence            98653

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

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

Probab=99.63  E-value=3.1e-17  Score=118.49  Aligned_cols=80  Identities=28%  Similarity=0.429  Sum_probs=76.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      .+.-|||+|||.++||.||..+|++||+|+.|.++.|..||+++||||+.|++..+...|+..|||..|.|+.|.|....
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999998654

>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=1.1e-15  Score=116.66  Aligned_cols=88  Identities=28%  Similarity=0.419  Sum_probs=81.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .+.......|||+.|...++-++|++.|.+||+|.+++|+.|..|++++||+||.|-+.++||.||..|+|..|..+.|.
T Consensus        56 k~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IR  135 (321)
T KOG0148|consen   56 KPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIR  135 (321)
T ss_pred             CCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceee
Confidence            33444467899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 029810           93 VERSRRKR  100 (187)
Q Consensus        93 v~~a~~~~  100 (187)
                      ..||..++
T Consensus       136 TNWATRKp  143 (321)
T KOG0148|consen  136 TNWATRKP  143 (321)
T ss_pred             ccccccCc
Confidence            99998765

>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=3e-15  Score=114.37  Aligned_cols=82  Identities=20%  Similarity=0.396  Sum_probs=75.6

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      ...+.+++|||+||+..+++++|++.|+.||.|.+|.|+++      +||+||.|++.|.|..||..+|+.+|.|+.|++
T Consensus       159 Qssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkC  232 (321)
T KOG0148|consen  159 QSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRC  232 (321)
T ss_pred             cCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEE
Confidence            34567899999999999999999999999999999999987      679999999999999999999999999999999


Q ss_pred             EeccCCCC
Q 029810           94 ERSRRKRP  101 (187)
Q Consensus        94 ~~a~~~~~  101 (187)
                      .|-+....
T Consensus       233 sWGKe~~~  240 (321)
T KOG0148|consen  233 SWGKEGDD  240 (321)
T ss_pred             eccccCCC
Confidence            99876544

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

Probab=99.62  E-value=7.4e-15  Score=96.97  Aligned_cols=81  Identities=23%  Similarity=0.362  Sum_probs=74.1

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      +++.+..|||.|||..+|.+++.++|.+||.|..|.|-..+.|   +|.|||.|++..+|.+|+.+|.|..+.+..|.|-
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vl   90 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKET---RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVL   90 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCc---CceEEEEehHhhhHHHHHHHhcccccCCceEEEE
Confidence            4566789999999999999999999999999999999766554   7899999999999999999999999999999998


Q ss_pred             eccC
Q 029810           95 RSRR   98 (187)
Q Consensus        95 ~a~~   98 (187)
                      +.++
T Consensus        91 yyq~   94 (124)
T KOG0114|consen   91 YYQP   94 (124)
T ss_pred             ecCH
Confidence            8765

>smart00360 RRM RNA recognition motif

Probab=99.61  E-value=4.1e-15  Score=92.62  Aligned_cols=71  Identities=44%  Similarity=0.615  Sum_probs=66.5

Q ss_pred             EcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           24 VTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        24 V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      |+|||..+++++|+++|.+||.|..+.+..+..++.++++|||+|.+.++|+.|+..|++..|.++.|.|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            67999999999999999999999999999888778889999999999999999999999999999998874

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

Probab=99.60  E-value=4.6e-15  Score=120.05  Aligned_cols=83  Identities=31%  Similarity=0.421  Sum_probs=77.2

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc-CCeEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVL-EGRYITV   93 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i-~g~~l~v   93 (187)
                      ...-++.|||+.||.++.|++|.-+|++.|+|-++.|++++.+|.++|||||+|.+.++|++||+.||+++| .|+.|.|
T Consensus        79 ~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igv  158 (506)
T KOG0117|consen   79 PPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGV  158 (506)
T ss_pred             CCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEE
Confidence            346789999999999999999999999999999999999999999999999999999999999999999988 5888888


Q ss_pred             Eecc
Q 029810           94 ERSR   97 (187)
Q Consensus        94 ~~a~   97 (187)
                      ..+.
T Consensus       159 c~Sv  162 (506)
T KOG0117|consen  159 CVSV  162 (506)
T ss_pred             EEee
Confidence            7654

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.59  E-value=1.2e-14  Score=123.63  Aligned_cols=80  Identities=26%  Similarity=0.363  Sum_probs=73.3

Q ss_pred             CCCCCeEEEcCCCC-CCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           16 GNPGNTLYVTGLST-RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~-~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ..++++|||+||++ .+++++|+++|++||.|..|+|+.+.     ++||||+|.+.++|+.||..||+..|.|+.|.|.
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~  346 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVC  346 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEE
Confidence            34678999999998 69999999999999999999998763     6899999999999999999999999999999999


Q ss_pred             eccCCC
Q 029810           95 RSRRKR  100 (187)
Q Consensus        95 ~a~~~~  100 (187)
                      +++.+.
T Consensus       347 ~s~~~~  352 (481)
T TIGR01649       347 PSKQQN  352 (481)
T ss_pred             Eccccc
Confidence            987654

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).

>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=99.59  E-value=2.4e-14  Score=89.96  Aligned_cols=74  Identities=47%  Similarity=0.630  Sum_probs=68.1

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        21 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      +|+|.|||..+++++|+++|..||.|..+.+..+..+ ...++|||+|.+.++|..|++.+++..+++..|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            5899999999999999999999999999999877654 5678999999999999999999999999999998864

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).

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

Probab=99.58  E-value=1.3e-14  Score=110.54  Aligned_cols=85  Identities=32%  Similarity=0.429  Sum_probs=80.3

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ..+.-+.|.|.-||.++|+++|+.+|...|+|+.|+++.|+.+|++.||+||.|-++++|++||..|||..+..+.|+|.
T Consensus        37 t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             cCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEE
Confidence            34556789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCC
Q 029810           95 RSRRK   99 (187)
Q Consensus        95 ~a~~~   99 (187)
                      +|++.
T Consensus       117 yARPS  121 (360)
T KOG0145|consen  117 YARPS  121 (360)
T ss_pred             eccCC
Confidence            99874

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

Probab=99.58  E-value=2.6e-15  Score=114.65  Aligned_cols=89  Identities=24%  Similarity=0.361  Sum_probs=84.2

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      ..+.+++++|||-.||.+..+.||.++|-.||.|+..+|+.|..|+.+++|+||.|+++.+|++||.+|||..|.-+.|+
T Consensus       279 qreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLK  358 (371)
T KOG0146|consen  279 QREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLK  358 (371)
T ss_pred             hhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhh
Confidence            45678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeccCCCC
Q 029810           93 VERSRRKRP  101 (187)
Q Consensus        93 v~~a~~~~~  101 (187)
                      |.+.+++..
T Consensus       359 VQLKRPkda  367 (371)
T KOG0146|consen  359 VQLKRPKDA  367 (371)
T ss_pred             hhhcCcccc
Confidence            999887643

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

Probab=99.58  E-value=1.4e-14  Score=112.88  Aligned_cols=80  Identities=44%  Similarity=0.595  Sum_probs=76.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccC
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR   98 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   98 (187)
                      ..+|||+|||..+++++|.++|.+||.|..+.|..+..++.++|||||+|.+.++|..|+..+++..|.|+.|.|.++..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            69999999999999999999999999999999999988999999999999999999999999999999999999999653

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

Probab=99.57  E-value=2.4e-14  Score=109.04  Aligned_cols=83  Identities=29%  Similarity=0.352  Sum_probs=78.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ..+..|||-||.++++|.-|+++|.+||.|..|+|+.|..|.+++||+||.+.+-++|..||..|||..+.++.|.|.+.
T Consensus       276 ~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFK  355 (360)
T KOG0145|consen  276 GGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFK  355 (360)
T ss_pred             CCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEe
Confidence            34789999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cCC
Q 029810           97 RRK   99 (187)
Q Consensus        97 ~~~   99 (187)
                      ..+
T Consensus       356 tnk  358 (360)
T KOG0145|consen  356 TNK  358 (360)
T ss_pred             cCC
Confidence            644

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.57  E-value=4.2e-15  Score=117.38  Aligned_cols=85  Identities=29%  Similarity=0.485  Sum_probs=80.8

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      +..+|.+.|||..|.+-|+.+||.-+|+.||.|..|.|+.+..||.+..||||+|++.+++++|.-+|++..|++..|+|
T Consensus       234 d~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHV  313 (479)
T KOG0415|consen  234 DVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHV  313 (479)
T ss_pred             ccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEe
Confidence            34577899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeccC
Q 029810           94 ERSRR   98 (187)
Q Consensus        94 ~~a~~   98 (187)
                      .+++.
T Consensus       314 DFSQS  318 (479)
T KOG0415|consen  314 DFSQS  318 (479)
T ss_pred             ehhhh
Confidence            99764

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

Probab=99.57  E-value=5.8e-15  Score=119.51  Aligned_cols=77  Identities=31%  Similarity=0.375  Sum_probs=71.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ..-..|||.||+.+||++.|+++|.+||.|..|+.+.|        ||||+|.+.++|.+||+.+|+++|+|..|.|.+|
T Consensus       257 s~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLA  328 (506)
T KOG0117|consen  257 SKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLA  328 (506)
T ss_pred             hheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEec
Confidence            34578999999999999999999999999999988744        9999999999999999999999999999999999


Q ss_pred             cCCCC
Q 029810           97 RRKRP  101 (187)
Q Consensus        97 ~~~~~  101 (187)
                      ++..+
T Consensus       329 KP~~k  333 (506)
T KOG0117|consen  329 KPVDK  333 (506)
T ss_pred             CChhh
Confidence            98654

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.56  E-value=2e-14  Score=122.17  Aligned_cols=76  Identities=21%  Similarity=0.326  Sum_probs=69.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh--CCCccCCeEEEEEe
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL--NQSVLEGRYITVER   95 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l--~g~~i~g~~l~v~~   95 (187)
                      ++.+|||+|||+.+++++|.++|++||.|..|.|+.+      ++||||+|++.++|++||+.|  ++..|.|+.|.|++
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            4689999999999999999999999999999998853      579999999999999999975  67899999999999


Q ss_pred             ccCC
Q 029810           96 SRRK   99 (187)
Q Consensus        96 a~~~   99 (187)
                      +..+
T Consensus        75 s~~~   78 (481)
T TIGR01649        75 STSQ   78 (481)
T ss_pred             cCCc
Confidence            8754

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).

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

Probab=99.55  E-value=7.4e-15  Score=113.22  Aligned_cols=72  Identities=33%  Similarity=0.539  Sum_probs=68.5

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccCC
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK   99 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   99 (187)
                      .+|||+|||.++++.+|+.+|++||+|.+|+|++        .|+||+.++...|+.||..||+.+|+|..|.|+.++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvK--------NYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVK--------NYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeec--------ccceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            5799999999999999999999999999999984        49999999999999999999999999999999998876

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

Probab=99.54  E-value=1.7e-14  Score=119.32  Aligned_cols=82  Identities=29%  Similarity=0.445  Sum_probs=79.0

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccCC
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK   99 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   99 (187)
                      ..|||+|||.++++++|.++|+..|.|..++++.|.+||+++||||++|.+.++|+.|++.||+.++.|.+|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999998755


Q ss_pred             CC
Q 029810          100 RP  101 (187)
Q Consensus       100 ~~  101 (187)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            43

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

Probab=99.54  E-value=2.1e-14  Score=115.93  Aligned_cols=89  Identities=26%  Similarity=0.400  Sum_probs=79.2

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC-ccCC--eE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS-VLEG--RY   90 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~-~i~g--~~   90 (187)
                      .++....++||+-||..++|.||+++|++||.|.+|.|++|+.|+.++|||||.|.+.++|.+|+.+||.. .|.|  ..
T Consensus        29 ~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~p  108 (510)
T KOG0144|consen   29 NPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHP  108 (510)
T ss_pred             CCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcc
Confidence            33456679999999999999999999999999999999999999999999999999999999999999986 4554  57


Q ss_pred             EEEEeccCCCCC
Q 029810           91 ITVERSRRKRPR  102 (187)
Q Consensus        91 l~v~~a~~~~~~  102 (187)
                      |.|++|....++
T Consensus       109 vqvk~Ad~E~er  120 (510)
T KOG0144|consen  109 VQVKYADGERER  120 (510)
T ss_pred             eeecccchhhhc
Confidence            899998876554

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

Probab=99.53  E-value=1.5e-14  Score=111.63  Aligned_cols=100  Identities=28%  Similarity=0.470  Sum_probs=85.6

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ....++|+|+||.+.++.++|++.|++||+|++++|+        ++|+||+|+-.++|..||..|++.+|.|+.++|++
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv--------kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~  146 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV--------KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQL  146 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeee--------cceeEEEEeeccchHHHHhcccccccccceeeeee
Confidence            4467899999999999999999999999999999998        45999999999999999999999999999999999


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 029810           96 SRRKRPRTPTPGHYLGLKSSRDIGRGDRGRYRS  128 (187)
Q Consensus        96 a~~~~~~~~~~~~~~g~~~~r~~g~g~~g~~~~  128 (187)
                      ++..-...+..+.     ...++.+|..|.|..
T Consensus       147 stsrlrtapgmgD-----q~~cyrcGkeghwsk  174 (346)
T KOG0109|consen  147 STSRLRTAPGMGD-----QSGCYRCGKEGHWSK  174 (346)
T ss_pred             eccccccCCCCCC-----HHHheeccccccccc
Confidence            9987766665542     234666676666643

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

Probab=99.52  E-value=1.3e-14  Score=117.07  Aligned_cols=86  Identities=30%  Similarity=0.521  Sum_probs=77.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC-ccCC--eEEEE
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS-VLEG--RYITV   93 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~-~i~g--~~l~v   93 (187)
                      ....+|||+.|+..++|.+|.++|.+||.|++|.|+.+.+ +.++|||||.|.+.+-|..||+.||+. ++.|  .+|.|
T Consensus       122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~-~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVV  200 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD-GLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVV  200 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheeccc-ccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEE
Confidence            4478999999999999999999999999999999999875 888999999999999999999999996 4654  58999


Q ss_pred             EeccCCCCCC
Q 029810           94 ERSRRKRPRT  103 (187)
Q Consensus        94 ~~a~~~~~~~  103 (187)
                      +||.+++.+.
T Consensus       201 kFADtqkdk~  210 (510)
T KOG0144|consen  201 KFADTQKDKD  210 (510)
T ss_pred             EecccCCCch
Confidence            9999887653

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

Probab=99.49  E-value=9.8e-14  Score=114.93  Aligned_cols=86  Identities=33%  Similarity=0.500  Sum_probs=77.7

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC-----C-CccC
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLN-----Q-SVLE   87 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~-----g-~~i~   87 (187)
                      ++...+.+|||.|||+++|+++|.+.|.+||+|..+.|+.++.|+.++|.|||.|.+..+|++||+...     + ..|.
T Consensus       287 en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~  366 (678)
T KOG0127|consen  287 ENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLD  366 (678)
T ss_pred             ccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEe
Confidence            445567999999999999999999999999999999999999999999999999999999999999762     3 5688


Q ss_pred             CeEEEEEeccCC
Q 029810           88 GRYITVERSRRK   99 (187)
Q Consensus        88 g~~l~v~~a~~~   99 (187)
                      |+.|.|..+-++
T Consensus       367 GR~Lkv~~Av~R  378 (678)
T KOG0127|consen  367 GRLLKVTLAVTR  378 (678)
T ss_pred             ccEEeeeeccch
Confidence            999999988654

>PF13893 RRM_5: RNA recognition motif

Probab=99.49  E-value=2.1e-13  Score=82.28  Aligned_cols=56  Identities=41%  Similarity=0.576  Sum_probs=50.5

Q ss_pred             HHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           36 LEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        36 L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      |.++|++||+|..+.+..+.     .++|||+|.+.++|+.|++.||+..|.|++|.|+||
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-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68899999999999997553     479999999999999999999999999999999986

(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 ....

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

Probab=99.49  E-value=1.2e-13  Score=114.37  Aligned_cols=82  Identities=28%  Similarity=0.494  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      +-..|+|.|||+.+.+.+|+.+|+.||.|..|.|+...+++. +|||||.|....+|+.||+.+|+..|+|++|.|.||-
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgkl-cGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKL-CGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCc-cceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            368999999999999999999999999999999997776555 4999999999999999999999999999999999987


Q ss_pred             CCC
Q 029810           98 RKR  100 (187)
Q Consensus        98 ~~~  100 (187)
                      ++.
T Consensus       195 ~Kd  197 (678)
T KOG0127|consen  195 DKD  197 (678)
T ss_pred             ccc
Confidence            653

>smart00361 RRM_1 RNA recognition motif

Probab=99.48  E-value=2.4e-13  Score=85.91  Aligned_cols=61  Identities=30%  Similarity=0.485  Sum_probs=55.0

Q ss_pred             HHHHHHHhh----cCCceeEEE-EeecCCC--CCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           33 ERDLEKHFS----KEGKVASCF-LVVEPRT--RISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        33 ~~~L~~~f~----~~G~i~~~~-i~~~~~~--~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      +++|+++|.    +||.|..|. |+.+..+  +.++|||||+|.+.++|++|+..|||..|.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578888888    999999995 7777666  888999999999999999999999999999999876

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

Probab=99.47  E-value=8.9e-13  Score=108.69  Aligned_cols=88  Identities=22%  Similarity=0.314  Sum_probs=72.6

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ..++.....+|||.|||.++++.+|+++|..||.|+...|..-...++..+||||+|.+.+.++.||++ +...|++++|
T Consensus       281 ~~~~~~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl  359 (419)
T KOG0116|consen  281 NQEPRADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKL  359 (419)
T ss_pred             CcceeecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeE
Confidence            344555667799999999999999999999999999987765443344448999999999999999995 4778999999


Q ss_pred             EEEeccCCC
Q 029810           92 TVERSRRKR  100 (187)
Q Consensus        92 ~v~~a~~~~  100 (187)
                      .|+..++..
T Consensus       360 ~Veek~~~~  368 (419)
T KOG0116|consen  360 NVEEKRPGF  368 (419)
T ss_pred             EEEeccccc
Confidence            999877543

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.43  E-value=2.1e-12  Score=104.72  Aligned_cols=79  Identities=22%  Similarity=0.378  Sum_probs=72.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhh-cCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFS-KEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~-~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ...+||+|||.++.|++|+++|. +.|+|..|.++.|. .++++|||.|||+++|.+++|++.||.+.++|+.|.|+...
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            45699999999999999999995 78999999999886 58999999999999999999999999999999999998765


Q ss_pred             C
Q 029810           98 R   98 (187)
Q Consensus        98 ~   98 (187)
                      .
T Consensus       123 d  123 (608)
T KOG4212|consen  123 D  123 (608)
T ss_pred             c
Confidence            3

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

Probab=99.40  E-value=2.5e-13  Score=107.93  Aligned_cols=77  Identities=30%  Similarity=0.452  Sum_probs=74.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      -+.|||+.|.+++.|+.|+..|..||+|+.|.+.+|..|+++++||||+|+-+|.|+.|++.||+..+.|+.|+|..
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence            37899999999999999999999999999999999999999999999999999999999999999999999999974

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.40  E-value=4.3e-13  Score=111.18  Aligned_cols=80  Identities=34%  Similarity=0.471  Sum_probs=75.5

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccCC
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK   99 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   99 (187)
                      ..|||+||..++++++|..+|+.||.|..|.+.++..||.++||+||+|.+.++|.+|++.|||.+|-|..|+|.....+
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            34999999999999999999999999999999999999999999999999999999999999999999999999876644

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

Probab=99.39  E-value=1.3e-12  Score=94.77  Aligned_cols=90  Identities=28%  Similarity=0.381  Sum_probs=81.3

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe
Q 029810           11 GRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVAS-CFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGR   89 (187)
Q Consensus        11 ~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~-~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~   89 (187)
                      ..+...+.+..|||+||.+++++..|.++|+.||.|.. -.++.+..|+.+++|+||.|++.+.+.+||+.|++..++..
T Consensus        88 ~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr  167 (203)
T KOG0131|consen   88 AHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNR  167 (203)
T ss_pred             cccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCC
Confidence            34556677799999999999999999999999998776 47888889999999999999999999999999999999999


Q ss_pred             EEEEEeccCCC
Q 029810           90 YITVERSRRKR  100 (187)
Q Consensus        90 ~l~v~~a~~~~  100 (187)
                      +|.|.++..+.
T Consensus       168 ~itv~ya~k~~  178 (203)
T KOG0131|consen  168 PITVSYAFKKD  178 (203)
T ss_pred             ceEEEEEEecC
Confidence            99999998653

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

Probab=99.36  E-value=2.2e-12  Score=110.35  Aligned_cols=75  Identities=21%  Similarity=0.409  Sum_probs=61.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcC------------CceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKE------------GKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQ   83 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~------------G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g   83 (187)
                      .....+|||+|||+.+|+++|.++|.++            +.|..+.+.      ..++||||+|.+.++|+.||+ |+|
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~------~~kg~afVeF~~~e~A~~Al~-l~g  244 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNIN------KEKNFAFLEFRTVEEATFAMA-LDS  244 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEEC------CCCCEEEEEeCCHHHHhhhhc-CCC
Confidence            4456799999999999999999999875            233444432      347899999999999999995 999


Q ss_pred             CccCCeEEEEEecc
Q 029810           84 SVLEGRYITVERSR   97 (187)
Q Consensus        84 ~~i~g~~l~v~~a~   97 (187)
                      ..|.|..|.|....
T Consensus       245 ~~~~g~~l~v~r~~  258 (509)
T TIGR01642       245 IIYSNVFLKIRRPH  258 (509)
T ss_pred             eEeeCceeEecCcc
Confidence            99999999997543

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

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

Probab=99.32  E-value=8.7e-12  Score=93.38  Aligned_cols=83  Identities=25%  Similarity=0.423  Sum_probs=73.3

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHH----HhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEK----HFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY   90 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~----~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~   90 (187)
                      +.+++.||||.||+..+..++|+.    +|++||.|..|.+..   |.+.+|-|||.|.+.+.|-.|+.+|+|..|.|+.
T Consensus         5 ~~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~   81 (221)
T KOG4206|consen    5 SVNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKP   81 (221)
T ss_pred             ccCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCch
Confidence            345566999999999999998877    999999999998774   3556889999999999999999999999999999


Q ss_pred             EEEEeccCCC
Q 029810           91 ITVERSRRKR  100 (187)
Q Consensus        91 l~v~~a~~~~  100 (187)
                      +.|++|+.+-
T Consensus        82 mriqyA~s~s   91 (221)
T KOG4206|consen   82 MRIQYAKSDS   91 (221)
T ss_pred             hheecccCcc
Confidence            9999998653

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

Probab=99.30  E-value=1.1e-11  Score=101.54  Aligned_cols=79  Identities=29%  Similarity=0.543  Sum_probs=73.2

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccCCCC
Q 029810           22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRP  101 (187)
Q Consensus        22 l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~~~  101 (187)
                      |||.||++.++..+|.++|+.||+|..|+|..+.. | ++|| ||+|+++++|++||+.|||..+.++.|.|.....+..
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhh
Confidence            99999999999999999999999999999998875 3 7999 9999999999999999999999999999988877665


Q ss_pred             CC
Q 029810          102 RT  103 (187)
Q Consensus       102 ~~  103 (187)
                      +.
T Consensus       156 r~  157 (369)
T KOG0123|consen  156 RE  157 (369)
T ss_pred             hc
Confidence            44

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.30  E-value=1.5e-11  Score=90.85  Aligned_cols=87  Identities=21%  Similarity=0.267  Sum_probs=77.6

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcC-CceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKE-GKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~-G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      .+.......+||..||..+.+.+|..+|.+| |.|..+.+..+..||.++|||||+|++++.|+-|.+.||+..|.++-|
T Consensus        43 ~p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL  122 (214)
T KOG4208|consen   43 KPEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLL  122 (214)
T ss_pred             CCccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhhee
Confidence            3445566788999999999999999999998 678888888999999999999999999999999999999999999999


Q ss_pred             EEEeccCC
Q 029810           92 TVERSRRK   99 (187)
Q Consensus        92 ~v~~a~~~   99 (187)
                      .|.+..+.
T Consensus       123 ~c~vmppe  130 (214)
T KOG4208|consen  123 ECHVMPPE  130 (214)
T ss_pred             eeEEeCch
Confidence            99886654

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

Probab=99.29  E-value=8.4e-12  Score=107.17  Aligned_cols=79  Identities=32%  Similarity=0.537  Sum_probs=72.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccC
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR   98 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   98 (187)
                      .+||||++|+..+++.||..+|+.||+|..|.++..      .+||||.+...++|++|+.+|....|.++.|+|.|+..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            489999999999999999999999999999998755      67999999999999999999999999999999999986


Q ss_pred             CCCCC
Q 029810           99 KRPRT  103 (187)
Q Consensus        99 ~~~~~  103 (187)
                      +-.+.
T Consensus       495 ~G~ks  499 (894)
T KOG0132|consen  495 KGPKS  499 (894)
T ss_pred             CCcch
Confidence            65443

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

Probab=99.28  E-value=8.9e-12  Score=99.31  Aligned_cols=87  Identities=28%  Similarity=0.454  Sum_probs=80.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ...+|||++||.++++++|+++|.+||.|..+.+++|..+...++|+||.|.+++++++++. ++-+.|+++.|.|..|.
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAI  174 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeecc
Confidence            46799999999999999999999999999999999999999999999999999999999988 77889999999999999


Q ss_pred             CCCCCCCC
Q 029810           98 RKRPRTPT  105 (187)
Q Consensus        98 ~~~~~~~~  105 (187)
                      ++....+.
T Consensus       175 pk~~~~~~  182 (311)
T KOG4205|consen  175 PKEVMQST  182 (311)
T ss_pred             chhhcccc
Confidence            88766544

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

Probab=99.27  E-value=1.7e-11  Score=96.81  Aligned_cols=79  Identities=30%  Similarity=0.484  Sum_probs=69.0

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh-CCCccCCeEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL-NQSVLEGRYIT   92 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l-~g~~i~g~~l~   92 (187)
                      ++...-++|||++|...+++.+|.+.|.+||+|..+.+...      +++|||+|.+.+.|+.|.+++ +...|+|..|.
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~  296 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLK  296 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEE
Confidence            34445689999999999999999999999999999998765      459999999999999988765 44578999999


Q ss_pred             EEeccC
Q 029810           93 VERSRR   98 (187)
Q Consensus        93 v~~a~~   98 (187)
                      |.|..+
T Consensus       297 i~Wg~~  302 (377)
T KOG0153|consen  297 IKWGRP  302 (377)
T ss_pred             EEeCCC
Confidence            999987

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

Probab=99.26  E-value=2.3e-11  Score=101.67  Aligned_cols=84  Identities=37%  Similarity=0.625  Sum_probs=76.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ..+.+|||.+|...|...+|+.||++||.|+-.+|+++..+--..+|+||++.+.++|.+||..||..+|.|+.|.|+.+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            34679999999999999999999999999999999988776666889999999999999999999999999999999998


Q ss_pred             cCCC
Q 029810           97 RRKR  100 (187)
Q Consensus        97 ~~~~  100 (187)
                      +..+
T Consensus       483 KNEp  486 (940)
T KOG4661|consen  483 KNEP  486 (940)
T ss_pred             ccCc
Confidence            7543

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

Probab=99.24  E-value=1e-11  Score=99.00  Aligned_cols=83  Identities=31%  Similarity=0.548  Sum_probs=75.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ..++|||++|+|+++++.|++.|.+||+|.+|.++.+..++.+.+|+||+|++.+.+.++|. ...+.|+++.|.++.+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            67899999999999999999999999999999999999999999999999999988888877 55678999999998887


Q ss_pred             CCCC
Q 029810           98 RKRP  101 (187)
Q Consensus        98 ~~~~  101 (187)
                      +...
T Consensus        84 ~r~~   87 (311)
T KOG4205|consen   84 SRED   87 (311)
T ss_pred             Cccc
Confidence            7654

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

Probab=99.21  E-value=3.8e-11  Score=95.61  Aligned_cols=83  Identities=23%  Similarity=0.472  Sum_probs=76.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ..-+.|||..+.++++++||+.+|+.||+|..|.+.....++.++||+||+|.+......||..||-..+.|+-|.|..+
T Consensus       208 k~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~  287 (544)
T KOG0124|consen  208 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  287 (544)
T ss_pred             HhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccc
Confidence            34589999999999999999999999999999999999999999999999999999999999999999999999999766


Q ss_pred             cCC
Q 029810           97 RRK   99 (187)
Q Consensus        97 ~~~   99 (187)
                      -..
T Consensus       288 vTP  290 (544)
T KOG0124|consen  288 VTP  290 (544)
T ss_pred             cCC
Confidence            543

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.20  E-value=5.1e-11  Score=101.57  Aligned_cols=78  Identities=33%  Similarity=0.477  Sum_probs=70.0

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCC---CcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTR---ISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~---~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ++|||.||++.++.++|..+|..+|.|..+.|.+.+...   .+.|||||+|.++++|+.|++.|+|+.|+|+.|.|+++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            449999999999999999999999999999887655321   23499999999999999999999999999999999998


Q ss_pred             c
Q 029810           97 R   97 (187)
Q Consensus        97 ~   97 (187)
                      .
T Consensus       596 ~  596 (725)
T KOG0110|consen  596 E  596 (725)
T ss_pred             c
Confidence            8

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=99.19  E-value=2.2e-10  Score=76.22  Aligned_cols=80  Identities=19%  Similarity=0.319  Sum_probs=71.0

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhc--CCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC----CeEEEE
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSK--EGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE----GRYITV   93 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~--~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~----g~~l~v   93 (187)
                      +||.|.|||...+.++|.+++..  .|....+.++.|..+..+.|||||.|.+++.|....+.++|..|.    .+.+.|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            79999999999999999998854  367778899999999999999999999999999999999999775    567889


Q ss_pred             EeccCC
Q 029810           94 ERSRRK   99 (187)
Q Consensus        94 ~~a~~~   99 (187)
                      .+|+-+
T Consensus        82 ~yAriQ   87 (97)
T PF04059_consen   82 SYARIQ   87 (97)
T ss_pred             ehhHhh
Confidence            988754

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=99.18  E-value=1.3e-10  Score=89.42  Aligned_cols=83  Identities=25%  Similarity=0.333  Sum_probs=74.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ....++|+|.||+..++++||+++|..||.++.+.|.++. .|.+.|.|-|.|...++|++||+.+++..++|..|+++.
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            3344889999999999999999999999999998888876 588899999999999999999999999999999999987


Q ss_pred             ccCC
Q 029810           96 SRRK   99 (187)
Q Consensus        96 a~~~   99 (187)
                      ..+.
T Consensus       159 i~~~  162 (243)
T KOG0533|consen  159 ISSP  162 (243)
T ss_pred             ecCc
Confidence            6643

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

Probab=99.17  E-value=9.9e-11  Score=96.05  Aligned_cols=74  Identities=38%  Similarity=0.513  Sum_probs=69.7

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccCC
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK   99 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   99 (187)
                      ..|||+   +++|+..|.++|+.+|+|..+.|+.+. |  +.|||||.|.++++|++||..||...|.|+.|.|-|+...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            468998   899999999999999999999999998 7  8999999999999999999999999999999999998744

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

Probab=99.17  E-value=3.9e-11  Score=92.02  Aligned_cols=84  Identities=25%  Similarity=0.441  Sum_probs=74.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC-ccCC--eEEEEE
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS-VLEG--RYITVE   94 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~-~i~g--~~l~v~   94 (187)
                      ...+|||+.|...-.|+|+..+|..||.|.+|.+....+ +.++|||||.|.+..+|++||..|||. ++-|  ..|.|+
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            568999999999999999999999999999999987764 788999999999999999999999997 4554  479999


Q ss_pred             eccCCCCC
Q 029810           95 RSRRKRPR  102 (187)
Q Consensus        95 ~a~~~~~~  102 (187)
                      ++...+++
T Consensus        97 ~ADTdkER  104 (371)
T KOG0146|consen   97 FADTDKER  104 (371)
T ss_pred             eccchHHH
Confidence            99876654

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

Probab=99.15  E-value=4.9e-11  Score=89.97  Aligned_cols=72  Identities=32%  Similarity=0.548  Sum_probs=66.9

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccCC
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK   99 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   99 (187)
                      ..|||++||+.+.+.+|.+||..||.|..|.|.        .+|+||+|++..+|+.||..||+.+|.+..+.|++++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            469999999999999999999999999999886        569999999999999999999999999999999998854

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.14  E-value=1.2e-10  Score=94.78  Aligned_cols=76  Identities=28%  Similarity=0.312  Sum_probs=67.9

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ....++|||.|||.++||+.|++-|..||.|..++|+.   .+++++  .|.|.++++|+.|+..|++..|+|+.|.|.+
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeee
Confidence            45568999999999999999999999999999998843   365565  9999999999999999999999999999986


Q ss_pred             c
Q 029810           96 S   96 (187)
Q Consensus        96 a   96 (187)
                      .
T Consensus       608 ~  608 (608)
T KOG4212|consen  608 F  608 (608)
T ss_pred             C
Confidence            3

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

Probab=99.13  E-value=5.7e-10  Score=83.58  Aligned_cols=87  Identities=21%  Similarity=0.331  Sum_probs=70.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccC---CeEE
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPR-TRISRGFAFVTMDGVEDAERCIKYLNQSVLE---GRYI   91 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~-~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~---g~~l   91 (187)
                      ...-.||||.+||.++...+|..+|..|--.+.+.|..... ....+.+|||+|.+.++|++|+.+|||..|+   ++.|
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            34468999999999999999999999987666655543322 2233579999999999999999999999885   7789


Q ss_pred             EEEeccCCCCC
Q 029810           92 TVERSRRKRPR  102 (187)
Q Consensus        92 ~v~~a~~~~~~  102 (187)
                      +|++++.....
T Consensus       111 hiElAKSNtK~  121 (284)
T KOG1457|consen  111 HIELAKSNTKR  121 (284)
T ss_pred             EeeehhcCccc
Confidence            99999876544

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.12  E-value=6.9e-11  Score=100.82  Aligned_cols=85  Identities=24%  Similarity=0.370  Sum_probs=77.5

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      .....+.|+|.|||..++..+|+++|..||.|..|.|+.....+.+.|||||+|-++.+|..|+.+|...-|.|+.|.++
T Consensus       609 ~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLE  688 (725)
T KOG0110|consen  609 KKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLE  688 (725)
T ss_pred             cccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhhee
Confidence            34447899999999999999999999999999999999776667778999999999999999999999889999999999


Q ss_pred             eccCC
Q 029810           95 RSRRK   99 (187)
Q Consensus        95 ~a~~~   99 (187)
                      |++..
T Consensus       689 wA~~d  693 (725)
T KOG0110|consen  689 WAKSD  693 (725)
T ss_pred             hhccc
Confidence            99854

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.09  E-value=5.3e-10  Score=88.46  Aligned_cols=83  Identities=25%  Similarity=0.347  Sum_probs=73.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeE--------EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVAS--------CFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE   87 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~--------~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~   87 (187)
                      ...++.|||.|||.++|.+++.++|++||.|..        |+|..+.. |+.+|=|+|.|...++++.||+.|++..|.
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCccccc
Confidence            445678999999999999999999999998764        66666654 889999999999999999999999999999


Q ss_pred             CeEEEEEeccCC
Q 029810           88 GRYITVERSRRK   99 (187)
Q Consensus        88 g~~l~v~~a~~~   99 (187)
                      |+.|.|+.|+-+
T Consensus       210 g~~~rVerAkfq  221 (382)
T KOG1548|consen  210 GKKLRVERAKFQ  221 (382)
T ss_pred             CcEEEEehhhhh
Confidence            999999988743

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

Probab=99.04  E-value=4.4e-10  Score=86.50  Aligned_cols=84  Identities=24%  Similarity=0.315  Sum_probs=78.5

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ...+...|||+|+...+|.++|...|+.||.|..+.|+.+..++++++|+||+|.+.+.++.|+. |++..|.+..|.|.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            45567899999999999999999999999999999999999999999999999999999999999 99999999999999


Q ss_pred             eccCC
Q 029810           95 RSRRK   99 (187)
Q Consensus        95 ~a~~~   99 (187)
                      +.+..
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            87755

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=99.01  E-value=1.3e-10  Score=86.78  Aligned_cols=81  Identities=19%  Similarity=0.139  Sum_probs=71.6

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ..+...||||+|+...++++.|.++|.+-|+|..|.|..++.. ..+ ||||+|.++..+.-|++.|||..+.+..|.|+
T Consensus         5 aae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~-~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~   82 (267)
T KOG4454|consen    5 AAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQ-EQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRT   82 (267)
T ss_pred             CcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccC-CCc-eeeeecccccchhhhhhhcccchhccchhhcc
Confidence            4556789999999999999999999999999999999887753 334 99999999999999999999999999888887


Q ss_pred             ecc
Q 029810           95 RSR   97 (187)
Q Consensus        95 ~a~   97 (187)
                      +-.
T Consensus        83 ~r~   85 (267)
T KOG4454|consen   83 LRC   85 (267)
T ss_pred             ccc
Confidence            643

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.95  E-value=2.8e-09  Score=84.83  Aligned_cols=85  Identities=21%  Similarity=0.300  Sum_probs=77.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeE--------EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVAS--------CFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE   87 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~--------~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~   87 (187)
                      .....+|||.+||..+++++|.++|.+++.|..        |+|-++++|++.++-|.|.|.+...|++||..++++.|.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            556789999999999999999999999998753        677788899999999999999999999999999999999


Q ss_pred             CeEEEEEeccCCC
Q 029810           88 GRYITVERSRRKR  100 (187)
Q Consensus        88 g~~l~v~~a~~~~  100 (187)
                      +.+|+|.+|..+.
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999998887554

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

Probab=98.90  E-value=4.2e-09  Score=90.14  Aligned_cols=83  Identities=25%  Similarity=0.320  Sum_probs=73.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecC---CCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEP---RTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~---~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .+.+++|||+||++.++++.|...|..||+|..|+|+...   +......|+||.|-+..+|++|++.|+|..|.+..++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            5667899999999999999999999999999999988544   2333456899999999999999999999999999999


Q ss_pred             EEeccC
Q 029810           93 VERSRR   98 (187)
Q Consensus        93 v~~a~~   98 (187)
                      +.|+++
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            999864

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

Probab=98.87  E-value=1.7e-09  Score=90.32  Aligned_cols=72  Identities=31%  Similarity=0.410  Sum_probs=64.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .-+..+|+|-|||..+++++|..+|+.||+|..|.....     ..+.+||+|.+..+|++|+++|++..|.|+.|.
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            345679999999999999999999999999999766443     367999999999999999999999999999887

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

Probab=98.87  E-value=1.1e-08  Score=84.47  Aligned_cols=81  Identities=25%  Similarity=0.379  Sum_probs=67.0

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      +......|-|.+|||++|++||.+||+.++ |..+.+  ...+++..|-|||+|++++++++|++ .+...+..+-|+|-
T Consensus         6 e~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~--~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf   81 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEI--PRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVF   81 (510)
T ss_pred             CCCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEE--eccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEE
Confidence            345567788899999999999999999985 566444  44568889999999999999999999 67778888889997


Q ss_pred             eccCC
Q 029810           95 RSRRK   99 (187)
Q Consensus        95 ~a~~~   99 (187)
                      .+...
T Consensus        82 ~~~~~   86 (510)
T KOG4211|consen   82 TAGGA   86 (510)
T ss_pred             ccCCc
Confidence            77543

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

Probab=98.83  E-value=9.6e-09  Score=77.62  Aligned_cols=74  Identities=36%  Similarity=0.486  Sum_probs=65.4

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ...+....+.|+|.+|+..+.+++|.+.|.++|.+..+.+.        .+++||+|++.++|..||..|++..|.++.|
T Consensus        92 ~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~--------~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l  163 (216)
T KOG0106|consen   92 YRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDAR--------RNFAFVEFSEQEDAKRALEKLDGKKLNGRRI  163 (216)
T ss_pred             cCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhhh--------ccccceeehhhhhhhhcchhccchhhcCcee
Confidence            34556677899999999999999999999999999555442        5589999999999999999999999999999


Q ss_pred             EE
Q 029810           92 TV   93 (187)
Q Consensus        92 ~v   93 (187)
                      ++
T Consensus       164 ~~  165 (216)
T KOG0106|consen  164 SV  165 (216)
T ss_pred             ee
Confidence            99

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.82  E-value=2.9e-08  Score=80.35  Aligned_cols=81  Identities=22%  Similarity=0.278  Sum_probs=72.4

Q ss_pred             CCeEEEcCCCC-CCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           19 GNTLYVTGLST-RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        19 ~~~l~V~~Lp~-~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      +..|.|.||.. .+|.+.|..+|..||+|..|+|+.++     +.-|+|.|.+...|+.|+++|+|+.|.|+.|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk-----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK-----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC-----CcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            67888999987 68999999999999999999999876     3479999999999999999999999999999999998


Q ss_pred             CCCCCCC
Q 029810           98 RKRPRTP  104 (187)
Q Consensus        98 ~~~~~~~  104 (187)
                      .....-+
T Consensus       372 H~~vqlp  378 (492)
T KOG1190|consen  372 HTNVQLP  378 (492)
T ss_pred             CccccCC
Confidence            7655433

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.76  E-value=1.1e-08  Score=78.03  Aligned_cols=85  Identities=21%  Similarity=0.332  Sum_probs=77.1

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      +-.+....||.+.|..+++.+.|-..|.+|-......++.+..|++++||+||.|.+++++..|+..|+|.-++...|++
T Consensus       185 ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpikl  264 (290)
T KOG0226|consen  185 EWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKL  264 (290)
T ss_pred             cCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHh
Confidence            34566789999999999999999999999998888999999999999999999999999999999999999999998887


Q ss_pred             EeccC
Q 029810           94 ERSRR   98 (187)
Q Consensus        94 ~~a~~   98 (187)
                      ..+..
T Consensus       265 RkS~w  269 (290)
T KOG0226|consen  265 RKSEW  269 (290)
T ss_pred             hhhhH
Confidence            65543

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

Probab=98.73  E-value=1.3e-08  Score=85.49  Aligned_cols=90  Identities=24%  Similarity=0.327  Sum_probs=81.6

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ..........|||++||..+++.++++++..||.+....++.+..++-+++|||.+|.+......|+..|||..+.+++|
T Consensus       282 ~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~l  361 (500)
T KOG0120|consen  282 STDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKL  361 (500)
T ss_pred             ccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCcee
Confidence            34445667899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeccCCCC
Q 029810           92 TVERSRRKRP  101 (187)
Q Consensus        92 ~v~~a~~~~~  101 (187)
                      .|+.|.....
T Consensus       362 vvq~A~~g~~  371 (500)
T KOG0120|consen  362 VVQRAIVGAS  371 (500)
T ss_pred             Eeehhhccch
Confidence            9998875443

>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=98.70  E-value=4.7e-08  Score=66.39  Aligned_cols=72  Identities=24%  Similarity=0.369  Sum_probs=45.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC-----ccCCeEEEE
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS-----VLEGRYITV   93 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~-----~i~g~~l~v   93 (187)
                      ++.|+|.+++..++.++|+++|.+||.|..|.+....      ..|||.|.+.+.|++|++++...     .|.+..+.+
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            3678999999999999999999999999999887543      37999999999999999876543     567777777


Q ss_pred             Eec
Q 029810           94 ERS   96 (187)
Q Consensus        94 ~~a   96 (187)
                      +..
T Consensus        75 ~vL   77 (105)
T PF08777_consen   75 EVL   77 (105)
T ss_dssp             E--
T ss_pred             EEC
Confidence            654

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

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

Probab=98.66  E-value=1.9e-07  Score=59.80  Aligned_cols=69  Identities=30%  Similarity=0.308  Sum_probs=47.6

Q ss_pred             CeEEEcCCCCCCcHHH----HHHHhhcCC-ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           20 NTLYVTGLSTRVTERD----LEKHFSKEG-KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~----L~~~f~~~G-~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      +.|+|.|||.+.+...    |++++.-+| .|..|.          .+.|+|.|.+.+.|+.|.+.|+|..+.|..|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            4689999999888765    566666776 566552          3589999999999999999999999999999999


Q ss_pred             eccC
Q 029810           95 RSRR   98 (187)
Q Consensus        95 ~a~~   98 (187)
                      +...
T Consensus        73 ~~~~   76 (90)
T PF11608_consen   73 FSPK   76 (90)
T ss_dssp             SS--
T ss_pred             EcCC
Confidence            9753

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=98.66  E-value=7.7e-08  Score=79.53  Aligned_cols=80  Identities=26%  Similarity=0.322  Sum_probs=66.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      .....|-|.+||+.||++||.+||+..-.|....++.....+.+.|.|||.|++.+.|++||. -|...|.-+-|+|-.+
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFRS  179 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeehh
Confidence            466889999999999999999999988766663433334457788999999999999999998 5677888888988765


Q ss_pred             c
Q 029810           97 R   97 (187)
Q Consensus        97 ~   97 (187)
                      .
T Consensus       180 s  180 (510)
T KOG4211|consen  180 S  180 (510)
T ss_pred             H
Confidence            4

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.62  E-value=1.1e-07  Score=75.69  Aligned_cols=75  Identities=21%  Similarity=0.298  Sum_probs=67.5

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCC--ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEG--KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G--~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ..+||+||-|++|++||.+.+...|  .|.+++++.+..+|+++|||+|...+.+..++.|+.|..++|.|+.-.|.
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            5789999999999999999998777  57778888888999999999999999999999999999999999866554

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

Probab=98.61  E-value=4.5e-08  Score=73.56  Aligned_cols=68  Identities=19%  Similarity=0.290  Sum_probs=55.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE   87 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~   87 (187)
                      .....+|||.||..+++|++|+.+|+.|-....++|...  .|  ...|||+|++.+.|..||..|+|..|.
T Consensus       207 ~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~g--~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  207 ARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--GG--MPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             chhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CC--cceEeecHHHHHHHHHHHHHhhcceec
Confidence            345679999999999999999999999986655555422  22  458999999999999999999987653

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

Probab=98.55  E-value=3.8e-07  Score=68.68  Aligned_cols=78  Identities=17%  Similarity=0.223  Sum_probs=68.3

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-CeEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE-GRYITV   93 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~-g~~l~v   93 (187)
                      ...++.++|+.|||.+++.+.|..+|.+|.....|.++...     .+.|||+|.+...|..|...|++..|- ...+.|
T Consensus       142 ~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i  216 (221)
T KOG4206|consen  142 MAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQI  216 (221)
T ss_pred             CCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEe
Confidence            35678899999999999999999999999988888887543     569999999999999999999998876 778888


Q ss_pred             Eecc
Q 029810           94 ERSR   97 (187)
Q Consensus        94 ~~a~   97 (187)
                      .+++
T Consensus       217 ~~a~  220 (221)
T KOG4206|consen  217 TFAK  220 (221)
T ss_pred             cccC
Confidence            8764

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=98.45  E-value=9e-08  Score=80.03  Aligned_cols=85  Identities=27%  Similarity=0.368  Sum_probs=76.6

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      +....+||+--|+..++.-+|.+||+.+|.|..|.|+.|..++.++|.|||+|.+.+.+..||. |.|..+.|.+|.|+.
T Consensus       176 ERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~  254 (549)
T KOG0147|consen  176 ERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQL  254 (549)
T ss_pred             HHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEecc
Confidence            3445788888889999999999999999999999999999999999999999999999999996 999999999999988


Q ss_pred             ccCCCC
Q 029810           96 SRRKRP  101 (187)
Q Consensus        96 a~~~~~  101 (187)
                      ....+.
T Consensus       255 sEaekn  260 (549)
T KOG0147|consen  255 SEAEKN  260 (549)
T ss_pred             cHHHHH
Confidence            765443

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

Probab=98.43  E-value=1.9e-06  Score=69.36  Aligned_cols=82  Identities=27%  Similarity=0.323  Sum_probs=72.5

Q ss_pred             CCCCCCCeEEEcCCCC-CCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           14 ETGNPGNTLYVTGLST-RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~-~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      ....++..++|.+|.. .+.-+.|..+|..||.|..|++++.+     .+.|.|++.+..+.+.|+..||+..+-|.+|.
T Consensus       282 ~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~  356 (494)
T KOG1456|consen  282 GGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLN  356 (494)
T ss_pred             CCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEE
Confidence            4456789999999988 56678899999999999999998765     57899999999999999999999999999999


Q ss_pred             EEeccCCC
Q 029810           93 VERSRRKR  100 (187)
Q Consensus        93 v~~a~~~~  100 (187)
                      |.+++...
T Consensus       357 v~~SkQ~~  364 (494)
T KOG1456|consen  357 VCVSKQNF  364 (494)
T ss_pred             Eeeccccc
Confidence            99988543

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.40  E-value=3.6e-07  Score=72.66  Aligned_cols=83  Identities=24%  Similarity=0.456  Sum_probs=74.2

Q ss_pred             CCCeEE-EcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           18 PGNTLY-VTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        18 ~~~~l~-V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ...++| |.+|+..+++++|+..|..+|.|..+.+..+..++..++||||.|.+...+..++.. +...|.+..+.|...
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEED  261 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccC
Confidence            344555 999999999999999999999999999999999999999999999999999999886 788899999999988


Q ss_pred             cCCCC
Q 029810           97 RRKRP  101 (187)
Q Consensus        97 ~~~~~  101 (187)
                      .+...
T Consensus       262 ~~~~~  266 (285)
T KOG4210|consen  262 EPRPK  266 (285)
T ss_pred             CCCcc
Confidence            76543

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

Probab=98.32  E-value=2.9e-06  Score=71.56  Aligned_cols=80  Identities=24%  Similarity=0.390  Sum_probs=65.7

Q ss_pred             CCCCeEEEcCCCCCCcH------HHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-Ce
Q 029810           17 NPGNTLYVTGLSTRVTE------RDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE-GR   89 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~------~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~-g~   89 (187)
                      .-.+.|+|.|+|.--..      .-|..+|+++|+|..+.++.+..+| .+||.|++|++..+|+.|++.|||+.|+ .+
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknH  134 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            55678999999873322      3477889999999999999887766 7999999999999999999999999874 67


Q ss_pred             EEEEEecc
Q 029810           90 YITVERSR   97 (187)
Q Consensus        90 ~l~v~~a~   97 (187)
                      ++.|..-+
T Consensus       135 tf~v~~f~  142 (698)
T KOG2314|consen  135 TFFVRLFK  142 (698)
T ss_pred             eEEeehhh
Confidence            77776543

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

Probab=98.23  E-value=8e-07  Score=68.07  Aligned_cols=73  Identities=18%  Similarity=0.260  Sum_probs=61.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCC--------CCcc----eEEEEEecCHHHHHHHHHHhCCCc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRT--------RISR----GFAFVTMDGVEDAERCIKYLNQSV   85 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~--------~~~~----g~afV~f~~~~~a~~ai~~l~g~~   85 (187)
                      ..-.|||++||+.+...-|+++|.+||+|-.|.|.....+        +.+.    --++|+|.+...|..+...||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            4568999999999999999999999999999988755433        2222    237899999999999999999999


Q ss_pred             cCCeE
Q 029810           86 LEGRY   90 (187)
Q Consensus        86 i~g~~   90 (187)
                      |.|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99874

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.23  E-value=3.7e-06  Score=66.96  Aligned_cols=80  Identities=25%  Similarity=0.485  Sum_probs=62.4

Q ss_pred             CCeEEEcCCCCCCcHHH----H--HHHhhcCCceeEEEEeecCCCC-CcceE--EEEEecCHHHHHHHHHHhCCCccCCe
Q 029810           19 GNTLYVTGLSTRVTERD----L--EKHFSKEGKVASCFLVVEPRTR-ISRGF--AFVTMDGVEDAERCIKYLNQSVLEGR   89 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~----L--~~~f~~~G~i~~~~i~~~~~~~-~~~g~--afV~f~~~~~a~~ai~~l~g~~i~g~   89 (187)
                      -+-|||-+|++.+..++    |  .++|.+||.|..|.|.+..... ...+.  .||+|.+.++|..||.+.+|..++|+
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            35688999999776665    3  6789999999998886433111 11122  49999999999999999999999999


Q ss_pred             EEEEEeccC
Q 029810           90 YITVERSRR   98 (187)
Q Consensus        90 ~l~v~~a~~   98 (187)
                      .|+..+...
T Consensus       194 ~lkatYGTT  202 (480)
T COG5175         194 VLKATYGTT  202 (480)
T ss_pred             eEeeecCch
Confidence            999988764

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

Probab=98.19  E-value=2.1e-05  Score=57.83  Aligned_cols=65  Identities=20%  Similarity=0.290  Sum_probs=57.8

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE   87 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~   87 (187)
                      ......|.|.+||+..+|+||++.+.+-|.|+...+..+       +++.|+|...++++-||.+|+...+.
T Consensus       112 rrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  112 RRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             cccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            344578999999999999999999999999999998765       38999999999999999999887654

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.19  E-value=5.9e-06  Score=71.25  Aligned_cols=76  Identities=16%  Similarity=0.235  Sum_probs=66.8

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      +.|-+.|+|++++-+||.+||..|-.+-.-.++.-.+.|...|-|.|.|++.++|..|...|++..|..++|.+.+
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            3777899999999999999999998776655555556789999999999999999999999999999999988764

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

Probab=98.18  E-value=1.3e-05  Score=64.59  Aligned_cols=83  Identities=27%  Similarity=0.296  Sum_probs=66.9

Q ss_pred             CCCCCCCCeEEEcCCCC--CCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-C-
Q 029810           13 TETGNPGNTLYVTGLST--RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE-G-   88 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~--~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~-g-   88 (187)
                      .+...++..|.+.=|.+  .+|.+.|..+....|+|..|.|++..     ---|.|||++.+.|++|.++|||..|. | 
T Consensus       114 ~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkn-----gVQAmVEFdsv~~AqrAk~alNGADIYsGC  188 (494)
T KOG1456|consen  114 DESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKN-----GVQAMVEFDSVEVAQRAKAALNGADIYSGC  188 (494)
T ss_pred             CCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEecc-----ceeeEEeechhHHHHHHHhhcccccccccc
Confidence            45556666666665544  78999999999999999999888652     226999999999999999999999875 3 


Q ss_pred             eEEEEEeccCCC
Q 029810           89 RYITVERSRRKR  100 (187)
Q Consensus        89 ~~l~v~~a~~~~  100 (187)
                      .+|+|++|++.+
T Consensus       189 CTLKIeyAkP~r  200 (494)
T KOG1456|consen  189 CTLKIEYAKPTR  200 (494)
T ss_pred             eeEEEEecCcce
Confidence            489999999754

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

Probab=98.15  E-value=3.7e-06  Score=67.93  Aligned_cols=80  Identities=19%  Similarity=0.287  Sum_probs=67.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCc-eeE--EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGK-VAS--CFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~-i~~--~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      .....|-+.+||...+.+||.+||..|.. |..  |+|+.+. .|...|-|||+|.+.++|.+|+...+++....+.|+|
T Consensus       278 ~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEv  356 (508)
T KOG1365|consen  278 RSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEV  356 (508)
T ss_pred             CCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEE
Confidence            33678899999999999999999999874 444  7777775 4888899999999999999999999988888888888


Q ss_pred             Eecc
Q 029810           94 ERSR   97 (187)
Q Consensus        94 ~~a~   97 (187)
                      -.+.
T Consensus       357 fp~S  360 (508)
T KOG1365|consen  357 FPCS  360 (508)
T ss_pred             eecc
Confidence            6554

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

Probab=98.13  E-value=9.3e-06  Score=67.86  Aligned_cols=69  Identities=20%  Similarity=0.292  Sum_probs=63.8

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhh-cCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHH
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFS-KEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY   80 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~-~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~   80 (187)
                      .+.+.++..||||++||..++.++|..+|. -||.|..+-|-+|++-+.++|-|=|+|.+..+-.+||.+
T Consensus       363 ~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  363 HNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            456778899999999999999999999998 899999999999988899999999999999999999883

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

Probab=98.10  E-value=8.5e-06  Score=48.29  Aligned_cols=52  Identities=17%  Similarity=0.443  Sum_probs=41.9

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHH
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI   78 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai   78 (187)
                      +.|-|.+.+....+. |...|..||+|..+.+...      ..+.+|.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            567889999877654 5558889999999888621      459999999999999985

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=98.08  E-value=6.9e-06  Score=67.18  Aligned_cols=75  Identities=23%  Similarity=0.302  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeec---CC--CCC--------cceEEEEEecCHHHHHH
Q 029810           10 RGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVE---PR--TRI--------SRGFAFVTMDGVEDAER   76 (187)
Q Consensus        10 ~~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~---~~--~~~--------~~g~afV~f~~~~~a~~   76 (187)
                      ..-..+..+..+|.+.|||.+-.-+.|.++|..+|.|+.|.|+..   ..  .+.        .+-+|||+|+..+.|.+
T Consensus       222 p~~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~K  301 (484)
T KOG1855|consen  222 PEFDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARK  301 (484)
T ss_pred             CCccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHH
Confidence            334455668899999999998888999999999999999999865   21  111        14579999999999999


Q ss_pred             HHHHhCCC
Q 029810           77 CIKYLNQS   84 (187)
Q Consensus        77 ai~~l~g~   84 (187)
                      |.+.|+..
T Consensus       302 A~e~~~~e  309 (484)
T KOG1855|consen  302 ARELLNPE  309 (484)
T ss_pred             HHHhhchh
Confidence            99988644

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.06  E-value=1.3e-05  Score=65.40  Aligned_cols=78  Identities=24%  Similarity=0.382  Sum_probs=64.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe-EEEEEe
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGR-YITVER   95 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~-~l~v~~   95 (187)
                      ++..+|.+.|||..++|++|+++|..-|...+......    +...+|++.+++.|+|..|+-.+|.+.+.+. -|.|.+
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~----kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSF  487 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQ----KDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSF  487 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeeecC----CCcceeecccCChhHhhhhccccccccCCCCceEEEEe
Confidence            56779999999999999999999998886654433322    2245999999999999999999999988655 899999


Q ss_pred             ccC
Q 029810           96 SRR   98 (187)
Q Consensus        96 a~~   98 (187)
                      ++.
T Consensus       488 Sks  490 (492)
T KOG1190|consen  488 SKS  490 (492)
T ss_pred             ecc
Confidence            874

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

Probab=98.05  E-value=1.4e-05  Score=67.43  Aligned_cols=64  Identities=20%  Similarity=0.235  Sum_probs=53.0

Q ss_pred             HHHHHHhhcCCceeEEEEeecC---CCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           34 RDLEKHFSKEGKVASCFLVVEP---RTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        34 ~~L~~~f~~~G~i~~~~i~~~~---~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ++|+..+.+||.|..|.|+.+.   ...-..|..||+|++.++++.|+++|+|.+|.+++|.+.|..
T Consensus       424 Edvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  424 EDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             HHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            3566677899999999998662   222335789999999999999999999999999999988754

>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=98.04  E-value=2.7e-05  Score=52.23  Aligned_cols=78  Identities=18%  Similarity=0.325  Sum_probs=51.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEE-EeecC------CCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCF-LVVEP------RTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY   90 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~-i~~~~------~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~   90 (187)
                      ..+-|.|-+.|+.. ...|.+.|++||+|.+.. +..+.      ..-....|..|.|+++.+|++||. .||..|.|..
T Consensus         5 ~~~wVtVFGfp~~~-~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPSA-SNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GGG-HHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE
T ss_pred             CCeEEEEEccCHHH-HHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE
Confidence            45668888999884 466888999999998764 10000      001124599999999999999999 8999998864


Q ss_pred             -EEEEecc
Q 029810           91 -ITVERSR   97 (187)
Q Consensus        91 -l~v~~a~   97 (187)
                       |-|.+.+
T Consensus        83 mvGV~~~~   90 (100)
T PF05172_consen   83 MVGVKPCD   90 (100)
T ss_dssp             EEEEEE-H
T ss_pred             EEEEEEcH
Confidence             4566654

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.

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

Probab=98.00  E-value=4.1e-05  Score=54.48  Aligned_cols=77  Identities=21%  Similarity=0.293  Sum_probs=52.6

Q ss_pred             CCCCCCeEEEcCCC----C--CCcH---HHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCc
Q 029810           15 TGNPGNTLYVTGLS----T--RVTE---RDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSV   85 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp----~--~~t~---~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~   85 (187)
                      ..++..||.|.=+.    .  ...+   .+|.+.|..||++.-+.+..+        .-+|+|.+-+.|.+|+. |+|.+
T Consensus        23 ~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~   93 (146)
T PF08952_consen   23 QGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQ   93 (146)
T ss_dssp             ---TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSE
T ss_pred             cCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcE
Confidence            34556677665444    1  1222   367888999999988887633        58999999999999999 99999


Q ss_pred             cCCeEEEEEeccCCC
Q 029810           86 LEGRYITVERSRRKR  100 (187)
Q Consensus        86 i~g~~l~v~~a~~~~  100 (187)
                      |+|+.|+|.+..+..
T Consensus        94 v~g~~l~i~LKtpdW  108 (146)
T PF08952_consen   94 VNGRTLKIRLKTPDW  108 (146)
T ss_dssp             ETTEEEEEEE-----
T ss_pred             ECCEEEEEEeCCccH
Confidence            999999999877643

; PDB: 1UFW_A 2DNR_A.

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=97.95  E-value=4.1e-05  Score=61.18  Aligned_cols=79  Identities=23%  Similarity=0.360  Sum_probs=63.0

Q ss_pred             CCCCeEEEcCCCC----CCc-------HHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCc
Q 029810           17 NPGNTLYVTGLST----RVT-------ERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSV   85 (187)
Q Consensus        17 ~~~~~l~V~~Lp~----~~t-------~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~   85 (187)
                      ....+|.|.||=.    ..+       +++|.+...+||.|..|.|.-    .++.|.+-|.|.+.++|+.||+.|+|..
T Consensus       263 r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d----~hPdGvvtV~f~n~eeA~~ciq~m~GR~  338 (382)
T KOG1548|consen  263 RADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYD----RHPDGVVTVSFRNNEEADQCIQTMDGRW  338 (382)
T ss_pred             cCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEec----cCCCceeEEEeCChHHHHHHHHHhcCee
Confidence            3457888888732    222       356777789999999998863    3347899999999999999999999999


Q ss_pred             cCCeEEEEEeccCC
Q 029810           86 LEGRYITVERSRRK   99 (187)
Q Consensus        86 i~g~~l~v~~a~~~   99 (187)
                      |.|++|+..+...+
T Consensus       339 fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  339 FDGRQLTASIWDGK  352 (382)
T ss_pred             ecceEEEEEEeCCc
Confidence            99999999876543

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

Probab=97.93  E-value=4.5e-06  Score=64.06  Aligned_cols=64  Identities=25%  Similarity=0.258  Sum_probs=52.5

Q ss_pred             HHHHHHhh-cCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccC
Q 029810           34 RDLEKHFS-KEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR   98 (187)
Q Consensus        34 ~~L~~~f~-~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   98 (187)
                      ++|...|+ +||+|.++.|..+-. -.-.|-++|.|..+++|++|+..||+..|.|++|.+++...
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~-~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLG-DHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccc-hhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            45555565 999999987765432 34467899999999999999999999999999999998753

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

Probab=97.85  E-value=6e-05  Score=63.12  Aligned_cols=67  Identities=15%  Similarity=0.279  Sum_probs=51.2

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecC---CCCCcce---EEEEEecCHHHHHHHHHHhC
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEP---RTRISRG---FAFVTMDGVEDAERCIKYLN   82 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~---~~~~~~g---~afV~f~~~~~a~~ai~~l~   82 (187)
                      ...-..+|||++||++++|+.|...|..||.|. |.++...   .--.++|   |+|+.|+++..+.+.|.++.
T Consensus       255 ~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~  327 (520)
T KOG0129|consen  255 SPRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS  327 (520)
T ss_pred             ccccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh
Confidence            345568999999999999999999999999865 4554211   1122356   99999999999888777654

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

Probab=97.81  E-value=2.1e-05  Score=66.89  Aligned_cols=77  Identities=18%  Similarity=0.308  Sum_probs=63.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhh-cCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc---CCeEE
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFS-KEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVL---EGRYI   91 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~-~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i---~g~~l   91 (187)
                      ....+.|+|.||-.-+|.-+|++++. ..|.|..++|  |.    .+-.|||.|.+.++|.+.+.+|||..|   +.+.|
T Consensus       441 ~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--Dk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L  514 (718)
T KOG2416|consen  441 KEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--DK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHL  514 (718)
T ss_pred             CCccceEeeecccccchHHHHHHHHhhccCchHHHHH--HH----hhcceeEecccHHHHHHHHHHHhccccCCCCCcee
Confidence            45679999999999999999999998 4556666633  22    256899999999999999999999876   56788


Q ss_pred             EEEeccC
Q 029810           92 TVERSRR   98 (187)
Q Consensus        92 ~v~~a~~   98 (187)
                      .|.|...
T Consensus       515 ~adf~~~  521 (718)
T KOG2416|consen  515 IADFVRA  521 (718)
T ss_pred             Eeeecch
Confidence            8888754

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.67  E-value=5.5e-05  Score=67.09  Aligned_cols=78  Identities=17%  Similarity=0.269  Sum_probs=68.5

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--eEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG--RYIT   92 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g--~~l~   92 (187)
                      ...+++.+||++|..++....|..+|..||.|..|.+-..      .-||+|.|++...|++|++.|.+..|.+  +.|.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg------q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~r  524 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG------QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLR  524 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC------CcceeeecccCccchhhHHHHhcCcCCCCCcccc
Confidence            4567789999999999999999999999999999887433      4599999999999999999999999875  5688


Q ss_pred             EEeccC
Q 029810           93 VERSRR   98 (187)
Q Consensus        93 v~~a~~   98 (187)
                      |.++..
T Consensus       525 vdla~~  530 (975)
T KOG0112|consen  525 VDLASP  530 (975)
T ss_pred             cccccC
Confidence            888764

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

Probab=97.63  E-value=0.0004  Score=42.24  Aligned_cols=55  Identities=16%  Similarity=0.195  Sum_probs=44.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcC---CceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKE---GKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL   81 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~---G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l   81 (187)
                      ..+|+|.||. +++.++|+.+|..|   .....|.++-|.       -|-|.|.+.+.|.+||.+|
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            4689999985 57778999999988   235678887664       5899999999999999865

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

Probab=97.63  E-value=0.00043  Score=44.46  Aligned_cols=57  Identities=18%  Similarity=0.275  Sum_probs=42.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQ   83 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g   83 (187)
                      -....+|+ +|.++...||.++|+.||.|. |.++.+       .-|||...+.+.|..|+..+..
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-------TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-------TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-------TEEEEEECCCHHHHHHHHHHTT
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-------CcEEEEeecHHHHHHHHHHhcc
Confidence            34566676 999999999999999999876 444433       2699999999999999998764

; 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.

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.55  E-value=0.00028  Score=55.41  Aligned_cols=65  Identities=23%  Similarity=0.279  Sum_probs=51.9

Q ss_pred             HHHHHHHhhcCCceeEEEEeecCCCCCc-ceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           33 ERDLEKHFSKEGKVASCFLVVEPRTRIS-RGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        33 ~~~L~~~f~~~G~i~~~~i~~~~~~~~~-~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ++++++.+++||.|..|.|+.....-.. .--.||+|+..++|.+|+-.|||..|.|+.+...|-.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            3568889999999999988766421111 1247999999999999999999999999999887754

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.42  E-value=0.00012  Score=63.58  Aligned_cols=83  Identities=19%  Similarity=0.132  Sum_probs=66.3

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      -+...+..|||..||..+++.++.++|...-.|++..++..--++...+.|||+|..++++.+|+..-+.+-+..+.|.|
T Consensus       429 ~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv  508 (944)
T KOG4307|consen  429 FPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRV  508 (944)
T ss_pred             CCCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEe
Confidence            45677899999999999999999999998888877433333345667789999999988888888766677777788888


Q ss_pred             Eec
Q 029810           94 ERS   96 (187)
Q Consensus        94 ~~a   96 (187)
                      .-.
T Consensus       509 ~si  511 (944)
T KOG4307|consen  509 DSI  511 (944)
T ss_pred             ech
Confidence            654

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

Probab=97.41  E-value=0.00022  Score=58.07  Aligned_cols=74  Identities=16%  Similarity=0.237  Sum_probs=57.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCC---CCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPR---TRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~---~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ..|.|.||.+.++.+++..||.-.|+|..+.|+.+..   .....-.|||-|.+...+..|.. |.+..|-+..|.|-
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~   84 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVR   84 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEE
Confidence            3899999999999999999999999999998875321   11223479999999998888877 66665555555554

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

Probab=97.41  E-value=0.00013  Score=59.91  Aligned_cols=76  Identities=34%  Similarity=0.459  Sum_probs=59.4

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC-ccCCeEEEEEeccC
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS-VLEGRYITVERSRR   98 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~-~i~g~~l~v~~a~~   98 (187)
                      +.+||+||.+.++..+|..+|..--.-..-.++..      .+|+||.+.+...|.+|++.++++ ++.|+.+.|+.+-+
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 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            47899999999999999999975421111111111      469999999999999999999987 68999999998766


Q ss_pred             CCC
Q 029810           99 KRP  101 (187)
Q Consensus        99 ~~~  101 (187)
                      +..
T Consensus        76 kkq   78 (584)
T KOG2193|consen   76 KKQ   78 (584)
T ss_pred             HHH
Confidence            543

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

Probab=97.39  E-value=0.00014  Score=64.25  Aligned_cols=80  Identities=23%  Similarity=0.180  Sum_probs=71.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccC
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR   98 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   98 (187)
                      ...|||.|+|+..|.++|+.++..+|.+..+.++..+ .|+++|.|||.|.++.+|..++...+...+....+.|+.+.+
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~vsnp  814 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            4678999999999999999999999999999877665 488899999999999999999998888888888888888766


Q ss_pred             C
Q 029810           99 K   99 (187)
Q Consensus        99 ~   99 (187)
                      .
T Consensus       815 ~  815 (881)
T KOG0128|consen  815 E  815 (881)
T ss_pred             c
Confidence            3

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

Probab=97.33  E-value=0.00094  Score=54.38  Aligned_cols=75  Identities=24%  Similarity=0.305  Sum_probs=53.0

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcC---C-ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKE---G-KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~---G-~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      -.|-+.+||.++++.++.+||.+-   + .+..|-++.. ..++..|-|||.|+.+++|+.||.+ |...|.-+.|++-.
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFR  239 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFR  239 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHH
Confidence            455668999999999999999632   2 2333433333 3477889999999999999999983 44455555555543


Q ss_pred             c
Q 029810           96 S   96 (187)
Q Consensus        96 a   96 (187)
                      +
T Consensus       240 S  240 (508)
T KOG1365|consen  240 S  240 (508)
T ss_pred             H
Confidence            3

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

Probab=97.33  E-value=0.00043  Score=58.59  Aligned_cols=57  Identities=21%  Similarity=0.357  Sum_probs=46.7

Q ss_pred             CCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC----CeEEEEEeccCC
Q 029810           43 EGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE----GRYITVERSRRK   99 (187)
Q Consensus        43 ~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~----g~~l~v~~a~~~   99 (187)
                      .|.-..+.++.|..+.++.|||||.|.+.+++..+.+++||+.|.    .+.+.|.||+-+
T Consensus       413 ~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYArIQ  473 (549)
T KOG4660|consen  413 KGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYARIQ  473 (549)
T ss_pred             cCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhhhh
Confidence            455566778888888899999999999999999999999998653    456678887654

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

Probab=97.18  E-value=2.1e-05  Score=69.29  Aligned_cols=68  Identities=24%  Similarity=0.430  Sum_probs=58.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE   87 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~   87 (187)
                      .++||.||+..+.+.+|...|..++.|..+.+.....++..+|+|||+|..+++|.+||...+...+.
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            57899999999999999999999998888777655667888999999999999999999865554444

>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=97.14  E-value=0.00093  Score=49.60  Aligned_cols=84  Identities=13%  Similarity=0.076  Sum_probs=51.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhc-CCce---eEEEEeecCC--CCCcceEEEEEecCHHHHHHHHHHhCCCccCC-
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSK-EGKV---ASCFLVVEPR--TRISRGFAFVTMDGVEDAERCIKYLNQSVLEG-   88 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~-~G~i---~~~~i~~~~~--~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g-   88 (187)
                      ....++|.|.+||+.+|++++.+.+.. ++..   ..+.-.....  ......-|||.|.+.+++...+..++|+.|.+ 
T Consensus         4 ~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~   83 (176)
T PF03467_consen    4 EKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDS   83 (176)
T ss_dssp             -----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-T
T ss_pred             cccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECC
Confidence            345679999999999999999887776 6654   2332112211  11123469999999999999999999986632 


Q ss_pred             ----eEEEEEeccCC
Q 029810           89 ----RYITVERSRRK   99 (187)
Q Consensus        89 ----~~l~v~~a~~~   99 (187)
                          ....|++|.-+
T Consensus        84 kg~~~~~~VE~Apyq   98 (176)
T PF03467_consen   84 KGNEYPAVVEFAPYQ   98 (176)
T ss_dssp             TS-EEEEEEEE-SS-
T ss_pred             CCCCcceeEEEcchh
Confidence                24567777643

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.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=97.04  E-value=0.0054  Score=43.48  Aligned_cols=77  Identities=17%  Similarity=0.210  Sum_probs=56.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCc----HHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 029810           13 TETGNPGNTLYVTGLSTRVT----ERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG   88 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t----~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g   88 (187)
                      +..+++-.+|.|.=|..++.    ...|...++.||+|..|.++     |  +.-|.|.|.+..+|-.|+.+++. ...|
T Consensus        80 ~~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----G--rqsavVvF~d~~SAC~Av~Af~s-~~pg  151 (166)
T PF15023_consen   80 NTKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----G--RQSAVVVFKDITSACKAVSAFQS-RAPG  151 (166)
T ss_pred             cCCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----C--CceEEEEehhhHHHHHHHHhhcC-CCCC
Confidence            34456667787865555443    34456667899999999875     2  44799999999999999998876 5667


Q ss_pred             eEEEEEecc
Q 029810           89 RYITVERSR   97 (187)
Q Consensus        89 ~~l~v~~a~   97 (187)
                      ..+.+.|-.
T Consensus       152 tm~qCsWqq  160 (166)
T PF15023_consen  152 TMFQCSWQQ  160 (166)
T ss_pred             ceEEeeccc
Confidence            777777743

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

Probab=97.01  E-value=0.001  Score=51.40  Aligned_cols=75  Identities=20%  Similarity=0.264  Sum_probs=60.4

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC----ccCCeEEEEEe
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS----VLEGRYITVER   95 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~----~i~g~~l~v~~   95 (187)
                      ..|||.||...++.+.|.+.|..||+|....++.|. .++..+-++|+|+..-.|.+|+..+.-.    ++.+..+.|..
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP  110 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            689999999999999999999999999887666554 3667788999999999999999877432    44455555544

>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=96.99  E-value=0.0056  Score=38.71  Aligned_cols=67  Identities=27%  Similarity=0.472  Sum_probs=40.2

Q ss_pred             eEEEc-CCCCCCcHHHHHHHhhcCC-----ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           21 TLYVT-GLSTRVTERDLEKHFSKEG-----KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        21 ~l~V~-~Lp~~~t~~~L~~~f~~~G-----~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ++||. +--..++..+|..++...+     .|-.|.|..        .|+||+... +.|+.++..|++..+.|+.|.|+
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~--------~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve   72 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFD--------NFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-S--------S-EEEEE-T-T-HHHHHHHHTT--SSS----EE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEee--------eEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEE
Confidence            56662 2234788899999987764     455677753        389999864 48899999999999999999998


Q ss_pred             ec
Q 029810           95 RS   96 (187)
Q Consensus        95 ~a   96 (187)
                      .|
T Consensus        73 ~A   74 (74)
T PF03880_consen   73 RA   74 (74)
T ss_dssp             E-
T ss_pred             EC
Confidence            75

; PDB: 2G0C_A 3MOJ_B.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=96.99  E-value=0.0013  Score=55.82  Aligned_cols=71  Identities=18%  Similarity=0.291  Sum_probs=56.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhc--CCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC--CccCCeEEE
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSK--EGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQ--SVLEGRYIT   92 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~--~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g--~~i~g~~l~   92 (187)
                      -.-+.|+|.-||..+..++|+.||..  +-.++.|.+..+.       -=||+|++..||+.|.+.|..  ++|.|+.|.
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            34577888999999999999999964  6678888876553       369999999999999998864  367777765


Q ss_pred             EE
Q 029810           93 VE   94 (187)
Q Consensus        93 v~   94 (187)
                      ..
T Consensus       246 AR  247 (684)
T KOG2591|consen  246 AR  247 (684)
T ss_pred             hh
Confidence            43

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.91  E-value=0.00021  Score=63.56  Aligned_cols=83  Identities=14%  Similarity=0.221  Sum_probs=67.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .++...+.+||++||+..+++.+|...|..+|.|..|.|....- ++-..|+||.|.+...+-.|+..+.+..|..-.+.
T Consensus       366 ~DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r  444 (975)
T KOG0112|consen  366 LDDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHR  444 (975)
T ss_pred             ccchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCCccccCccc
Confidence            45566788999999999999999999999999999998875532 22245999999999999999988988877655555


Q ss_pred             EEec
Q 029810           93 VERS   96 (187)
Q Consensus        93 v~~a   96 (187)
                      +.+.
T Consensus       445 ~glG  448 (975)
T KOG0112|consen  445 IGLG  448 (975)
T ss_pred             cccc
Confidence            5554

>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=96.91  E-value=0.02  Score=39.07  Aligned_cols=70  Identities=10%  Similarity=0.043  Sum_probs=49.0

Q ss_pred             CCCCeEE-EcCCCCCCcHHHHHHHhhcCC-ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 029810           17 NPGNTLY-VTGLSTRVTERDLEKHFSKEG-KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG   88 (187)
Q Consensus        17 ~~~~~l~-V~~Lp~~~t~~~L~~~f~~~G-~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g   88 (187)
                      ...+.|. +...|..++.++|..+.+.+- .|..+.|+.+...  +.-.++|.|.+.++|.+..+.+||+.++.
T Consensus        10 ~~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~p--nrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   10 ERRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTP--NRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             CCCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCC--ceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            3334444 444555666667766666654 5667888876532  34578999999999999999999997653

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=96.85  E-value=0.0004  Score=55.53  Aligned_cols=81  Identities=25%  Similarity=0.422  Sum_probs=61.6

Q ss_pred             CCeEEEcCCCCCCcHHHH---HHHhhcCCceeEEEEeecCC--CC-CcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           19 GNTLYVTGLSTRVTERDL---EKHFSKEGKVASCFLVVEPR--TR-ISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L---~~~f~~~G~i~~~~i~~~~~--~~-~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .+-+||-+|+..+..+++   .+.|.+||.|..|.+..+..  .. ....-++|+|+..++|..||...+|..+.++.|+
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            356788889887665554   35688999999998876551  11 1122489999999999999999999999999888


Q ss_pred             EEeccCC
Q 029810           93 VERSRRK   99 (187)
Q Consensus        93 v~~a~~~   99 (187)
                      +.+...+
T Consensus       157 a~~gttk  163 (327)
T KOG2068|consen  157 ASLGTTK  163 (327)
T ss_pred             HhhCCCc
Confidence            7776654

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=96.82  E-value=0.049  Score=48.34  Aligned_cols=70  Identities=9%  Similarity=0.155  Sum_probs=51.2

Q ss_pred             CeEEEc-CCCCCCcHHHHHHHhhcCCce-----eEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           20 NTLYVT-GLSTRVTERDLEKHFSKEGKV-----ASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        20 ~~l~V~-~Lp~~~t~~~L~~~f~~~G~i-----~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      ..+||. +-...++..+|..++..-+.|     -.|.|.        ..|.||+.. .+.|...+..|++..|.|+.|.|
T Consensus       487 ~~~~~~~g~~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~--------~~~s~v~~~-~~~~~~~~~~~~~~~~~~~~~~~  557 (629)
T PRK11634        487 QLYRIEVGRDDGVEVRHIVGAIANEGDISSRYIGNIKLF--------ASHSTIELP-KGMPGEVLQHFTRTRILNKPMNM  557 (629)
T ss_pred             EEEEEecccccCCCHHHHHHHHHhhcCCChhhCCcEEEe--------CCceEEEcC-hhhHHHHHHHhccccccCCceEE
Confidence            345552 223478888998888766644     345554        238999985 45688899999999999999999


Q ss_pred             EeccC
Q 029810           94 ERSRR   98 (187)
Q Consensus        94 ~~a~~   98 (187)
                      +.+..
T Consensus       558 ~~~~~  562 (629)
T PRK11634        558 QLLGD  562 (629)
T ss_pred             EECCC
Confidence            98753

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=96.36  E-value=0.0019  Score=53.85  Aligned_cols=73  Identities=21%  Similarity=0.226  Sum_probs=59.5

Q ss_pred             CCeEEEcCCCCCC-cHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           19 GNTLYVTGLSTRV-TERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        19 ~~~l~V~~Lp~~~-t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      .+.|-|.-+|..+ +-++|...|.+||+|..|.|-+.      .-.|.|+|.+..+|-.|.. .++..|+++.|+|.|-+
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whn  444 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHN  444 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-cccceecCceeEEEEec
Confidence            4455566666644 56889999999999999988544      3379999999999988877 78999999999999987


Q ss_pred             C
Q 029810           98 R   98 (187)
Q Consensus        98 ~   98 (187)
                      +
T Consensus       445 p  445 (526)
T KOG2135|consen  445 P  445 (526)
T ss_pred             C
Confidence            6

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=96.36  E-value=0.018  Score=45.64  Aligned_cols=69  Identities=16%  Similarity=0.247  Sum_probs=51.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE-EEEEe
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY-ITVER   95 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~-l~v~~   95 (187)
                      .+=|-|-++|+... .-|..+|++||+|++....      .+-.|-+|.|.+..+|++||. .+|..|+|.. |-|+.
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkp  266 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKP  266 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeee
Confidence            34455567777543 4578899999999887654      124599999999999999999 7898888764 34444

>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=96.08  E-value=0.019  Score=42.88  Aligned_cols=61  Identities=18%  Similarity=0.159  Sum_probs=45.2

Q ss_pred             cHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC--CCccCCeEEEEEeccC
Q 029810           32 TERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLN--QSVLEGRYITVERSRR   98 (187)
Q Consensus        32 t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~--g~~i~g~~l~v~~a~~   98 (187)
                      ..+.|+++|..|+.+..+.++...      +=..|.|.+.++|++|...|+  +..|.|..|.|-++..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            457899999999998888776442      358999999999999999999  8899999999988754

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.

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

Probab=95.96  E-value=0.001  Score=54.21  Aligned_cols=73  Identities=8%  Similarity=0.061  Sum_probs=56.1

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      .+|+|++|+..+...++.++|..+|+|....|....    ...+|.|+|........|+. ++|..+.-+...+...+
T Consensus       152 Rt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~ask~----~s~~c~~sf~~qts~~halr-~~gre~k~qhsr~ai~k  224 (479)
T KOG4676|consen  152 RTREVQSLISAAILPESGESFERKGEVSYAHTASKS----RSSSCSHSFRKQTSSKHALR-SHGRERKRQHSRRAIIK  224 (479)
T ss_pred             hhhhhhcchhhhcchhhhhhhhhcchhhhhhhhccC----CCcchhhhHhhhhhHHHHHH-hcchhhhhhhhhhhhcC
Confidence            678999999999999999999999999988776433    24578899998888888888 67777664444433333

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=95.91  E-value=0.0054  Score=53.17  Aligned_cols=73  Identities=18%  Similarity=0.181  Sum_probs=62.9

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      .+.++..+|||+||...+..+-++.++..+|.|..+....         |+|.+|..+..+..|+..|+...++++.+.+
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~  105 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIE  105 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhc
Confidence            4556778999999999999999999999999888765532         8999999999999999999998998887766


Q ss_pred             Ee
Q 029810           94 ER   95 (187)
Q Consensus        94 ~~   95 (187)
                      ..
T Consensus       106 ~~  107 (668)
T KOG2253|consen  106 NV  107 (668)
T ss_pred             cc
Confidence            54

>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=95.85  E-value=0.06  Score=33.21  Aligned_cols=55  Identities=20%  Similarity=0.310  Sum_probs=43.0

Q ss_pred             CCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           30 RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        30 ~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      .++-++|+..|..|.-   ..|..++ |    | -||.|.+.++|++|....++..+....|.+
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 GVTVEDFKKRLRKYRW---DRIRDDR-T----G-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc---ceEEecC-C----E-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            6778999999999973   2333343 2    2 689999999999999999999888777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=95.79  E-value=0.0092  Score=53.24  Aligned_cols=77  Identities=21%  Similarity=0.226  Sum_probs=62.3

Q ss_pred             EEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc--CCeEEEEEeccCCC
Q 029810           23 YVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVL--EGRYITVERSRRKR  100 (187)
Q Consensus        23 ~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i--~g~~l~v~~a~~~~  100 (187)
                      ++.|.+-.++-..|..+|.+||.|..++.+.+.      ..|.|+|...+.|..|+.+|+|+++  .|-+.+|.+|+..+
T Consensus       302 ~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~  375 (1007)
T KOG4574|consen  302 SLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLP  375 (1007)
T ss_pred             hhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccc
Confidence            344445556667899999999999999887663      3899999999999999999999864  57789999998776


Q ss_pred             CCCCC
Q 029810          101 PRTPT  105 (187)
Q Consensus       101 ~~~~~  105 (187)
                      ...+.
T Consensus       376 ~~ep~  380 (1007)
T KOG4574|consen  376 MYEPP  380 (1007)
T ss_pred             cccCC
Confidence            55443

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=95.72  E-value=0.053  Score=45.30  Aligned_cols=68  Identities=13%  Similarity=0.194  Sum_probs=57.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCC-ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEG-KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG   88 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G-~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g   88 (187)
                      ++.|+|-.+|..++-.||..|+..+- .|..+.|+.+....  .=.++|.|.+.++|....+.+||..|+.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pn--rymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPN--RYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCc--eEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            88999999999999999999998665 67889888864322  3368999999999999999999998764

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=95.44  E-value=0.01  Score=47.45  Aligned_cols=80  Identities=18%  Similarity=0.146  Sum_probs=64.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ..+++|++++.+.+.+.++..++..+|.+..+.+........+++++.|.|+..+.+..|+.......+.+..+...+..
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            56899999999999999999999999988777666655667789999999999999999999554456665555544443

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.36  E-value=0.26  Score=42.60  Aligned_cols=81  Identities=20%  Similarity=0.191  Sum_probs=60.2

Q ss_pred             CCCCCeEEEcCCCC-CCcHHHHHHHhhcC----CceeEEEEeecC----------CCCC---------------------
Q 029810           16 GNPGNTLYVTGLST-RVTERDLEKHFSKE----GKVASCFLVVEP----------RTRI---------------------   59 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~-~~t~~~L~~~f~~~----G~i~~~~i~~~~----------~~~~---------------------   59 (187)
                      ...++.|-|.|+.| .+...+|.-+|..|    |.|..|.|....          ..|-                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            45678999999999 67889999998766    478888775211          1111                     


Q ss_pred             ----------------cceEEEEEecCHHHHHHHHHHhCCCccCCe--EEEEEec
Q 029810           60 ----------------SRGFAFVTMDGVEDAERCIKYLNQSVLEGR--YITVERS   96 (187)
Q Consensus        60 ----------------~~g~afV~f~~~~~a~~ai~~l~g~~i~g~--~l~v~~a   96 (187)
                                      ..=||.|+|.+++.|.++.+.++|.+|...  .|.+.|.
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFI  305 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFI  305 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeec
Confidence                            123799999999999999999999988755  4444443

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

Probab=93.86  E-value=0.0037  Score=51.62  Aligned_cols=77  Identities=17%  Similarity=0.261  Sum_probs=63.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEe-ecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLV-VEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~-~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      .+++-|.|||+...|+.|..++.+||.+..|..+ .+.+    ....-|+|...+.+..||.+|++..+....++|.|..
T Consensus        80 srk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e----tavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiP  155 (584)
T KOG2193|consen   80 SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE----TAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIP  155 (584)
T ss_pred             hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH----HHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCc
Confidence            4568899999999999999999999999988653 3332    2245678899999999999999999999999998865


Q ss_pred             CC
Q 029810           98 RK   99 (187)
Q Consensus        98 ~~   99 (187)
                      ..
T Consensus       156 de  157 (584)
T KOG2193|consen  156 DE  157 (584)
T ss_pred             hh
Confidence            43

>smart00596 PRE_C2HC PRE_C2HC domain

Probab=93.33  E-value=0.19  Score=31.08  Aligned_cols=61  Identities=21%  Similarity=0.280  Sum_probs=46.8

Q ss_pred             HHHHHHhhcCC-ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           34 RDLEKHFSKEG-KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        34 ~~L~~~f~~~G-~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ++|++.|...| ++..+..+....+..+...-||+.....+...   .|+=+.|+++.|.|+-..
T Consensus         2 ~~I~~~L~~~G~~v~~i~~m~~~~~r~P~nmf~vel~~~~~~~~---Il~ik~Lg~~~V~VEr~~   63 (69)
T smart00596        2 SQIEEALKDIGFPVLFIHNMLNRDTKNPQNMFEVELVPAANGKE---ILNIKTLGGQRVTVERPH   63 (69)
T ss_pred             HHHHHHHHHcCCceeEEEcccccCCCCcceeEEEEeeecCCCcc---eEeehhhCCeeEEEecCc
Confidence            46888898888 78888888888777777888999876654444   455568899999998754

>PF07530 PRE_C2HC: Associated with zinc fingers; InterPro: IPR006579 This domain is present in proteins found exclusively in the arthropods, including a number of Drosophila species, the silk moth and the gypsy moth

Probab=93.13  E-value=0.23  Score=30.79  Aligned_cols=62  Identities=18%  Similarity=0.337  Sum_probs=45.9

Q ss_pred             HHHHHHhhcCC-ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccC
Q 029810           34 RDLEKHFSKEG-KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR   98 (187)
Q Consensus        34 ~~L~~~f~~~G-~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   98 (187)
                      ++|.+.|...| +|..|.-+....+.......||+++...+...   .++=..|++..|+|+....
T Consensus         2 ~~I~~~L~~~G~~v~~i~~~~~~~~k~pl~mf~veL~p~~~~k~---i~~Ik~l~~~~V~vE~~~k   64 (68)
T PF07530_consen    2 EEIKEELKDQGHPVRNIHNMHSRNTKKPLNMFFVELEPKPNNKE---IYKIKTLCGQRVKVERPRK   64 (68)
T ss_pred             HHHHHHHHHcCCceEEEEccccCCCCCCceEEEEeeccCccccc---eeehHhhCCeEEEEecCCC
Confidence            56788888888 77888777777667777889999887655333   3445678999999987654

These proteins are possibly involved in RNA binding or single strand DNA binding.

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=92.60  E-value=0.55  Score=37.28  Aligned_cols=49  Identities=18%  Similarity=0.192  Sum_probs=37.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCce-eEEEEeecCCCCCcceEEEEEecCH
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKV-ASCFLVVEPRTRISRGFAFVTMDGV   71 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i-~~~~i~~~~~~~~~~g~afV~f~~~   71 (187)
                      ...+-|+|+||+.++...||+..+.+.+.+ ..+.|.-      ..+-||++|.+.
T Consensus       328 ~~~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswkg------~~~k~flh~~~~  377 (396)
T KOG4410|consen  328 GAKTDIKLTNLSRDIRVKDLKSELRKRECTPMSISWKG------HFGKCFLHFGNR  377 (396)
T ss_pred             ccccceeeccCccccchHHHHHHHHhcCCCceeEeeec------CCcceeEecCCc
Confidence            345679999999999999999999988744 3455532      245799999764

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.24  E-value=0.46  Score=39.39  Aligned_cols=57  Identities=16%  Similarity=0.167  Sum_probs=46.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCc-eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHH
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGK-VASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY   80 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~-i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~   80 (187)
                      +-.+.|-|.++|.....+||..+|+.|+. -..|.|+.+.       .||..|.+...|..||..
T Consensus       389 dlpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt~  446 (528)
T KOG4483|consen  389 DLPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALTL  446 (528)
T ss_pred             cccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhhc
Confidence            34578889999999999999999999974 3456666443       799999999999999884

>KOG2891 consensus Surface glycoprotein [General function prediction only]

Probab=91.15  E-value=0.11  Score=41.06  Aligned_cols=39  Identities=21%  Similarity=0.411  Sum_probs=30.0

Q ss_pred             CCCCCCeEEEcCCCCC------------CcHHHHHHHhhcCCceeEEEEee
Q 029810           15 TGNPGNTLYVTGLSTR------------VTERDLEKHFSKEGKVASCFLVV   53 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~------------~t~~~L~~~f~~~G~i~~~~i~~   53 (187)
                      +.....|||+.+||..            .+++-|...|..||.|..|.|+.
T Consensus       145 pgerpdti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdipi  195 (445)
T KOG2891|consen  145 PGERPDTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIPI  195 (445)
T ss_pred             CCCCCCceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCCcc
Confidence            3444578999999863            24567999999999999998863

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

Probab=90.37  E-value=6.6  Score=29.96  Aligned_cols=59  Identities=17%  Similarity=0.059  Sum_probs=35.0

Q ss_pred             CcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH--HhCCCccCCe
Q 029810           31 VTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK--YLNQSVLEGR   89 (187)
Q Consensus        31 ~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~--~l~g~~i~g~   89 (187)
                      -+---|.+-+...|.|---.-....+..-+.-+-|-.=.+.++|++||.  .|+|.+|--+
T Consensus        28 d~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq   88 (256)
T KOG4207|consen   28 DDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQ   88 (256)
T ss_pred             HHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeeh
Confidence            3445566667777765432222222222223356666678999999996  6889887543

>KOG4019 consensus Calcineurin-mediated signaling pathway inhibitor DSCR1 [Signal transduction mechanisms; General function prediction only]

Probab=89.55  E-value=0.37  Score=35.67  Aligned_cols=76  Identities=12%  Similarity=0.095  Sum_probs=54.0

Q ss_pred             CCCCeEEEcCCCCCCcH-----HHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe-E
Q 029810           17 NPGNTLYVTGLSTRVTE-----RDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGR-Y   90 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~-----~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~-~   90 (187)
                      +-.+++++.+|+..+-.     .....+|.+|.+.....++..      .+..-|.|.+++.|..|..+++...|.++ .
T Consensus         8 dlp~~~~~c~i~~~VF~~~~~k~~~~~lFrq~n~~~~fq~lrs------frrvRi~f~~p~~a~~a~i~~~~~~f~~~~~   81 (193)
T KOG4019|consen    8 DLPTAIIACDIHEEVFVNREDKALFENLFRQINEDATFQLLRS------FRRVRINFSNPEAAADARIKLHSTSFNGKNE   81 (193)
T ss_pred             cccceeeeecccHHhhccHHHHHHHHhHHhhhCcchHHHHHHh------hceeEEeccChhHHHHHHHHhhhcccCCCce
Confidence            34467788888875422     234566777766665555432      44678999999999999999999999988 6


Q ss_pred             EEEEeccC
Q 029810           91 ITVERSRR   98 (187)
Q Consensus        91 l~v~~a~~   98 (187)
                      ++.-++.+
T Consensus        82 ~k~yfaQ~   89 (193)
T KOG4019|consen   82 LKLYFAQP   89 (193)
T ss_pred             EEEEEccC
Confidence            66666654

>KOG2295 consensus C2H2 Zn-finger protein [General function prediction only]

Probab=84.78  E-value=0.12  Score=44.45  Aligned_cols=73  Identities=12%  Similarity=0.046  Sum_probs=53.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGR   89 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~   89 (187)
                      -..++|||.||+++++-++|..++..+-.+..+.+-.........-+.+|+|.---....|+.+||+..+...
T Consensus       229 hke~sll~rni~Pnis~aeIe~~ck~i~~~lrfals~~~aek~~~r~lwv~fk~~~ni~~a~~aLn~irl~s~  301 (648)
T KOG2295|consen  229 HKECSLLVRNILPNISVAEIENLCKGIPGFLRFALSTINAEKNFERRLWVTFKRGTNIKEACWALNGIRLRSN  301 (648)
T ss_pred             hHHHHHHHhccCCcccHHHHHHHhccCchheeeeccCchHHHHHHHHhhHhhccccchHHHHHHhhhcccccc
Confidence            3457899999999999999999999887776666554433333455788999876677777777877655433

>PF03468 XS: XS domain; InterPro: IPR005380 The XS (rice gene X and SGS3) domain is found in a family of plant proteins including gene X Q9SBW2 from SWISSPROT and SGS3 Q9LDX1 from SWISSPROT

Probab=84.12  E-value=2.5  Score=29.11  Aligned_cols=56  Identities=11%  Similarity=0.166  Sum_probs=29.0

Q ss_pred             eEEEcCCCCCC---------cHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecC-HHHHHHHHH
Q 029810           21 TLYVTGLSTRV---------TERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDG-VEDAERCIK   79 (187)
Q Consensus        21 ~l~V~~Lp~~~---------t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~-~~~a~~ai~   79 (187)
                      ++.|.|++...         +.++|.+.|..|..++ +..+.+..  -..++++|+|.. -.-...|+.
T Consensus        10 mgIi~N~~~~~~~~g~~~g~~~~~l~~~l~~f~p~k-v~~l~~~~--gh~g~aiv~F~~~w~Gf~~A~~   75 (116)
T PF03468_consen   10 MGIIVNIPTEKDDDGRWVGMSNEELLDKLAEFNPLK-VKPLYGKQ--GHTGFAIVEFNKDWSGFKNAMR   75 (116)
T ss_dssp             EEEEE----EE-TTS-EE---SHHHHHHHHH---SE-EEEEEETT--EEEEEEEEE--SSHHHHHHHHH
T ss_pred             EEEEEcCccccCCCCceeccCHHHHHHHHHhcCCce-eEECcCCC--CCcEEEEEEECCChHHHHHHHH
Confidence            56677886543         4578999999998875 44445542  357899999975 333333443

SGS3 is thought to be involved in post-transcriptional gene silencing (PTGS). This domain contains a conserved aspartate residue that may be functionally important. The XS domain containing proteins contain coiled-coils, which suggests that they will oligomerise. Most coiled-coil proteins form either a dimeric or a trimeric structure. It is possible that different members of the XS domain family could oligomerise via their coiled-coils forming a variety of complexes [].; PDB: 4E8U_C.

>COG5638 Uncharacterized conserved protein [Function unknown]

Probab=80.15  E-value=6.6  Score=32.97  Aligned_cols=77  Identities=25%  Similarity=0.290  Sum_probs=55.0

Q ss_pred             CCCCCCCCeEEEcCCCC-CCcHHHHHHHhhcC----CceeEEEEeecC--------------------------------
Q 029810           13 TETGNPGNTLYVTGLST-RVTERDLEKHFSKE----GKVASCFLVVEP--------------------------------   55 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~-~~t~~~L~~~f~~~----G~i~~~~i~~~~--------------------------------   55 (187)
                      .+..+++..|-|-||.| .+...+|..+|+.|    |.|..|.|....                                
T Consensus       140 pe~G~~tkrLAvVnmDWd~v~a~DLf~~fsSf~P~ggkl~kV~iypsefGkeRm~~e~vqGpprdif~~~d~~~ssqk~~  219 (622)
T COG5638         140 PEEGNPTKRLAVVNMDWDRVDAKDLFKIFSSFLPYGGKLSKVKIYPSEFGKERMAAEHVQGPPRDIFTPADNQPSSQKFG  219 (622)
T ss_pred             cCCCCcccceeEeecccccchHHHHHHHHHhhCCCCCccceeEechhhhhHHHHhHhhccCCchhhccccccCcchhccC
Confidence            34467788999999999 67888999888765    467766653110                                


Q ss_pred             ----CCCCc-----------------------------ceEEEEEecCHHHHHHHHHHhCCCccCCe
Q 029810           56 ----RTRIS-----------------------------RGFAFVTMDGVEDAERCIKYLNQSVLEGR   89 (187)
Q Consensus        56 ----~~~~~-----------------------------~g~afV~f~~~~~a~~ai~~l~g~~i~g~   89 (187)
                          .+...                             .=||.|+|.+.+.+..+...++|.++...
T Consensus       220 ~dn~~sd~d~g~d~~~Egd~g~e~d~~~lrqyqlerlryYyAvvec~d~~tsK~iY~~CDG~Eye~s  286 (622)
T COG5638         220 DDNVFSDRDAGEDALIEGDRGNEFDMVKLRQYQLERLRYYYAVVECEDIETSKNIYSACDGVEYENS  286 (622)
T ss_pred             CccchhhhhcchhhhhhcccccchhHHHHHHHHhhhheeEEEEEEeccchhhHHHHhccCccccccc
Confidence                00000                             22689999999999999999999877543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	187
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		2e-09
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		2e-09
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		3e-09
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		3e-09
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		6e-09
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		2e-07
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		9e-07
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		1e-06
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		2e-06
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-06
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		4e-06
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		4e-06
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		4e-06
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-06
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		5e-06
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		5e-06
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		5e-06
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		5e-06
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		5e-06
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		5e-06
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		7e-06
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		1e-05
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		2e-05
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		2e-05
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		2e-05
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		2e-05
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		3e-05
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		3e-05
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		3e-05
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		4e-05
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		4e-05
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		4e-05
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		5e-05
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		5e-05
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		6e-05
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		8e-05
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		1e-04
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		2e-04
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		2e-04
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		2e-04
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		2e-04
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		3e-04
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		4e-04
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		4e-04
1sxl_A	97	Resonance Assignments And Solution Structure Of The		5e-04
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		5e-04
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		6e-04
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		6e-04
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		6e-04
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		7e-04
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		7e-04
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		7e-04
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		8e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		8e-04
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		8e-04
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		9e-04

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/75 (44%), Positives = 45/75 (60%)
Query: 17  NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
           +P   L V GLS   TERDL + FSK G +A   +V + ++R SRGFAFV  + V+DA+ 
Sbjct: 44  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 103
Query: 77  CIKYLNQSVLEGRYI 91
             +  N   L+GR I
Sbjct: 104 AKERANGMELDGRRI 118

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 58.2 bits (139), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/75 (44%), Positives = 45/75 (60%)
Query: 17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
          +P   L V GLS   TERDL + FSK G +A   +V + ++R SRGFAFV  + V+DA+ 
Sbjct: 13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 77 CIKYLNQSVLEGRYI 91
            +  N   L+GR I
Sbjct: 73 AKERANGMELDGRRI 87

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 58.2 bits (139), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 33/75 (44%), Positives = 45/75 (60%)
Query: 17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
          +P   L V GLS   TERDL + FSK G +A   +V + ++R SRGFAFV  + V+DA+ 
Sbjct: 13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 77 CIKYLNQSVLEGRYI 91
            +  N   L+GR I
Sbjct: 73 AKERANGMELDGRRI 87

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 58.2 bits (139), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 33/75 (44%), Positives = 45/75 (60%)
Query: 17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
          +P   L V GLS   TERDL + FSK G +A   +V + ++R SRGFAFV  + V+DA+ 
Sbjct: 10 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 69
Query: 77 CIKYLNQSVLEGRYI 91
            +  N   L+GR I
Sbjct: 70 AKERANGMELDGRRI 84

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 57.0 bits (136), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 44/70 (62%)
Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V GLS    E+ LE+ FSK G+++   +V +  T+ SRGF FVT + ++DA+  +  +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 82 NQSVLEGRYI 91
          N   ++GR I
Sbjct: 75 NGKSVDGRQI 84

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
          E  +PG  L++ GL+    E+ L+  F K G ++   L+ + RT  SRGFAF+T +   D
Sbjct: 3  EADHPG-KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPAD 60
Query: 74 AERCIKYLNQSVLEGRYI 91
          A+   K +N   L G+ I
Sbjct: 61 AKNAAKDMNGKSLHGKAI 78

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 49.7 bits (117), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 40/61 (65%)
Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
           LYV+GL   +T+++LE+ FS+ G++ +  ++V+  T +SRG  F+  D   +AE  IK L
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 82  N 82
           N
Sbjct: 151 N 151

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 39/71 (54%)
Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          T+YV+ L   +T  DL + FSK GKV    ++ +  TR S+G AF+     + A+ C + 
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 81 LNQSVLEGRYI 91
          +N   L GR I
Sbjct: 78 INNKQLFGRVI 88

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 38/61 (62%)
Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
           LY++GL   +T++D+E  FS+ G++ +  ++V+  T +SRG AF+  D   +AE  I   
Sbjct: 91  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 82  N 82
           N
Sbjct: 151 N 151

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 38/61 (62%)
Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
           LY++GL   +T++D+E  FS+ G++ +  ++V+  T +SRG AF+  D   +AE  I   
Sbjct: 91  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 82  N 82
           N
Sbjct: 151 N 151

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 40/62 (64%)
Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           LYV+GL   ++++++E+ FS+ G++ +  ++++  T +SRG  F+  D   +AE  IK 
Sbjct: 3  NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 81 LN 82
          LN
Sbjct: 63 LN 64

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L++ GLS   T+  L  HF + G +  C ++ +P T+ SRGF FVT   VE+ +  +   
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 76
Query: 82 NQSVLEGRYI 91
             V +GR +
Sbjct: 77 PHKV-DGRVV 85

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L++ GLS   T+  L  HF + G +  C ++ +P T+ SRGF FVT   VE+ +  +   
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 82 NQSVLEGRYI 91
             V +GR +
Sbjct: 75 PHKV-DGRVV 83

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L++ GLS   T+  L  HF + G +  C ++ +P T+ SRGF FVT   VE+ +  +   
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 82 NQSVLEGRYI 91
             V +GR +
Sbjct: 76 PHKV-DGRVV 84

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L++ GLS   T+  L  HF + G +  C ++ +P T+ SRGF FVT   VE+ +  +   
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 82 NQSVLEGRYI 91
             V +GR +
Sbjct: 74 PHKV-DGRVV 82

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L++ GLS   T+  L  HF + G +  C ++ +P T+ SRGF FVT   VE+ +  +   
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 82 NQSVLEGRYI 91
             V +GR +
Sbjct: 76 PHKV-DGRVV 84

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L++ GLS   T+  L  HF + G +  C ++ +P T+ SRGF FVT   VE+ +  +   
Sbjct: 9  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 82 NQSVLEGRYI 91
             V +GR +
Sbjct: 69 PHKV-DGRVV 77

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 40/62 (64%)
Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
            LYV+GL   ++++++E+ FS+ G++ +  ++++  T +SRG  F+  D   +AE  IK 
Sbjct: 92  NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 151
Query: 81  LN 82
           LN
Sbjct: 152 LN 153

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 5/71 (7%)
Query: 23 YVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLN 82
          +V GLS   +++DL+ +F+K G+V  C +  +P T  SRGF F+     +DA    K L+
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF---KDAASVEKVLD 71
Query: 83 QSV--LEGRYI 91
          Q    L+GR I
Sbjct: 72 QKEHRLDGRVI 82

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 43/72 (59%), Gaps = 5/72 (6%)
Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          +++ GLS   T++DL+ +FSK G+V  C L ++P T  SRGF FV     +++E   K +
Sbjct: 2  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLF---KESESVDKVM 58
Query: 82 NQS--VLEGRYI 91
          +Q    L G+ I
Sbjct: 59 DQKEHKLNGKVI 70

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 47.0 bits (110), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVE 72
          +  G+ G  +++ GLS + T+  L ++F + G+V  C ++ +P T+ SRGF FVT     
Sbjct: 19 SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF---M 75
Query: 73 DAERCIKYLNQS 84
          D     K L QS
Sbjct: 76 DQAGVDKVLAQS 87

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 37/71 (52%)
Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          TL V  L+ R +   L + F K G+V   ++  EP T+  RGFAFV      DA+     
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 81 LNQSVLEGRYI 91
          ++ + L+GR +
Sbjct: 75 MDGAELDGREL 85

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 39/71 (54%)
Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           +L V  L+ R +   L + F K G+V   ++  +  T+ SRGFAFV      DAE  +  
Sbjct: 49  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 81  LNQSVLEGRYI 91
           ++ +VL+GR +
Sbjct: 109 MDGAVLDGREL 119

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 36/71 (50%)
Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           LYV GL+  V ++ L   F   G +    + ++  T   RGFAFV  +  EDA   I  
Sbjct: 14 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73
Query: 81 LNQSVLEGRYI 91
          +N+S L GR I
Sbjct: 74 MNESELFGRTI 84

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVE 72
          TE  +    L+V+ +  R  + DL + F + GK+    ++   R   S+GF FVT +   
Sbjct: 23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSA 80
Query: 73 DAERCIKYLNQSVLEGRYI 91
          DA+R  + L+ +V+EGR I
Sbjct: 81 DADRAREKLHGTVVEGRKI 99

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L++ GLS   TE  L  ++ + GK+  C ++ +P ++ SRGF FVT   + + +  +   
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89
Query: 82 NQSVLEGRYI 91
            S+ +GR +
Sbjct: 90 PHSI-DGRVV 98

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 36/71 (50%)
Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           LYV GL+  V ++ L   F   G +    + ++  T   RGFAFV  +  EDA   I  
Sbjct: 4  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 63
Query: 81 LNQSVLEGRYI 91
          +N+S L GR I
Sbjct: 64 MNESELFGRTI 74

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 36/71 (50%)
Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           LYV GL+  V ++ L   F   G +    + ++  T   RGFAFV  +  EDA   I  
Sbjct: 7  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66
Query: 81 LNQSVLEGRYI 91
          +N+S L GR I
Sbjct: 67 MNESELFGRTI 77

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 36/71 (50%)
Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           LYV GL+  V ++ L   F   G +    + ++  T   RGFAFV  +  EDA   I  
Sbjct: 9  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68
Query: 81 LNQSVLEGRYI 91
          +N+S L GR I
Sbjct: 69 MNESELFGRTI 79

>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 = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 39/74 (52%)
Query: 18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
          P  +LYV  L   VTE  L + FS  G + S  +  +  TR S G+A+V      DAER 
Sbjct: 14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 73
Query: 78 IKYLNQSVLEGRYI 91
          +  +N  V++G+ +
Sbjct: 74 LDTMNFDVIKGKPV 87

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V+ +  R  + DL + F + GK+    ++   R   S+GF FVT +   DA+R  + L
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 75
Query: 82 NQSVLEGRYI 91
          + +V+EGR I
Sbjct: 76 HGTVVEGRKI 85

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 38/69 (55%)
Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           +L V  L+ R +   L + F K G+V   ++  +  T+ SRGFAFV      DAE  +  
Sbjct: 72  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 81  LNQSVLEGR 89
           ++ +VL+GR
Sbjct: 132 MDGAVLDGR 140

>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 = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 39/74 (52%)
Query: 18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
          P  +LYV  L   VTE  L + FS  G + S  +  +  TR S G+A+V      DAER 
Sbjct: 9  PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 68
Query: 78 IKYLNQSVLEGRYI 91
          +  +N  V++G+ +
Sbjct: 69 LDTMNFDVIKGKPV 82

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 37/71 (52%)
Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           TLYV  LS   TE  + + FSK G +    + ++   + + GF FV      DAE  ++Y
Sbjct: 41  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 81  LNQSVLEGRYI 91
           +N + L+ R I
Sbjct: 101 INGTRLDDRII 111

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 37/70 (52%)
Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L+V  LS   +E DLEK FS  G ++     ++  T+  +GFAFVT    E A +    +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 82 NQSVLEGRYI 91
          +  V +GR +
Sbjct: 71 DGQVFQGRML 80

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 43.5 bits (101), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 36/71 (50%)
Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
            LYV GL+  V ++ L   F   G +    + ++  T   RGFAFV  +  EDA   I  
Sbjct: 65  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124
Query: 81  LNQSVLEGRYI 91
           +N+S L GR I
Sbjct: 125 MNESELFGRTI 135

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 33/49 (67%), Gaps = 1/49 (2%)
Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVT-MD 69
          +++ GLS + T+  L ++F + G+V  C ++ +P T+ SRGF FVT MD
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 51

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 37/70 (52%)
Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V  LS  +T  D++  F+  GK++   +V +  T  S+G+ FV+     DAE  I ++
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 82 NQSVLEGRYI 91
              L GR I
Sbjct: 78 GGQWLGGRQI 87

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/72 (25%), Positives = 38/72 (52%)
Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
           N +YV  +   +++ D++  F   GK+ SC L  +P T   +G+ F+  +  + ++  + 
Sbjct: 111 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 170
Query: 80  YLNQSVLEGRYI 91
            +N   L G+Y+
Sbjct: 171 SMNLFDLGGQYL 182

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 37/70 (52%)
Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V  LS  +T  D++  F+  G+++   +V +  T  S+G+ FV+     DAE  I+ +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 82 NQSVLEGRYI 91
              L GR I
Sbjct: 78 GGQWLGGRQI 87

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          +++ GL+   TE +L ++F K G V    ++ +P T  SRGF F++ +     +  +K  
Sbjct: 6  MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK-- 63
Query: 82 NQSVLEGRYI 91
           Q +L+G+ I
Sbjct: 64 TQHILDGKVI 73

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V GL    T+  L K+F   G +    ++ + +T  SRG+ FVTM     AER  K  
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 82 NQSVLEGR 89
          N  +++GR
Sbjct: 80 N-PIIDGR 86

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 32/58 (55%)
Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          T+ VT LS    E DL++ F   G ++  +L  +  T  S+GFAF++    EDA R I
Sbjct: 17 TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 18/72 (25%), Positives = 37/72 (51%)
Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
           N +YV  +   +++ D++  F   GK+ SC L  +P T   +G+ F+  +  + ++  + 
Sbjct: 110 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 169
Query: 80  YLNQSVLEGRYI 91
             N   L G+Y+
Sbjct: 170 SXNLFDLGGQYL 181

>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 = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 34/68 (50%)
Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           LYVT L   +T+  L+  F K G +    ++ +  T   RG AFV  +  E+A+  I  
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 81 LNQSVLEG 88
          LN  + EG
Sbjct: 75 LNNVIPEG 82

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 40/73 (54%)
Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          G  L+VTG+    TE D+   F++ G++ +  L ++ RT   +G+  V  +  ++A+  +
Sbjct: 9  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 68
Query: 79 KYLNQSVLEGRYI 91
          + LN   L G+ I
Sbjct: 69 EGLNGQDLMGQPI 81

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 40/73 (54%)
Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          G  L+VTG+    TE D+   F++ G++ +  L ++ RT   +G+  V  +  ++A+  +
Sbjct: 23 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 82
Query: 79 KYLNQSVLEGRYI 91
          + LN   L G+ I
Sbjct: 83 EGLNGQDLMGQPI 95

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 3/74 (4%)
Query: 18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
          P  TL+V GLS   TE  L++ F  +G V    +V +  T  S+GF FV  +  EDA+  
Sbjct: 14 PSKTLFVKGLSEDTTEETLKESF--DGSV-RARIVTDRETGSSKGFGFVDFNSEEDAKAA 70
Query: 78 IKYLNQSVLEGRYI 91
           + +    ++G  +
Sbjct: 71 KEAMEDGEIDGNKV 84

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 40/73 (54%)
Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          G  L+VTG+    TE D+   F++ G++ +  L ++ RT   +G+  V  +  ++A+  +
Sbjct: 7  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 79 KYLNQSVLEGRYI 91
          + LN   L G+ I
Sbjct: 67 EGLNGQDLMGQPI 79

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 40/73 (54%)
Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          G  L+VTG+    TE D+   F++ G++ +  L ++ RT   +G+  V  +  ++A+  +
Sbjct: 7  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 79 KYLNQSVLEGRYI 91
          + LN   L G+ I
Sbjct: 67 EGLNGQDLMGQPI 79

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          TLYV  LS   TE  + + FSK G +    + ++ + + + GF FV      DAE  ++Y
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD-KMKTACGFCFVEYYSRADAENAMRY 78
Query: 81 LNQSVLEGRYI 91
          +N + L+ R I
Sbjct: 79 INGTRLDDRII 89

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 34/68 (50%)
Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
            LYVT L   +T+  L+  F K G +    ++ +  T   RG AFV  +  E+A+  I  
Sbjct: 102 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 161
Query: 81  LNQSVLEG 88
           LN  + EG
Sbjct: 162 LNNVIPEG 169

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 40.0 bits (92), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 34/68 (50%)
Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
            LYVT L   +T+  L+  F K G +    ++ +  T   RG AFV  +  E+A+  I  
Sbjct: 91  NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 150
Query: 81  LNQSVLEG 88
           LN  + EG
Sbjct: 151 LNNVIPEG 158

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 40.0 bits (92), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 40/73 (54%)
Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          G  L+VTG+    TE D+   F++ G++ +  L ++ RT   +G+  V  +  ++A+  +
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
Query: 79 KYLNQSVLEGRYI 91
          + LN   L G+ I
Sbjct: 82 EGLNGQDLMGQPI 94

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 40.0 bits (92), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 36/68 (52%)
Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LYV  L   +TE  L   F   G++ S  L+++  T  S+G+ F+T    E A++ ++ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 82 NQSVLEGR 89
          N   L GR
Sbjct: 89 NGFELAGR 96

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 40.0 bits (92), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 40/73 (54%)
Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
          G  L+VTG+    TE D+   F++ G++ +  L ++ RT   +G+  V  +  ++A+  +
Sbjct: 7  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 79 KYLNQSVLEGRYI 91
          + LN   L G+ I
Sbjct: 67 EGLNGQDLMGQPI 79

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	187
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-31
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-27
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-27
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-26
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-26
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-25
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	8e-25
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	5e-23
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	5e-23
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	4e-22
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-22
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-16
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	8e-22
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	8e-22
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	8e-22
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	9e-22
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-21
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-21
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-21
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-21
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-21
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-21
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-21
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-19
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-13
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-21
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	5e-21
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	8e-19
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-21
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	8e-21
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	8e-21
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-20
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-20
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-20
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-20
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-20
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-20
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-20
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-20
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	5e-20
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	7e-19
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	7e-20
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-20
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	9e-18
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	8e-20
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	9e-20
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-19
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-19
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-19
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-19
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-19
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-19
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-19
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-19
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-19
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-19
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	4e-19
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	6e-19
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	7e-19
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-18
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	7e-19
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	9e-19
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-19
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-17
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-18
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-18
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-18
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-18
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-18
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	6e-14
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-18
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-18
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-18
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-06
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-18
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-18
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-18
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	4e-18
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-18
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	4e-18
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-18
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	5e-18
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-18
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-13
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	7e-18
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	7e-18
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	7e-18
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	8e-18
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	9e-18
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-17
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-17
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-17
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-17
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-17
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-17
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-17
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-17
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-17
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-17
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-17
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-16
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	9e-17
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	9e-17
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-16
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-16
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-16
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-16
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-16
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-16
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-16
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	5e-15
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-16
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-16
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	6e-16
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	7e-16
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-16
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-15
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-15
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-15
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-15
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-12
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-15
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	5e-15
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	5e-15
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-14
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	6e-15
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	8e-15
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	8e-15
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	8e-15
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	8e-15
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	9e-15
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-14
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-14
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-14
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	9e-14
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-14
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-11
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-14
2div_A	99	TRNA selenocysteine associated protein; structural	2e-14
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-14
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-14
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-14
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-14
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	5e-14
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-14
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	6e-14
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	8e-14
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	8e-14
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-13
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-13
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-13
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-13
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-13
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	3e-13
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	3e-13
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	6e-13
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	7e-13
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	8e-13
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-12
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-12
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-12
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-12
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	5e-12
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-12
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	6e-12
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-11
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-11
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-11
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	5e-11
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	5e-11
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	5e-11
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-10
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-10
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	8e-10
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-09
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-09
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-09
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-09
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-09
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	4e-09
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-08
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	2e-08
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-07
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-07
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	9e-07
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	6e-06
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	1e-05
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	1e-05
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-05
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-05
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	4e-05
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	5e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	3e-04

>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 =  108 bits (273), Expect = 2e-31
 Identities = 29/95 (30%), Positives = 44/95 (46%)

Query: 14  ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
             G P   LY+  LS RVTERDL   F++  +     +     T   RG AF+T    E 
Sbjct: 20  NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEI 79

Query: 74  AERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGH 108
           A + +  +N   L G+ + +E  + K+ R+  P  
Sbjct: 80  AWQALHLVNGYKLYGKILVIEFGKNKKQRSSGPSS 114

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 99.0 bits (247), Expect = 1e-27
 Identities = 21/85 (24%), Positives = 36/85 (42%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
           P   +    L+  V E  L+    K G+V    +++ PRTR   G A V       A+  
Sbjct: 5   PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKET 64

Query: 78  IKYLNQSVLEGRYITVERSRRKRPR 102
           +K L+ + + G  I  +   + + R
Sbjct: 65  VKNLHLTSVMGNIIHAQLDIKGQQR 89

>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 = 98.4 bits (246), Expect = 2e-27
 Identities = 29/101 (28%), Positives = 47/101 (46%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G     +   T+ VT LS    E DL++ F   G ++  +L  +  T  S+GFAF+
Sbjct: 3   SGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFI 62

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
           +    EDA R I  ++    +   + VE ++      P+ G
Sbjct: 63  SFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSGPSSG 103

>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 = 96.5 bits (241), Expect = 1e-26
 Identities = 37/92 (40%), Positives = 49/92 (53%)

Query: 7  SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
          S S G     +P   L V GLS   TERDL + FSK G +A   +V + ++R SRGFAFV
Sbjct: 3  SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 62

Query: 67 TMDGVEDAERCIKYLNQSVLEGRYITVERSRR 98
            + V+DA+   +  N   L+GR I V     
Sbjct: 63 YFENVDDAKEAKERANGMELDGRRIRVSGPSS 94

>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 = 95.4 bits (238), Expect = 3e-26
 Identities = 30/102 (29%), Positives = 51/102 (50%), Gaps = 2/102 (1%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G +E+ +    L+V+ +  R  + DL + F + GK+    ++   R   S+GF FV
Sbjct: 3   SGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFV 60

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGH 108
           T +   DA+R  + L+ +V+EGR I V  +  +      P  
Sbjct: 61  TFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSGPSS 102

>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 = 95.2 bits (237), Expect = 1e-25
 Identities = 41/98 (41%), Positives = 54/98 (55%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
              SR  G     +P   L V GLS   TERDL + FSK G +A   +V + ++R SRGF
Sbjct: 31  GRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF 90

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRP 101
           AFV  + V+DA+   +  N   L+GR I V+ S  KRP
Sbjct: 91  AFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRP 128

>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 = 91.9 bits (229), Expect = 8e-25
 Identities = 29/100 (29%), Positives = 45/100 (45%)

Query: 8   RSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVT 67
            S       +   TL V  L+ R +   L + F K G+V   ++  EP T+  RGFAFV 
Sbjct: 2   SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61

Query: 68  MDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
                DA+     ++ + L+GR + V+ +R  R     P 
Sbjct: 62  FHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPS 101

>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 = 87.3 bits (217), Expect = 5e-23
 Identities = 31/100 (31%), Positives = 45/100 (45%)

Query: 9   SRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTM 68
           S G +        LYV GL+  V ++ L   F   G +    + ++  T   RGFAFV  
Sbjct: 2   SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61

Query: 69  DGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGH 108
           +  EDA   I  +N+S L GR I V  ++  R +   P  
Sbjct: 62  ELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKESGPSS 101

>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 = 87.3 bits (217), Expect = 5e-23
 Identities = 31/99 (31%), Positives = 54/99 (54%)

Query: 9   SRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTM 68
           S G +   +    L+V GLS    E+ LE+ FSK G+++   +V +  T+ SRGF FVT 
Sbjct: 2   SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61

Query: 69  DGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
           + ++DA+  +  +N   ++GR I V+++ +       P 
Sbjct: 62  ENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGPS 100

>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 = 85.4 bits (212), Expect = 4e-22
 Identities = 24/105 (22%), Positives = 46/105 (43%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
           +    + G  + G  G  L++  L     ++DL + F   G V S  + ++ +T +S+ F
Sbjct: 10  QQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCF 69

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGH 108
            FV+ D    A+  I+ +N   +  + + V+  R K      P  
Sbjct: 70  GFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGPSS 114

>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 = 86.9 bits (216), Expect = 5e-22
 Identities = 18/92 (19%), Positives = 38/92 (41%), Gaps = 2/92 (2%)

Query: 17  NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
                L++  L+   +  +L+   S+         VV+ RT  +R F +V  +  ED E+
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDFESAEDLEK 69

Query: 77  CIKYLNQSVLEGRYITVERSRRKRPRTPTPGH 108
            ++ L    + G  I +E+ + +  +      
Sbjct: 70  ALE-LTGLKVFGNEIKLEKPKGRDSKKVRAAR 100

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 72.6 bits (179), Expect = 1e-16
 Identities = 18/98 (18%), Positives = 43/98 (43%), Gaps = 6/98 (6%)

Query: 2   VFRSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISR 61
           +   + + R   +      TL    LS  +TE +L++ F    ++      +  +   S+
Sbjct: 83  IKLEKPKGRDSKKV-RAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSK 136

Query: 62  GFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK 99
           G A++      DAE+ ++    + ++GR +++  +  K
Sbjct: 137 GIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174

>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 = 84.2 bits (209), Expect = 8e-22
 Identities = 29/102 (28%), Positives = 45/102 (44%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G     N   T+YV GL  +V+E  L + F + G V +  +  +  T   +G+ FV
Sbjct: 3   SGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFV 62

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGH 108
                EDA+  IK ++   L G+ I V ++         P  
Sbjct: 63  EFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPSS 104

>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 = 83.9 bits (208), Expect = 8e-22
 Identities = 32/103 (31%), Positives = 43/103 (41%), Gaps = 8/103 (7%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G  +T +    LYV  L    +E  +EK F+     A        R +  R +AFV
Sbjct: 3   SGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVE------RVKKIRDYAFV 56

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVE--RSRRKRPRTPTPG 107
                EDA   +K LN  VL+G  I V   +   K    P+ G
Sbjct: 57  HFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGPSSG 99

>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 = 84.7 bits (210), Expect = 8e-22
 Identities = 30/122 (24%), Positives = 52/122 (42%), Gaps = 12/122 (9%)

Query: 16  GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAE 75
            +    L++ GL+    E+ L+  F K G ++   L+ + RT  SRGFAF+T +   DA+
Sbjct: 4   ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAK 62

Query: 76  RCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDRGRYRSGRDDYGY 135
              K +N   L G+ I VE++++   ++                     R RS      +
Sbjct: 63  NAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRR-----------RPPASSRNRSPSGSLEH 111

Query: 136 RR 137
             
Sbjct: 112 HH 113

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 84.3 bits (209), Expect = 9e-22
 Identities = 28/96 (29%), Positives = 47/96 (48%), Gaps = 2/96 (2%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
                S   TE  +    L+V+ +  R  + DL + F + GK+    ++   R   S+GF
Sbjct: 14  LVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGF 71

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK 99
            FVT +   DA+R  + L+ +V+EGR I V  +  +
Sbjct: 72  GFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 87.0 bits (216), Expect = 1e-21
 Identities = 24/104 (23%), Positives = 42/104 (40%)

Query: 3   FRSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRG 62
              R  +  R       + +YV  +   + E  + + F+  G + S  +  +  T   +G
Sbjct: 12  QMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKG 71

Query: 63  FAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTP 106
           FAFV  +  E A+  ++ +N  +L GR I V R        P  
Sbjct: 72  FAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPII 115

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 85.4 bits (212), Expect = 4e-21
 Identities = 21/104 (20%), Positives = 46/104 (44%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
           +++       E     N +YV  +   +++ D++  F   GK+ S  L  +P T   +G+
Sbjct: 110 QAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGY 169

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
            F+  +  + ++  +  +N   L G+Y+ V ++        TP 
Sbjct: 170 GFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPA 213

>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 = 85.7 bits (212), Expect = 1e-21
 Identities = 29/98 (29%), Positives = 46/98 (46%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
             S             +L V  L+ R +   L + F K G+V   ++  +  T+ SRGFA
Sbjct: 56  EGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFA 115

Query: 65  FVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPR 102
           FV      DAE  +  ++ +VL+GR + V+ +R  RP 
Sbjct: 116 FVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP 153

>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 = 82.7 bits (205), Expect = 2e-21
 Identities = 25/93 (26%), Positives = 40/93 (43%), Gaps = 3/93 (3%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRT---RISRGFAFVTMDGVEDA 74
             + L++  L+   TE  L+  FSK G + SC +  +       +S GF FV     E A
Sbjct: 4   GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63

Query: 75  ERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
           ++ +K L    ++G  + V  S R       P 
Sbjct: 64  QKALKQLQGHTVDGHKLEVRISERATKPASGPS 96

>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 = 82.7 bits (205), Expect = 2e-21
 Identities = 26/102 (25%), Positives = 41/102 (40%), Gaps = 6/102 (5%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G  +T    + L+V  L   +TE ++ K F K GK    F+         +GF F+
Sbjct: 3   SGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK------DKGFGFI 56

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGH 108
            ++    AE     L+   L G+ + V  +      T  P  
Sbjct: 57  RLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGPSS 98

>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 = 82.3 bits (204), Expect = 3e-21
 Identities = 28/101 (27%), Positives = 41/101 (40%), Gaps = 8/101 (7%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G       GNTLYV G    +T   L   FS  G +              R  AFV
Sbjct: 3   SGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDL------SMDPPRNCAFV 54

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
           T + +E A++ +  LN + +E   + V  +R++      P 
Sbjct: 55  TYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDSGPS 95

>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 = 86.6 bits (215), Expect = 4e-21
 Identities = 21/85 (24%), Positives = 32/85 (37%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
               L V  L   +T++  E+     G +  CFLV   RT  S+G+ F      + A R 
Sbjct: 94  TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153

Query: 78  IKYLNQSVLEGRYITVERSRRKRPR 102
              L    L  R + V  +   +  
Sbjct: 154 KSDLLGKPLGPRTLYVHWTDAGQLT 178

>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 = 82.0 bits (203), Expect = 3e-19
 Identities = 19/99 (19%), Positives = 31/99 (31%), Gaps = 2/99 (2%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERD-LEKHFSKEGKVASCFLVVEPRTRISRGF 63
             + +   T        L V  L     + D L +  S       C L      +  +GF
Sbjct: 170 HWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQ-LKGF 228

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPR 102
           A +  +  E AE   +  +   L G ++ V       P 
Sbjct: 229 AVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPG 267

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 65.8 bits (161), Expect = 2e-13
 Identities = 23/94 (24%), Positives = 35/94 (37%), Gaps = 7/94 (7%)

Query: 6  RSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAF 65
          R R             + + GL   VT +++    S    +  CF          +G AF
Sbjct: 9  RKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCF------VDKYKGTAF 61

Query: 66 VTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK 99
          VT+   E AE  I   +QS L  R ++V+     
Sbjct: 62 VTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD 95

>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 = 81.8 bits (203), Expect = 4e-21
 Identities = 21/86 (24%), Positives = 45/86 (52%), Gaps = 1/86 (1%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPR-TRISRGFAFVTMDGVEDAER 76
               +++  L+  VT+  + + FS  GK+    + VE     +S+G+A+V  +  ++AE+
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

Query: 77  CIKYLNQSVLEGRYITVERSRRKRPR 102
            +K+++   ++G+ IT        PR
Sbjct: 63  ALKHMDGGQIDGQEITATAVLAPWPR 88

>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 = 83.8 bits (208), Expect = 5e-21
 Identities = 23/85 (27%), Positives = 39/85 (45%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
            L V  L   +T+R+L   F   G + +C ++ + +T  S G+AFV      D++R IK 
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 81  LNQSVLEGRYITVERSRRKRPRTPT 105
           LN   +  + + V  +R        
Sbjct: 65  LNGITVRNKRLKVSYARPGGESIKD 89

>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 = 78.0 bits (193), Expect = 8e-19
 Identities = 27/83 (32%), Positives = 40/83 (48%), Gaps = 1/83 (1%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S +R   E+    N LYVT L   +T+  L+  F K G +    ++ +  T   RG AFV
Sbjct: 78  SYARPGGESIKDTN-LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFV 136

Query: 67  TMDGVEDAERCIKYLNQSVLEGR 89
             +  E+A+  I  LN  + EG 
Sbjct: 137 RYNKREEAQEAISALNNVIPEGG 159

>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 = 81.9 bits (203), Expect = 6e-21
 Identities = 27/90 (30%), Positives = 43/90 (47%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
               L+V  LS   +E DLEK FS  G ++     ++  T+  +GFAFVT    E A + 
Sbjct: 7   GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66

Query: 78  IKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
              ++  V +GR + V  S  K+  + +  
Sbjct: 67  YAEVDGQVFQGRMLHVLPSTIKKEASQSGP 96

>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 = 82.0 bits (203), Expect = 8e-21
 Identities = 27/109 (24%), Positives = 46/109 (42%), Gaps = 8/109 (7%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G       G T+++  LS    E  L +   + G +    +V+ P T  S+G AF 
Sbjct: 3   SGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFA 62

Query: 67  TMDGVEDAERCIKYLNQS------VLEGRYITVE--RSRRKRPRTPTPG 107
                E A++C+   +         L+GR + V+   +R +    P+ G
Sbjct: 63  QFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSSG 111

>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 = 81.1 bits (201), Expect = 8e-21
 Identities = 26/76 (34%), Positives = 40/76 (52%)

Query: 18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
            +T+YV+ L   +T  DL + FSK GKV    ++ +  TR S+G AF+     + A+ C
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74

Query: 78 IKYLNQSVLEGRYITV 93
           + +N   L GR I  
Sbjct: 75 TRAINNKQLFGRVIKA 90

>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 = 81.6 bits (202), Expect = 1e-20
 Identities = 27/104 (25%), Positives = 44/104 (42%), Gaps = 1/104 (0%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
             R      +       T++   L+ R+  RDLE  FS  GKV    ++ +  +R S+G 
Sbjct: 10  PVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGI 69

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
           A+V    ++     I  L    L G  I V+ S+ ++ R   P 
Sbjct: 70  AYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKNRLSGPS 112

>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 = 80.7 bits (200), Expect = 1e-20
 Identities = 27/81 (33%), Positives = 39/81 (48%)

Query: 17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
               LYV GL+  V ++ L   F   G +    + ++  T   RGFAFV  +  EDA  
Sbjct: 5  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64

Query: 77 CIKYLNQSVLEGRYITVERSR 97
           I  +N+S L GR I V  ++
Sbjct: 65 AIDNMNESELFGRTIRVNLAK 85

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 82.1 bits (203), Expect = 1e-20
 Identities = 29/99 (29%), Positives = 46/99 (46%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
           R                +L V  L+ R +   L + F K G+V   ++  +  T+ SRGF
Sbjct: 32  RGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGF 91

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPR 102
           AFV      DAE  +  ++ +VL+GR + V+ +R  RP 
Sbjct: 92  AFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP 130

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 80.4 bits (199), Expect = 2e-20
 Identities = 17/88 (19%), Positives = 40/88 (45%), Gaps = 6/88 (6%)

Query: 17 NPGNTLYVTGLSTRVTERDLEKHFSKEGK--VASCFLVVEPRTRISRGFAFVTMDGVEDA 74
          +  +T+ +  ++       +    S      V +  L+ + +T+ +RGFAFV +    DA
Sbjct: 7  HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDA 66

Query: 75 ERCIKYLNQS----VLEGRYITVERSRR 98
           + ++ L        ++G+ I V+ ++ 
Sbjct: 67 SQLLQILQSLHPPLKIDGKTIGVDFAKS 94

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

 Score = 81.7 bits (202), Expect = 2e-20
 Identities = 29/89 (32%), Positives = 40/89 (44%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
               S G   +      LYV GL+  V ++ L   F   G +    + ++  T   RGFA
Sbjct: 49  GSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 108

Query: 65  FVTMDGVEDAERCIKYLNQSVLEGRYITV 93
           FV  +  EDA   I  +N+S L GR I V
Sbjct: 109 FVEFELAEDAAAAIDNMNESELFGRTIRV 137

>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 = 81.8 bits (202), Expect = 2e-20
 Identities = 32/137 (23%), Positives = 54/137 (39%), Gaps = 4/137 (2%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
             R  +  + +      TLYV  LS   TE  + + FSK G +    + ++   + + GF
Sbjct: 24  HFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGF 83

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDR 123
            FV      DAE  ++Y+N + L+ R I  +     +            +S   +    R
Sbjct: 84  CFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYG----RGRSGGQVRDEYR 139

Query: 124 GRYRSGRDDYGYRRSPR 140
             Y +GR  YG     +
Sbjct: 140 QDYDAGRGGYGKLAQNQ 156

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 80.9 bits (200), Expect = 2e-20
 Identities = 23/94 (24%), Positives = 45/94 (47%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
            + + + G+   G  G  L++  L    T+ DL   F   G V S  + ++ +T +S+ F
Sbjct: 25  AAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCF 84

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR 97
            FV+ D  + A+  IK +N   +  + + V+  +
Sbjct: 85  GFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>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 = 79.5 bits (197), Expect = 3e-20
 Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 1/83 (1%)

Query: 16 GNPGNT-LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDA 74
          G+ G++ LY+ GL    T++DL K     GK+ S   +++  T   +G+ FV  D    A
Sbjct: 1  GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60

Query: 75 ERCIKYLNQSVLEGRYITVERSR 97
          ++ +  L  S ++ +        
Sbjct: 61 QKAVTALKASGVQAQMAKQSGPS 83

>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 = 81.5 bits (202), Expect = 5e-20
 Identities = 25/85 (29%), Positives = 37/85 (43%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
            L V  L   +T+ +    F   G++ SC LV +  T  S G+ FV     +DAE+ I  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 81  LNQSVLEGRYITVERSRRKRPRTPT 105
           LN   L+ + I V  +R        
Sbjct: 64  LNGLRLQTKTIKVSYARPSSASIRD 88

>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 = 78.4 bits (194), Expect = 7e-19
 Identities = 31/89 (34%), Positives = 50/89 (56%), Gaps = 3/89 (3%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S +R  + +    N LYV+GL   +T+++LE+ FS+ G++ +  ++V+  T +SRG  F+
Sbjct: 77  SYARPSSASIRDAN-LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFI 135

Query: 67  TMDGVEDAERCIKYLNQSVLEG--RYITV 93
             D   +AE  IK LN     G    ITV
Sbjct: 136 RFDKRIEAEEAIKGLNGQKPSGATEPITV 164

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

 Score = 79.2 bits (196), Expect = 7e-20
 Identities = 23/99 (23%), Positives = 40/99 (40%), Gaps = 2/99 (2%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
           S S    R  T    + L+++GL    T+ +LE+     G V    LV   R    +G A
Sbjct: 3   SGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLA 61

Query: 65  FVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRT 103
           +V  +    A + +  ++   ++   I V  S    P +
Sbjct: 62  YVEYENESQASQAVMKMDGMTIKENIIKVAIS-NSGPSS 99

>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 = 81.6 bits (202), Expect = 7e-20
 Identities = 18/93 (19%), Positives = 41/93 (44%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
                    T   +  + L++ GL   + +  +++  +  G + +  LV +  T +S+G+
Sbjct: 99  SVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGY 158

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERS 96
           AF     +   ++ I  LN   L  + + V+R+
Sbjct: 159 AFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 191

>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 = 76.2 bits (188), Expect = 9e-18
 Identities = 15/97 (15%), Positives = 37/97 (38%), Gaps = 6/97 (6%)

Query: 16  GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFL-----VVEPRTRISRGFAFVTMDG 70
           G     LYV  +   +TE  +   F+ + ++          V+  +    + FAF+    
Sbjct: 1   GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60

Query: 71  VEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
           V++  + +   +  + +G+ + + R    +P      
Sbjct: 61  VDETTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSE 96

>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 = 78.4 bits (194), Expect = 8e-20
 Identities = 29/96 (30%), Positives = 51/96 (53%), Gaps = 11/96 (11%)

Query: 15  TGNPGNT--LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVE 72
           +G+ GNT  ++V  +S   T ++L   F + G+V  C +V        + +AFV M+   
Sbjct: 3   SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEA 54

Query: 73  DAERCIKYLNQSVLEGRYITVERSRRKRPRT-PTPG 107
           DA+  I  LN   ++G+ I VE S + + ++ P+ G
Sbjct: 55  DAKAAIAQLNGKEVKGKRINVELSTKGQKKSGPSSG 90

>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 = 78.8 bits (195), Expect = 9e-20
 Identities = 28/103 (27%), Positives = 45/103 (43%), Gaps = 2/103 (1%)

Query: 6   RSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAF 65
            S S G   T      LYV  L   + +  L K FS  G + S  +++E     S+GF F
Sbjct: 2   SSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGF 59

Query: 66  VTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGH 108
           V     E+A + +  +N  ++  + + V  ++RK  R   P  
Sbjct: 60  VCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQSGPSS 102

>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 = 79.3 bits (196), Expect = 1e-19
 Identities = 22/103 (21%), Positives = 43/103 (41%), Gaps = 1/103 (0%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
               G  E    G  L V+ L   V++ D+++ F++ G +    +  + R+  S G A V
Sbjct: 23  DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADV 81

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHY 109
             +   DA + +K      L+GR + ++    +        H+
Sbjct: 82  HFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 124

>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 = 78.9 bits (195), Expect = 1e-19
 Identities = 24/103 (23%), Positives = 44/103 (42%), Gaps = 2/103 (1%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPR-TRISRGFAF 65
           S S G+       + + V  +  +  +R++ + FS  G++ +  L  +   T   RGF F
Sbjct: 3   SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62

Query: 66  VTMDGVEDAERCIKYLNQSV-LEGRYITVERSRRKRPRTPTPG 107
           V     +DA++    L  S  L GR + +E +  +      P 
Sbjct: 63  VDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPS 105

>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 = 78.5 bits (194), Expect = 1e-19
 Identities = 27/96 (28%), Positives = 46/96 (47%), Gaps = 1/96 (1%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G  + G  G+T++V  L  +V  + L++ FS  G V    ++ +   + SRG   V
Sbjct: 3   SGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGK-SRGIGTV 61

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPR 102
           T +   +A + I   N  +L  R + V+   R  P+
Sbjct: 62  TFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPK 97

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

 Score = 78.0 bits (193), Expect = 2e-19
 Identities = 19/93 (20%), Positives = 36/93 (38%), Gaps = 9/93 (9%)

Query: 18  PGNTLYVTGLSTR-VTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
           P + L++  L  + V++ DL + FS  G +            I   F F+  D  +    
Sbjct: 9   PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQI--------NIKNAFGFIQFDNPQSVRD 60

Query: 77  CIKYLNQSVLEGRYITVERSRRKRPRTPTPGHY 109
            I+  +Q +  G+ + +E S          G +
Sbjct: 61  AIECESQEMNFGKKLILEVSSSNARPQFDHGDH 93

>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 = 78.4 bits (194), Expect = 2e-19
 Identities = 26/93 (27%), Positives = 45/93 (48%), Gaps = 3/93 (3%)

Query: 16  GNPGNT-LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDA 74
           G  G+  +++  L   +  + L   FS  G + SC +V +     S+G+ FV  +  E A
Sbjct: 1   GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAA 58

Query: 75  ERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
           ER I+ +N  +L  R + V R + ++ R    G
Sbjct: 59  ERAIEKMNGMLLNDRKVFVGRFKSRKEREAELG 91

>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 = 78.2 bits (193), Expect = 2e-19
 Identities = 26/109 (23%), Positives = 45/109 (41%), Gaps = 8/109 (7%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRI------- 59
           S S G  +  +  + +YV GL+  VT  DL   F + G V       +P   I       
Sbjct: 3   SGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETG 62

Query: 60  -SRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
             +G A V+ +    A+  +++ +    +G  + V  +R+K P    P 
Sbjct: 63  KPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPS 111

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

 Score = 77.7 bits (192), Expect = 2e-19
 Identities = 23/84 (27%), Positives = 45/84 (53%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
            G  L+VTG+    TE D+   F++ G++ +  L ++ RT   +G+  V  +  ++A+  
Sbjct: 22  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81

Query: 78  IKYLNQSVLEGRYITVERSRRKRP 101
           ++ LN   L G+ I+V+    + P
Sbjct: 82  MEGLNGQDLMGQPISVDWCFVRGP 105

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

 Score = 77.7 bits (192), Expect = 2e-19
 Identities = 22/97 (22%), Positives = 35/97 (36%), Gaps = 8/97 (8%)

Query: 6   RSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAF 65
            S    R E       L+V      V E +L + F   G +           +I  GFAF
Sbjct: 18  GSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEV--------KILNGFAF 69

Query: 66  VTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPR 102
           V  +  E A + I+ ++      + + V  S+    R
Sbjct: 70  VEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKR 106

>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 = 77.2 bits (191), Expect = 3e-19
 Identities = 26/92 (28%), Positives = 40/92 (43%)

Query: 17  NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
           +  + LYV  L   +TE  L   F   GK+ +  L+ +  T  S+G+ F+T    E A R
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62

Query: 77  CIKYLNQSVLEGRYITVERSRRKRPRTPTPGH 108
            ++ LN   L GR + V     +      P  
Sbjct: 63  ALEQLNGFELAGRPMRVGHVTERLDGGSGPSS 94

>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 = 77.3 bits (191), Expect = 3e-19
 Identities = 28/103 (27%), Positives = 43/103 (41%), Gaps = 4/103 (3%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G  E      TLYV  LS  VTE  + + FS+ G   SC ++ E  +     + FV
Sbjct: 3   SGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFV 60

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVE--RSRRKRPRTPTPG 107
                 DA   +  +N   + G+ + V    +   +   P+ G
Sbjct: 61  EFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSGPSSG 103

>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 = 78.2 bits (193), Expect = 4e-19
 Identities = 24/104 (23%), Positives = 39/104 (37%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
           +            +    L V  + T V E  L + F + G + S  +V +  TR SRG+
Sbjct: 27  QQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGY 86

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
            FV       A++ I  LN   +  + + V  +     R    G
Sbjct: 87  GFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAG 130

>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 = 76.5 bits (189), Expect = 6e-19
 Identities = 23/92 (25%), Positives = 32/92 (34%), Gaps = 1/92 (1%)

Query: 5  SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
          S   S           T++V  L  RV E  L + F + G +    +  +   +  + F 
Sbjct: 2  SSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGK-PKSFG 60

Query: 65 FVTMDGVEDAERCIKYLNQSVLEGRYITVERS 96
          FV     E     I  LN   L GR I V   
Sbjct: 61 FVCFKHPESVSYAIALLNGIRLYGRPINVSGP 92

>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 = 78.4 bits (194), Expect = 7e-19
 Identities = 18/88 (20%), Positives = 38/88 (43%), Gaps = 1/88 (1%)

Query: 8   RSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVT 67
           R             L++ GL   + +  +++  +  G + +  LV +  T +S+G+AF  
Sbjct: 84  RPHDYQPLPGAHK-LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE 142

Query: 68  MDGVEDAERCIKYLNQSVLEGRYITVER 95
              +   ++ I  LN   L  + + V+R
Sbjct: 143 YVDINVTDQAIAGLNGMQLGDKKLLVQR 170

>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 = 76.5 bits (189), Expect = 4e-18
 Identities = 14/90 (15%), Positives = 36/90 (40%), Gaps = 6/90 (6%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFL-----VVEPRTRISRGFAFVTMDGVEDAE 75
            LYV  +   +TE  +   F+ + ++          V+  +    + FAF+    V++  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 76  RCIKYLNQSVLEGRYITVERSRRKRPRTPT 105
           + +   +  + +G+ + + R    +P    
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRPHDYQPLPGA 94

>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 = 78.3 bits (193), Expect = 7e-19
 Identities = 22/104 (21%), Positives = 44/104 (42%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
                     +    G  L+VT +     E ++++ F   G++ +  L ++ RT  S+G+
Sbjct: 57  EDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGY 116

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
           A V  +  + A    + LN + + G+ I V+    K P+     
Sbjct: 117 ALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKS 160

>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 = 78.0 bits (193), Expect = 9e-19
 Identities = 18/88 (20%), Positives = 40/88 (45%), Gaps = 1/88 (1%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
            LYV  L   +TE  L+++F   G +A+  ++++ +   +  +AFV      DA   ++ 
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQT 60

Query: 81  LNQSVLEGRYITVERSRRKRPRTPTPGH 108
           LN   +E   + +  + + +  +     
Sbjct: 61  LNGKQIENNIVKINWAFQSQQSSSDDTF 88

>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 = 73.7 bits (182), Expect = 4e-17
 Identities = 18/90 (20%), Positives = 39/90 (43%)

Query: 9   SRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTM 68
            + +  + +    L+V  L+  V +  L   F       S  ++ + +T  SRG+ FV+ 
Sbjct: 77  FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSF 136

Query: 69  DGVEDAERCIKYLNQSVLEGRYITVERSRR 98
              +DA+  +  +    L GR + +  + +
Sbjct: 137 TSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166

>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 = 76.1 bits (188), Expect = 1e-18
 Identities = 28/102 (27%), Positives = 45/102 (44%), Gaps = 3/102 (2%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G      P  TL+V GLS   TE  L++ F          +V +  T  S+GF FV
Sbjct: 3   SGSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFV 59

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGH 108
             +  EDA+   + +    ++G  +T++ ++ K      P  
Sbjct: 60  DFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGPSS 101

>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 = 75.7 bits (187), Expect = 1e-18
 Identities = 23/95 (24%), Positives = 45/95 (47%), Gaps = 2/95 (2%)

Query: 16  GNPGN-TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVV-EPRTRISRGFAFVTMDGVED 73
           G+ G+  +++  L   + E+ L   FS  G +     ++ +P T  S+G+AF+     + 
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60

Query: 74  AERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGH 108
           ++  I+ +N   L  R ITV  + +K  +   P  
Sbjct: 61  SDAAIEAMNGQYLCNRPITVSYAFKKDSKGSGPSS 95

>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 = 75.3 bits (186), Expect = 1e-18
 Identities = 24/93 (25%), Positives = 41/93 (44%), Gaps = 8/93 (8%)

Query: 16  GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAE 75
           G     L+V  +S   T ++L   F + G V  C +V        + +AFV M+  EDA 
Sbjct: 7   GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAV 58

Query: 76  RCIKYLNQSVLEGRYITVERSRRKRPRTPTPGH 108
             I+ L+ +  +G+ + V+ S  +      P  
Sbjct: 59  EAIRGLDNTEFQGKRMHVQLSTSRLRTASGPSS 91

>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 = 75.8 bits (187), Expect = 1e-18
 Identities = 22/85 (25%), Positives = 43/85 (50%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
            G  L+VT +     E ++++ F   G++ +  L ++ RT  S+G+A V  +  + A   
Sbjct: 25  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84

Query: 78  IKYLNQSVLEGRYITVERSRRKRPR 102
            + LN + + G+ I V+    K P+
Sbjct: 85  KEALNGAEIMGQTIQVDWCFVKGPK 109

>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 = 79.0 bits (195), Expect = 2e-18
 Identities = 22/95 (23%), Positives = 43/95 (45%), Gaps = 6/95 (6%)

Query: 4  RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
            +S  +   +T      L+V  L T +TE D ++ F + G+ +  F+    R    RGF
Sbjct: 7  DIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI---NR---DRGF 60

Query: 64 AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR 98
           F+ ++    AE     L+ ++L+ R + +  +  
Sbjct: 61 GFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH 95

>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 = 67.0 bits (164), Expect = 6e-14
 Identities = 23/89 (25%), Positives = 34/89 (38%), Gaps = 5/89 (5%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
            G  L V  LS  V+   LE+ FS+ G V    +VV+ R R + G  FV       A + 
Sbjct: 95  HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGR-ATGKGFVEFAAKPPARKA 153

Query: 78  IKYLNQSVLEG----RYITVERSRRKRPR 102
           ++             R + VE   +    
Sbjct: 154 LERCGDGAFLLTTTPRPVIVEPMEQFDDE 182

>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 = 75.5 bits (186), Expect = 3e-18
 Identities = 30/113 (26%), Positives = 51/113 (45%), Gaps = 9/113 (7%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
            G  L+VTG+    TE D+   F++ G++ +  L ++ RT   +G+  V  +  ++A+  
Sbjct: 21  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 80

Query: 78  IKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDRGRYRSGR 130
           ++ LN   L G+ I+V+       R P  G        R   R  R   R  R
Sbjct: 81  MEGLNGQDLMGQPISVDWC---FVRGPPKGKR------RGGRRRSRSPDRRRR 124

>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 = 76.0 bits (187), Expect = 3e-18
 Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 5/95 (5%)

Query: 14  ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASC-----FLVVEPRTRISRGFAFVTM 68
           E G P   +YV  L+  V E+DL+  F +    +S      F +   +    +G AF+ +
Sbjct: 40  EPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGL 99

Query: 69  DGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRT 103
              + A + +K  N  VL G+ + V+ +R  RP+ 
Sbjct: 100 PNEKAAAKALKEANGYVLFGKPMVVQFARSARPKQ 134

>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 = 79.2 bits (194), Expect = 3e-18
 Identities = 29/165 (17%), Positives = 56/165 (33%), Gaps = 10/165 (6%)

Query: 18  PGNTLYVTGLSTRVTERDLEKH----FSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
           P +T+Y+  L+ ++ + +L+K     FS+ G++      +  R+   RG AFV    V  
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDI---LVSRSLKMRGQAFVIFKEVSS 64

Query: 74  AERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDRGRYRSGRDDY 133
           A   ++ +       + + ++ ++             G    RD  R  R          
Sbjct: 65  ATNALRSMQGFPFYDKPMRIQYAKTDSDI---IAKMKGTFVERDRKREKRKPKSQETPAT 121

Query: 134 GYRRSPRRSPYRGGRDYSPRHSPPYGGRSRRERSRSVPRSPYGSP 178
                   +    G    P    P   ++ R       + PY  P
Sbjct: 122 KKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPP 166

>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 = 45.6 bits (107), Expect = 2e-06
 Identities = 15/83 (18%), Positives = 27/83 (32%), Gaps = 6/83 (7%)

Query: 17  NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
            P + L++T L     E  L   F++        LV           AFV  D    A  
Sbjct: 205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG-----RHDIAFVEFDNEVQAGA 259

Query: 77  CIKYLN-QSVLEGRYITVERSRR 98
               L    + +   + +  +++
Sbjct: 260 ARDALQGFKITQNNAMKISFAKK 282

>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 = 75.5 bits (186), Expect = 3e-18
 Identities = 30/115 (26%), Positives = 52/115 (45%), Gaps = 1/115 (0%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
           S   S  + +T N  + ++V  LS  +T  D++  F+  G+++   +V +  T  S+G+ 
Sbjct: 2   SSGSSGQKKDTSNHFH-VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60

Query: 65  FVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIG 119
           FV+     DAE  I+ +    L GR I    + RK P   +       +S    G
Sbjct: 61  FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPSSG 115

>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 = 74.5 bits (184), Expect = 3e-18
 Identities = 25/89 (28%), Positives = 40/89 (44%), Gaps = 1/89 (1%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
            +YV  L    T   +++ FS+ GKV +  L+ +  T+  +GF FV M   E     I  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 81  LNQSVLEGRYITVERSRRKRPRTPTPGHY 109
           L+ +   GR I V  +  K+       H+
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLEHHHHHH 90

>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 = 75.0 bits (185), Expect = 4e-18
 Identities = 19/99 (19%), Positives = 39/99 (39%), Gaps = 1/99 (1%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
            S  +++   +       LY++ L   + E++LE      G+V S  ++ +  +  SRG 
Sbjct: 10  ASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGV 68

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPR 102
            F  M+  E  E  I + N   ++        +     +
Sbjct: 69  GFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCK 107

>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 = 74.6 bits (184), Expect = 4e-18
 Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 8/83 (9%)

Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
             L+V  L+  VTE  LEK FS+ GK+           +  + +AF+  D  + A + ++
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQFGKLERV--------KKLKDYAFIHFDERDGAVKAME 63

Query: 80  YLNQSVLEGRYITVERSRRKRPR 102
            +N   LEG  I +  ++    +
Sbjct: 64  EMNGKDLEGENIEIVFAKPPDQK 86

>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 = 74.1 bits (183), Expect = 4e-18
 Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 1/84 (1%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
              ++YV  +    T  +LE HF   G V    ++ +  +   +GFA++     E     
Sbjct: 5   DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64

Query: 78  IKYLNQSVLEGRYITVERSRRKRP 101
           +  L++S+  GR I V   R  RP
Sbjct: 65  LA-LDESLFRGRQIKVIPKRTNRP 87

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 74.7 bits (184), Expect = 4e-18
 Identities = 20/95 (21%), Positives = 36/95 (37%), Gaps = 8/95 (8%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRI--------SRGFAFVTMD 69
             NT++V GL   VT   +  +F + G + +     +P   +         +G A V+ D
Sbjct: 6   DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65

Query: 70  GVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTP 104
               A+  I + +     G  I V  + R+     
Sbjct: 66  DPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNR 100

>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 = 73.7 bits (182), Expect = 4e-18
 Identities = 18/80 (22%), Positives = 35/80 (43%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
            L+V  L+  V +  L   F       S  ++ + +T  SRG+ FV+    +DA+  + 
Sbjct: 2  FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 80 YLNQSVLEGRYITVERSRRK 99
           +    L GR + +  + + 
Sbjct: 62 SMQGQDLNGRPLRINWAAKL 81

>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 = 74.2 bits (183), Expect = 5e-18
 Identities = 26/88 (29%), Positives = 40/88 (45%), Gaps = 7/88 (7%)

Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
           N LY+  LS  VT  DL + F          L +  +  +  G+AFV       A R I+
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIE 62

Query: 80  YLN-QSVLEGRYITVERSRRKRPRTPTP 106
            L+ +  L G+ + V+ S  K+ R+  P
Sbjct: 63  TLSGKVELHGKIMEVDYSVSKKLRSSGP 90

>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 = 78.5 bits (194), Expect = 6e-18
 Identities = 22/88 (25%), Positives = 36/88 (40%)

Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
            TL++T      T+R++         VA    +   R   SR FA++ +   EDA  C++
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177

Query: 80  YLNQSVLEGRYITVERSRRKRPRTPTPG 107
            LN   +EG  +  + S        T  
Sbjct: 178 KLNGLKIEGYTLVTKVSNPLEKSKRTDS 205

>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 = 73.9 bits (182), Expect = 3e-16
 Identities = 21/98 (21%), Positives = 42/98 (42%), Gaps = 3/98 (3%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVT-ERDLEKHFSKEGKVASCFLVV-EPRTRISR 61
               +S+        G  + +  LST +  E  L + F   G +    +   +     + 
Sbjct: 195 NPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNN 254

Query: 62  GFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK 99
             AF+  +  + AER ++ +N+S+L  R I+V  + +K
Sbjct: 255 CCAFMVFENKDSAERALQ-MNRSLLGNREISVSLADKK 291

>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 = 65.0 bits (159), Expect = 4e-13
 Identities = 16/95 (16%), Positives = 30/95 (31%), Gaps = 4/95 (4%)

Query: 7   SRSRGRTETGNPGN-TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAF 65
           S+      T N    T+ V  L     +  + K+F   G +    +    +   +  FA 
Sbjct: 28  SKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFAR 85

Query: 66  VTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKR 100
           +     + A   I   ++ V+    I V       
Sbjct: 86  IEFARYDGALAAITKTHK-VVGQNEIIVSHLTECT 119

>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 = 73.8 bits (182), Expect = 7e-18
 Identities = 17/88 (19%), Positives = 41/88 (46%), Gaps = 7/88 (7%)

Query: 16 GNPGNTLYVTGLSTRVTERDLEKH----FSKEGKVASCFLVVEPRTRISRGFAFVTMDGV 71
            P +T+Y+  L+ ++ + +L+K     FS+ G++     ++  R+   RG AFV    V
Sbjct: 5  TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEV 61

Query: 72 EDAERCIKYLNQSVLEGRYITVERSRRK 99
            A   ++ +       + + ++ ++  
Sbjct: 62 SSATNALRSMQGFPFYDKPMRIQYAKTD 89

>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 = 73.9 bits (182), Expect = 7e-18
 Identities = 25/104 (24%), Positives = 43/104 (41%), Gaps = 4/104 (3%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G    G     L+V  L+ + +E D+ + F   G +  C ++  P    S+G AFV
Sbjct: 3   SGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGS-SKGCAFV 61

Query: 67  TMDGVEDAERCIKYLNQSVLE---GRYITVERSRRKRPRTPTPG 107
                 +A+  I  L+ S         + V+ +   +   P+ G
Sbjct: 62  KFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESGPSSG 105

>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 = 73.4 bits (181), Expect = 7e-18
 Identities = 24/86 (27%), Positives = 38/86 (44%), Gaps = 8/86 (9%)

Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
           L++  L    TE+++   F + GKV  C         I + + FV ++    AE  I+ L
Sbjct: 11  LFIGNLPREATEQEIRSLFEQYGKVLEC--------DIIKNYGFVHIEDKTAAEDAIRNL 62

Query: 82  NQSVLEGRYITVERSRRKRPRTPTPG 107
           +   L G  I VE S+ K   +  P 
Sbjct: 63  HHYKLHGVNINVEASKNKSKASSGPS 88

>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 = 73.4 bits (181), Expect = 8e-18
 Identities = 22/82 (26%), Positives = 38/82 (46%)

Query: 18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
              ++V  LS  +T   +   F+  G+++   +V +  T  S+G+ FV+     DAE  
Sbjct: 5  SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64

Query: 78 IKYLNQSVLEGRYITVERSRRK 99
          I+ +    L GR I    + RK
Sbjct: 65 IQQMGGQWLGGRQIRTNWATRK 86

>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 = 74.0 bits (182), Expect = 9e-18
 Identities = 24/105 (22%), Positives = 44/105 (41%), Gaps = 9/105 (8%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLST-RVTERDLEKHFSKEGKVASCFLVVEPRTRISRG 62
              S    + +  +  + +++  L+T  V + D+E  FSK G+VA C         + +G
Sbjct: 12  LQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGC--------SVHKG 63

Query: 63  FAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
           +AFV       A   +   N  VL G+ + +  +   +P    P 
Sbjct: 64  YAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSGPS 108

>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 = 73.9 bits (182), Expect = 1e-17
 Identities = 19/95 (20%), Positives = 41/95 (43%), Gaps = 6/95 (6%)

Query: 13  TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVE 72
            ++     T+Y  G+++ +T++ + + FS  G++    +  E      +G++FV     E
Sbjct: 19  NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHE 72

Query: 73  DAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
            A   I  +N + +EG  +     +     T  P 
Sbjct: 73  SAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPS 107

>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 = 73.5 bits (181), Expect = 1e-17
 Identities = 24/96 (25%), Positives = 43/96 (44%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
            + + +    +       LYV  L   +TE  L   F   G++ S  L+++  T  S+G+
Sbjct: 11  MAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGY 70

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK 99
            F+T    E A++ ++ LN   L GR + V     +
Sbjct: 71  GFITFSDSECAKKALEQLNGFELAGRPMKVGHVTER 106

>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 = 73.1 bits (180), Expect = 1e-17
 Identities = 27/101 (26%), Positives = 45/101 (44%), Gaps = 6/101 (5%)

Query: 9   SRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTM 68
           S G +       TL ++ LS   TE  L++ F K   +     V + +   S+G+AF+  
Sbjct: 5   SSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEF 60

Query: 69  DGVEDAERCIKYLNQSVLEGRYITV--ERSRRKRPRTPTPG 107
              EDA+  +   N+  +EGR I +  +  R      P+ G
Sbjct: 61  ASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGPSSG 101

>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 = 73.1 bits (180), Expect = 1e-17
 Identities = 26/102 (25%), Positives = 36/102 (35%), Gaps = 3/102 (2%)

Query: 6   RSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAF 65
                 R   GN    +YV  L   +  +D+E  F K G +    L      R    FAF
Sbjct: 9   SGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAF 65

Query: 66  VTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
           V  +   DAE  +   +    +G  + VE  R  R     P 
Sbjct: 66  VEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSGPS 107

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 72.9 bits (179), Expect = 2e-17
 Identities = 19/88 (21%), Positives = 28/88 (31%), Gaps = 3/88 (3%)

Query: 7  SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
          S S G          L +  +   +    L+    + G V SC  V    T        V
Sbjct: 3  SGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQV---NTDSETAVVNV 59

Query: 67 TMDGVEDAERCIKYLNQSVLEGRYITVE 94
          T    + A + +  LN   LE   + V 
Sbjct: 60 TYSSKDQARQALDKLNGFQLENFTLKVA 87

>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 = 72.7 bits (179), Expect = 2e-17
 Identities = 18/97 (18%), Positives = 35/97 (36%), Gaps = 9/97 (9%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTR-VTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
               S       +  + L++  L  + V++ DL + FS  G +            I   F
Sbjct: 8   HHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQI--------NIKNAF 59

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKR 100
            F+  D  +     I+  +Q +  G+ + +E S    
Sbjct: 60  GFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA 96

>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 = 72.7 bits (179), Expect = 2e-17
 Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 8/84 (9%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRI--------SRGFAFVTMDGV 71
          NT++V GL   VT   +  +F + G + +     +P   +         +G A V+ D  
Sbjct: 14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 72 EDAERCIKYLNQSVLEGRYITVER 95
            A+  I + +     G  I V  
Sbjct: 74 PSAKAAIDWFDGKEFSGNPIKVSF 97

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

 Score = 72.2 bits (178), Expect = 2e-17
 Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 2/90 (2%)

Query: 13  TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVE 72
           +   +    ++V  L    T + L+  F++ G V    + +E     S+G   V  +  E
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPE 59

Query: 73  DAERCIKYLNQSVLEGRYITVERSRRKRPR 102
            AER  + +N   L GR I V   R     
Sbjct: 60  VAERACRMMNGMKLSGREIDVRIDRNASGP 89

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 73.0 bits (179), Expect = 3e-17
 Identities = 13/88 (14%), Positives = 32/88 (36%), Gaps = 7/88 (7%)

Query: 16  GNPGNTLYVTGLSTRVTERDLEKH----FSKEGKVASCFLVVEPRTRISRGFAFVTMDGV 71
             P   + +T ++  V +  L+       S +G +     +V   +  + G A++     
Sbjct: 26  TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILD---IVVDLSDDNSGKAYIVFATQ 82

Query: 72  EDAERCIKYLNQSVLEGRYITVERSRRK 99
           E A+  ++       +G  + +  S   
Sbjct: 83  ESAQAFVEAFQGYPFQGNPLVITFSETP 110

>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 = 72.3 bits (178), Expect = 3e-17
 Identities = 20/83 (24%), Positives = 45/83 (54%), Gaps = 3/83 (3%)

Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
           NT++V G+  R+ E ++   F++ G V    ++ + RT +S+G+ FV+     D ++ ++
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVE 68

Query: 80  YLNQSVLEGRYITVERSRRKRPR 102
             +Q    G+ + +  + RK+  
Sbjct: 69  --SQINFHGKKLKLGPAIRKQNL 89

>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 = 75.0 bits (185), Expect = 3e-17
 Identities = 29/100 (29%), Positives = 46/100 (46%)

Query: 9   SRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTM 68
           S   +    P  +LYV  L   VTE  L + FS  G + S  +  +  TR S G+A+V  
Sbjct: 5   SMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNF 64

Query: 69  DGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGH 108
               DAER +  +N  V++G+ + +  S+R      +   
Sbjct: 65  QQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVG 104

>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 = 73.9 bits (182), Expect = 1e-16
 Identities = 25/99 (25%), Positives = 45/99 (45%), Gaps = 2/99 (2%)

Query: 9   SRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTM 68
            R  +   +    +++  L   +  + L   FS  G + SC +V +     S+G+ FV  
Sbjct: 93  QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHF 150

Query: 69  DGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
           +  E AER I+ +N  +L  R + V R + ++ R    G
Sbjct: 151 ETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELG 189

>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 = 71.1 bits (175), Expect = 9e-17
 Identities = 17/87 (19%), Positives = 43/87 (49%), Gaps = 1/87 (1%)

Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
           ++V G+     E +L ++F K G V    ++ +   +  RGF F+T +  +  ++ +  +
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-M 71

Query: 82  NQSVLEGRYITVERSRRKRPRTPTPGH 108
           +   + G+ + V+R+  +  ++  P  
Sbjct: 72  HFHDIMGKKVEVKRAEPRDSKSSGPSS 98

>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 = 74.0 bits (181), Expect = 9e-17
 Identities = 28/174 (16%), Positives = 48/174 (27%), Gaps = 8/174 (4%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEG--KVASCFLVVEPRTRISRGFA 64
           +              LY+  L+   T+ DL +     G   +             S+GFA
Sbjct: 56  AAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFA 115

Query: 65  FVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDRG 124
            V +     +++ +  L +  L G+   V    ++             +S +  G G  G
Sbjct: 116 LVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAG 175

Query: 125 RYRSGRDDYGYRRSPRRSPYRGGRDYSPRHSPPYGGRSRRERSRSVPRSPYGSP 178
                      +    R  + G      R   P G           P  P G  
Sbjct: 176 PPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPG------GPPPPFPAGQT 223

>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 = 70.8 bits (174), Expect = 1e-16
 Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 1/86 (1%)

Query: 9   SRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTM 68
             G       G  L V+ L   V++ D+++ F++ G +    +  + R+  S G A V  
Sbjct: 19  GFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHF 77

Query: 69  DGVEDAERCIKYLNQSVLEGRYITVE 94
           +   DA + +K  N   L+GR + ++
Sbjct: 78  ERKADALKAMKQYNGVPLDGRPMNIQ 103

>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 = 71.3 bits (175), Expect = 1e-16
 Identities = 19/82 (23%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           ++YV  +    T +DLE HFS  G +    ++ +  +   +G+A++        +  +  
Sbjct: 38  SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA- 96

Query: 81  LNQSVLEGRYITVERSRRKRPR 102
           ++++V  GR I V   R   P 
Sbjct: 97  MDETVFRGRTIKVLPKRTNMPG 118

>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 = 70.5 bits (173), Expect = 2e-16
 Identities = 19/84 (22%), Positives = 36/84 (42%), Gaps = 3/84 (3%)

Query: 17  NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
                LY+  L  ++T  ++   F K G +     +    T  +RG A+V  + + DA+ 
Sbjct: 6   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKN 62

Query: 77  CIKYLNQSVLEGRYITVERSRRKR 100
            + +L+   +  RY+ V      R
Sbjct: 63  AVDHLSGFNVSNRYLVVLYYNANR 86

>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 = 70.4 bits (173), Expect = 2e-16
 Identities = 23/105 (21%), Positives = 45/105 (42%), Gaps = 6/105 (5%)

Query: 9   SRGRTETGNPGNT-LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVT 67
           S G +   +     L++  +   + E+DL+  F + GK+    ++ +  T + +G AF+T
Sbjct: 2   SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61

Query: 68  MDGVEDAERCIKYLNQSVL---EGRYITVE--RSRRKRPRTPTPG 107
               E A +    L++        R I V+   S  +    P+ G
Sbjct: 62  YCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRGGSGPSSG 106

>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 = 69.6 bits (171), Expect = 2e-16
 Identities = 20/92 (21%), Positives = 40/92 (43%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
           P   +Y+  +    TE  +    S  G V +  ++ +P+T  S+G+AF+    +E +   
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 78  IKYLNQSVLEGRYITVERSRRKRPRTPTPGHY 109
           ++ LN   L  R++    S        +  H+
Sbjct: 61  VRNLNGYQLGSRFLKCGYSSNSDISGVSLEHH 92

>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 = 70.0 bits (172), Expect = 2e-16
 Identities = 22/95 (23%), Positives = 39/95 (41%)

Query: 17  NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
               +++V  +    TE  L+  FS+ G V S  LV +  T   +G+ F      E A  
Sbjct: 6   RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65

Query: 77  CIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLG 111
            ++ LN     GR + V+ +  ++ +        G
Sbjct: 66  AMRNLNGREFSGRALRVDNAASEKNKEELKSLGTG 100

>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 = 71.9 bits (177), Expect = 3e-16
 Identities = 14/84 (16%), Positives = 30/84 (35%), Gaps = 2/84 (2%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRI--SRGFAFVTMDGVEDAERCI 78
            ++V  +    +E+DL + F + G V    ++ +       S+G  FVT    + A    
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 79  KYLNQSVLEGRYITVERSRRKRPR 102
             L+   +        + +     
Sbjct: 65  NALHNMKVLPGMHHPIQMKPADSE 88

>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 = 68.4 bits (168), Expect = 5e-15
 Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 2/81 (2%)

Query: 9   SRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTM 68
           +            L++  +S + TE D+   FS  G++  C ++  P    SRG AFVT 
Sbjct: 85  ADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGL-SRGCAFVTF 143

Query: 69  DGVEDAERCIKYLNQS-VLEG 88
                A+  IK ++Q+  +EG
Sbjct: 144 TTRAMAQTAIKAMHQAQTMEG 164

>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 = 69.6 bits (171), Expect = 3e-16
 Identities = 18/89 (20%), Positives = 37/89 (41%), Gaps = 2/89 (2%)

Query: 14  ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
                   L++  L+   +  +L+   S+         VV+ RT  +R F +V  +  ED
Sbjct: 12  SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAED 70

Query: 74  AERCIKYLNQSVLEGRYITVERSRRKRPR 102
            E+ ++ L    + G  I +E+ + +   
Sbjct: 71  LEKALE-LTGLKVFGNEIKLEKPKGRDGT 98

>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 = 69.6 bits (171), Expect = 4e-16
 Identities = 26/103 (25%), Positives = 47/103 (45%), Gaps = 2/103 (1%)

Query: 6   RSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAF 65
            S S G        + L V GL  + TE+DL+++FS  G+V    +  + +T  S+GF F
Sbjct: 2   SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF 61

Query: 66  VTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGH 108
           V     E   + +   +  +++GR+   +    K+ +   P  
Sbjct: 62  VRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQDSGPSS 102

>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 = 68.8 bits (169), Expect = 6e-16
 Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 2/83 (2%)

Query: 22  LYVTGLSTRVTERDLEKHFSKEG--KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
           LY+  L+   T+ DL +     G   +             S+GFA V +     +++ + 
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 80  YLNQSVLEGRYITVERSRRKRPR 102
            L +  L G+   V  S +    
Sbjct: 64  LLPKRELHGQNPVVTPSNKLEHH 86

>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 = 69.2 bits (170), Expect = 7e-16
 Identities = 28/92 (30%), Positives = 45/92 (48%), Gaps = 2/92 (2%)

Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
           ++V GL    T+  L K+F   G +    ++ + +T  SRG+ FVTM     AER  K  
Sbjct: 20  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79

Query: 82  NQSVLEGRYITVER-SRRKRPRTPTPGHYLGL 112
           N  +++GR   V       +PR+   G  +G+
Sbjct: 80  NP-IIDGRKANVNLAYLGAKPRSLQTGFAIGV 110

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 68.5 bits (168), Expect = 9e-16
 Identities = 19/73 (26%), Positives = 26/73 (35%), Gaps = 6/73 (8%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          T Y+  +    TE DL   F   G +       E      +G  F+  D  E A  CI  
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVA 82

Query: 81 LNQSVLEGRYITV 93
          L     +GR +  
Sbjct: 83 LANFPFQGRNLRT 95

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

 Score = 68.2 bits (167), Expect = 1e-15
 Identities = 18/73 (24%), Positives = 33/73 (45%)

Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
               +      V ++ L   FSK GKV +    ++  T  ++GF FV    + DA++ I
Sbjct: 12 NGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKII 71

Query: 79 KYLNQSVLEGRYI 91
          K  +   L+ ++ 
Sbjct: 72 KSFHGKRLDLKHR 84

>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 = 68.0 bits (166), Expect = 2e-15
 Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 6/86 (6%)

Query: 20  NTLYVTGLSTRVTERDLEK---HFSKEGKVASCFLV---VEPRTRISRGFAFVTMDGVED 73
           N ++V GLS R+ + ++ K   +F K GK+    +        ++     A+VT    ED
Sbjct: 16  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75

Query: 74  AERCIKYLNQSVLEGRYITVERSRRK 99
           A R I+ +N  V++GR +       K
Sbjct: 76  ALRAIQCVNNVVVDGRTLKASLGTTK 101

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 66.3 bits (163), Expect = 3e-15
 Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V GLS   T  D++ +F + GKV    L+ +  T   RGF FVT +  +  E+  +  
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 82 NQSVLEGRYITVER 95
              +  + +  ++
Sbjct: 62 FH-EINNKMVECKK 74

>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 = 69.2 bits (169), Expect = 4e-15
 Identities = 28/125 (22%), Positives = 46/125 (36%), Gaps = 9/125 (7%)

Query: 16  GNPGNTLYVTGLST-RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDA 74
           GN    L V+ L+  RVT + L   F   G V    ++        +  A V M     A
Sbjct: 2   GNS--VLLVSNLNPERVTPQSLFILFGVYGDVQRVKIL-----FNKKENALVQMADGNQA 54

Query: 75  ERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDRGRYRSGRDDYG 134
           +  + +LN   L G+ I +  S+ +  + P  G       ++D G     R++       
Sbjct: 55  QLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQE-DQGLTKDYGNSPLHRFKKPGSKNF 113

Query: 135 YRRSP 139
               P
Sbjct: 114 QNIFP 118

>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 = 62.6 bits (152), Expect = 1e-12
 Identities = 23/96 (23%), Positives = 41/96 (42%), Gaps = 5/96 (5%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
            +  S+       P  TL+++ +   V+E DL+  FS  G V   F   +      R  A
Sbjct: 106 KKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMA 161

Query: 65  FVTMDGVEDAERCIKYLN-QSVLEGRYITVERSRRK 99
            + M  VE+A + +  L+   + E  ++ V  S+  
Sbjct: 162 LIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 197

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 68.7 bits (168), Expect = 4e-15
 Identities = 21/99 (21%), Positives = 41/99 (41%), Gaps = 1/99 (1%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
                  G  E    G  L V+ L   V++ D+++ F++ G +    +  + R+  S G 
Sbjct: 73  DLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGT 131

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPR 102
           A V  +   DA + +K      L+GR + ++    +   
Sbjct: 132 ADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDL 170

>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 = 66.5 bits (163), Expect = 5e-15
 Identities = 17/90 (18%), Positives = 40/90 (44%), Gaps = 5/90 (5%)

Query: 13  TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVE 72
           ++      TL    LS  +TE +L++ F    ++      +  +   S+G A++      
Sbjct: 10  SKKVRAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEA 64

Query: 73  DAERCIKYLNQSVLEGRYITVERSRRKRPR 102
           DAE+ ++    + ++GR +++  +  K   
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGEKGGT 94

>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 = 67.9 bits (167), Expect = 5e-15
 Identities = 24/85 (28%), Positives = 46/85 (54%), Gaps = 4/85 (4%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
            +++ GL+   TE +L ++F K G V    ++ +P T  SRGF F++ +     +  +K 
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK- 63

Query: 81  LNQSVLEGRYITVER--SRRKRPRT 103
             Q +L+G+ I  +R   R ++ +T
Sbjct: 64  -TQHILDGKVIDPKRAIPRDEQDKT 87

>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 = 66.0 bits (162), Expect = 3e-14
 Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 1/83 (1%)

Query: 14  ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
           +  +    ++V G+   V  ++ E+ FS+ G +    L+++  T  SRGF FVT D  + 
Sbjct: 82  DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141

Query: 74  AERCIKYLNQSVLEGRYITVERS 96
            +R  +       + R I ++R+
Sbjct: 142 VDRVCQ-NKFIDFKDRKIEIKRA 163

>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 = 66.4 bits (162), Expect = 6e-15
 Identities = 21/101 (20%), Positives = 36/101 (35%), Gaps = 8/101 (7%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G     +    ++V GL   V E DL +   K G +    +         +  A V
Sbjct: 3   SGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM------MPFKRQALV 56

Query: 67  TMDGVEDAERCIKYL--NQSVLEGRYITVERSRRKRPRTPT 105
             + ++ A+ C+ +       + G+      S  KR   P 
Sbjct: 57  EFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPG 97

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 67.6 bits (165), Expect = 8e-15
 Identities = 18/101 (17%), Positives = 35/101 (34%), Gaps = 2/101 (1%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEG--KVASCFLVVEPRTRISR 61
           ++ +     +   N    +YV   S   T++ L +     G   V             S+
Sbjct: 40  KTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSK 99

Query: 62  GFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPR 102
           G+A V +       + ++ L   VL G  + V  + R+   
Sbjct: 100 GYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLS 140

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 65.2 bits (160), Expect = 8e-15
 Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          +++ GLS + T+  L ++F + G+V  C ++ +P T+ SRGF FVT       ++ +   
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 82 NQSVLEGRYITVER 95
              L+ + I  + 
Sbjct: 63 RH-ELDSKTIDPKV 75

>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 = 65.4 bits (160), Expect = 8e-15
 Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 12/85 (14%)

Query: 15 TGNPGN-----TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMD 69
          +G+ G      TLYV GL   +TE DL  HF + G++ +  +V        +  AF+   
Sbjct: 3  SGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFA 56

Query: 70 GVEDAERCIKY-LNQSVLEGRYITV 93
            + AE   +   N+ ++ GR + V
Sbjct: 57 TRQAAEVAAEKSFNKLIVNGRRLNV 81

>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 = 65.2 bits (160), Expect = 8e-15
 Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V GLS    E  + ++F   G+V S  L ++ +T   RGF F+T    E  ++ ++  
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 82 NQSVLEGRYITVER 95
              +      ++ 
Sbjct: 62 YH-NVGLSKCEIKV 74

>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 = 65.7 bits (161), Expect = 9e-15
 Identities = 30/105 (28%), Positives = 44/105 (41%), Gaps = 7/105 (6%)

Query: 9   SRGRTETGNPGNT----LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
           S G +   N G      L+V GL    T+  L  +FS+ G+V  C ++ +  T  SRGF 
Sbjct: 2   SSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFG 61

Query: 65  FVTMDGVEDAERCIKYLNQSVLEGRYITVER--SRRKRPRTPTPG 107
           FV           +       L+GR I  +    R  +P  P+ G
Sbjct: 62  FVKFKDPNCVGTVLASRPH-TLDGRNIDPKPCTPRGMQPSGPSSG 105

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 65.6 bits (160), Expect = 1e-14
 Identities = 18/98 (18%), Positives = 33/98 (33%), Gaps = 5/98 (5%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
           S        E       +YV  L       DL++   + G V      +    +  R  A
Sbjct: 5   SSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-----LRLTWQGPRRRA 59

Query: 65  FVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPR 102
           F+       A++ +  L    L    + V  +R++R +
Sbjct: 60  FLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRDK 97

>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 = 65.4 bits (160), Expect = 1e-14
 Identities = 13/90 (14%), Positives = 29/90 (32%)

Query: 7  SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
          S S G +        + V  +   V+  ++   F     +     +      +  G A V
Sbjct: 3  SGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62

Query: 67 TMDGVEDAERCIKYLNQSVLEGRYITVERS 96
            +  ++A   +  LN   +  R + +   
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKVKLSGP 92

>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 = 67.8 bits (165), Expect = 1e-14
 Identities = 25/127 (19%), Positives = 41/127 (32%), Gaps = 7/127 (5%)

Query: 16  GNPGNTLYVTGLST-RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDA 74
           G     L V GL   ++    +   F   G V     +     +   G A V M      
Sbjct: 1   GADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFM-----KSKPGAAMVEMADGYAV 55

Query: 75  ERCIKYLNQSVLEGRYITVERSRRKRPRTPTP-GHYLGLKSSRDIGRGDRGRYRSGRDDY 133
           +R I +LN + + G+ + V  S++         G   G  S +D       R+ +     
Sbjct: 56  DRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAA 115

Query: 134 GYRRSPR 140
             R    
Sbjct: 116 KNRIQHP 122

>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 = 65.5 bits (159), Expect = 9e-14
 Identities = 14/94 (14%), Positives = 28/94 (29%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
           S      +    +P N L+       VTE +  +   + G      + V           
Sbjct: 109 STPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSG 168

Query: 65  FVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR 98
            +  D   DA   + +LN   ++        + +
Sbjct: 169 LLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLK 202

>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 = 68.1 bits (166), Expect = 2e-14
 Identities = 26/141 (18%), Positives = 47/141 (33%), Gaps = 6/141 (4%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLST-RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
              R       G   + L V+ L+  RVT + L   F   G V    ++        +  
Sbjct: 20  HMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKEN 74

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDR 123
           A V M     A+  + +LN   L G+ I +  S+ +  + P  G      +         
Sbjct: 75  ALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLH 134

Query: 124 GRYRSGRDDYGYRRSPRRSPY 144
              + G  ++     P  + +
Sbjct: 135 RFKKPGSKNFQNIFPPSATLH 155

>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 = 58.1 bits (140), Expect = 7e-11
 Identities = 23/96 (23%), Positives = 41/96 (42%), Gaps = 5/96 (5%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
            +  S+       P  TL+++ +   V+E DL+  FS  G V   F       +  R  A
Sbjct: 137 KKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF----KFFQKDRKMA 192

Query: 65  FVTMDGVEDAERCIKYLN-QSVLEGRYITVERSRRK 99
            + M  VE+A + +  L+   + E  ++ V  S+  
Sbjct: 193 LIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228

>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 = 65.0 bits (159), Expect = 2e-14
 Identities = 13/93 (13%), Positives = 29/93 (31%)

Query: 7  SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
          S S G +        + V  +   V+  ++   F     +     +      +  G A V
Sbjct: 3  SGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62

Query: 67 TMDGVEDAERCIKYLNQSVLEGRYITVERSRRK 99
            +  ++A   +  LN   +  R + +      
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP 95

>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 = 65.0 bits (159), Expect = 2e-14
 Identities = 19/84 (22%), Positives = 35/84 (41%), Gaps = 1/84 (1%)

Query: 11 GRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEG-KVASCFLVVEPRTRISRGFAFVTMD 69
          G + +     +L++  L   + E  + + F+  G  V S  ++    T I  G+ FV   
Sbjct: 1  GSSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFA 60

Query: 70 GVEDAERCIKYLNQSVLEGRYITV 93
           +  AE+C+  +N   L G     
Sbjct: 61 DLATAEKCLHKINGKPLPGATPAK 84

>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 = 64.5 bits (158), Expect = 2e-14
 Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V GLS   +++DL+ +F+K G+V  C + ++P T  SRGF F+        E+ +   
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73

Query: 82 NQSVLEGRYITVER 95
              L+GR I  ++
Sbjct: 74 EH-RLDGRVIDPKK 86

>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 = 64.8 bits (158), Expect = 2e-14
 Identities = 24/104 (23%), Positives = 39/104 (37%), Gaps = 8/104 (7%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G    G P   L++  L   VTE ++       GKV +  ++        +  AF+
Sbjct: 3   SGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK------GKNQAFL 56

Query: 67  TMDGVEDAERCIKY--LNQSVLEGRYITVERSRRKRPRTPTPGH 108
            +   E A   + Y       L  + I ++ S  K  +T  P  
Sbjct: 57  ELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELKTSGPSS 100

>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 = 65.0 bits (159), Expect = 2e-14
 Identities = 23/83 (27%), Positives = 44/83 (53%), Gaps = 3/83 (3%)

Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
           +++ GLS + T+  L ++F + G+V  C ++ +P T+ SRGF FVT       ++ +   
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87

Query: 82  NQSVLEGRYITVER--SRRKRPR 102
               L+ + I  +    RR +P+
Sbjct: 88  RH-ELDSKTIDPKVAFPRRAQPK 109

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

 Score = 64.6 bits (158), Expect = 3e-14
 Identities = 27/103 (26%), Positives = 43/103 (41%), Gaps = 5/103 (4%)

Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
           +YV  L T   + +LE+ FS  G + + ++      R   GFAFV  +   DAE  ++ L
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIA-----RNPPGFAFVEFEDPRDAEDAVRGL 57

Query: 82  NQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDRG 124
           +  V+ G  + VE S     R+         K    +  G   
Sbjct: 58  DGKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEVLFNGPLE 100

>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 = 63.6 bits (155), Expect = 5e-14
 Identities = 13/88 (14%), Positives = 28/88 (31%), Gaps = 7/88 (7%)

Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
           + + V  L      +++               +       ++  AFVT+   E A+  I+
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 80  YLNQSVLEGRYITVERSRRKRPRTPTPG 107
             +Q    G+ + V+           P 
Sbjct: 59  MFHQYSFRGKDLIVQLQPTDALLCSGPS 86

>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 = 63.4 bits (155), Expect = 6e-14
 Identities = 20/101 (19%), Positives = 38/101 (37%), Gaps = 10/101 (9%)

Query: 6   RSRSRGRTETG--NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
            S S G+   G  NP   L+V GL    +   L + F + G + +              F
Sbjct: 2   SSGSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTI------DHVKGDSF 55

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEG--RYITVERSRRKRPR 102
           A++  + ++ A+     +    L G  R + V+ ++     
Sbjct: 56  AYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPSS 96

>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 = 63.8 bits (156), Expect = 6e-14
 Identities = 21/101 (20%), Positives = 43/101 (42%), Gaps = 3/101 (2%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRI-SRGFAF 65
           S S G     +P  T ++  L   VTE  +++ F     +++  L  EP      +GF +
Sbjct: 3   SGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFR-GLNISAVRLPREPSNPERLKGFGY 61

Query: 66  VTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTP 106
              + ++     +  LN+  L  + I V+ + + + +   P
Sbjct: 62  AEFEDLDSLLSALS-LNEESLGNKRIRVDVADQAQDKDSGP 101

>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 = 65.4 bits (160), Expect = 8e-14
 Identities = 19/100 (19%), Positives = 37/100 (37%), Gaps = 1/100 (1%)

Query: 8   RSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVT 67
               R         ++V G+     E  L  +F + GK+    ++ +  +   RGFAFVT
Sbjct: 93  EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVT 152

Query: 68  MDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
            D  +  ++ +       + G    V ++  K+       
Sbjct: 153 FDDHDSVDKIVI-QKYHTVNGHNCEVRKALSKQEMASASS 191

>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 = 65.4 bits (160), Expect = 8e-14
 Identities = 26/92 (28%), Positives = 44/92 (47%), Gaps = 1/92 (1%)

Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
           L++ GLS   T+  L  HF + G +  C ++ +P T+ SRGF FVT   VE+ +  +   
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-A 74

Query: 82  NQSVLEGRYITVERSRRKRPRTPTPGHYLGLK 113
               ++GR +  +R+  +        H    K
Sbjct: 75  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKK 106

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 62.9 bits (153), Expect = 1e-13
 Identities = 18/104 (17%), Positives = 34/104 (32%), Gaps = 10/104 (9%)

Query: 1   MVFRSRSRSRGRTETGN--PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTR 58
           M            +         +++ GL   V E DL +   + G ++   ++      
Sbjct: 1   MGHHHHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------ 54

Query: 59  ISRGFAFVTMDGVEDAERCIKYL--NQSVLEGRYITVERSRRKR 100
             +  A V  + V  A   + Y   NQ  + G    V  S  ++
Sbjct: 55  PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK 98

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 63.1 bits (154), Expect = 1e-13
 Identities = 23/103 (22%), Positives = 42/103 (40%), Gaps = 3/103 (2%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
           S   S     T  P  T YV  L     + D++  F  +  + S  LV +  T   +GF 
Sbjct: 2   SSGSSGKELPT-EPPYTAYVGNLPFNTVQGDIDAIFK-DLSIRSVRLVRDKDTDKFKGFC 59

Query: 65  FVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
           +V  D V+  +  +   + ++L  R + V+ +  ++     P 
Sbjct: 60  YVEFDEVDSLKEALT-YDGALLGDRSLRVDIAEGRKQDKSGPS 101

>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 = 62.7 bits (153), Expect = 2e-13
 Identities = 22/86 (25%), Positives = 43/86 (50%), Gaps = 1/86 (1%)

Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
           L++ GLS   TE  L  ++ + GK+  C ++ +P ++ SRGF FVT   + + +  +   
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89

Query: 82  NQSVLEGRYITVERSRRKRPRTPTPG 107
               ++GR +  +R+  +      P 
Sbjct: 90  PH-SIDGRVVEPKRAVAREESGSGPS 114

>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 = 62.5 bits (152), Expect = 2e-13
 Identities = 16/89 (17%), Positives = 31/89 (34%), Gaps = 4/89 (4%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGK-VASCFLVVEPR-TRISRGFAFVTMDGVEDAE 75
               L++ G+       ++ +  +K  + V    +         +RGFAFV  +    A 
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 76  RCIKYLNQS--VLEGRYITVERSRRKRPR 102
              + L      L G  I V+ +  +   
Sbjct: 67  MARRKLMPGRIQLWGHQIAVDWAEPEIDV 95

>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 = 63.4 bits (154), Expect = 2e-13
 Identities = 22/98 (22%), Positives = 38/98 (38%), Gaps = 5/98 (5%)

Query: 3   FRSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRG 62
                      ++      +YV  L     + +LE+ F   G + S ++      R   G
Sbjct: 57  GSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVA-----RNPPG 111

Query: 63  FAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKR 100
           FAFV  +   DA   ++ L+   L G  + VE S  ++
Sbjct: 112 FAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK 149

>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 = 61.5 bits (150), Expect = 3e-13
 Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 7/87 (8%)

Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
           ++V   +  +TE +L + FS+ G V   F+      +  R FAFVT    + A+      
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIAQSLCG-- 60

Query: 82  NQSVLEGRYITVERSRRKRPRTPTPGH 108
              +++G  + +  +  K      P  
Sbjct: 61  EDLIIKGISVHISNAEPKHNSNSGPSS 87

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 62.1 bits (151), Expect = 3e-13
 Identities = 18/97 (18%), Positives = 35/97 (36%), Gaps = 1/97 (1%)

Query: 6   RSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAF 65
            S S G  +  +     ++T +   +T+ D+ +         +   V+        G A 
Sbjct: 2   SSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQAL 61

Query: 66  VTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPR 102
           V     +DA +  + L++  L GR   V     +  R
Sbjct: 62  VQFKNEDDARKSER-LHRKKLNGREAFVHVVTLEDMR 97

>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 = 60.8 bits (148), Expect = 6e-13
 Identities = 20/84 (23%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDA 74
          +G   +T+ + G    VTE+++ +  +   K  +  +V         G+ FV     E+ 
Sbjct: 6  SGTTCHTVKLRGAPFNVTEKNVMEFLA-PLKPVAIRIVRNAHGN-KTGYIFVDFSNEEEV 63

Query: 75 ERCIKYLNQSVLEGRYITVERSRR 98
          ++ +K  N+  + GRYI V R + 
Sbjct: 64 KQALK-CNREYMGGRYIEVFREKS 86

>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 = 60.9 bits (148), Expect = 7e-13
 Identities = 25/100 (25%), Positives = 42/100 (42%), Gaps = 1/100 (1%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G +        + + GL    ++ ++ + FS    V +   +       S G AFV
Sbjct: 3   SGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFV 62

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTP 106
                E AE+ +K  ++  +  RYI + +S R   RT  P
Sbjct: 63  QFASQEIAEKALK-KHKERIGHRYIEIFKSSRAEVRTSGP 101

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 60.6 bits (147), Expect = 8e-13
 Identities = 23/102 (22%), Positives = 40/102 (39%), Gaps = 8/102 (7%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
             S       +G P   +++  L   VTE ++       GKV +  ++        +  A
Sbjct: 2   RGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK------GKNQA 55

Query: 65  FVTMDGVEDAERCIKYL--NQSVLEGRYITVERSRRKRPRTP 104
           F+ M+  E A   + Y      VL G+ I ++ S  K  +T 
Sbjct: 56  FIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTD 97

>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 = 60.7 bits (147), Expect = 1e-12
 Identities = 23/102 (22%), Positives = 39/102 (38%), Gaps = 8/102 (7%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
             S        G P   +++  L   VTE ++       GKV +  ++        +  A
Sbjct: 17  RGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK------GKNQA 70

Query: 65  FVTMDGVEDAERCIKY--LNQSVLEGRYITVERSRRKRPRTP 104
           F+ M+  E A   + Y      VL G+ I ++ S  K  +T 
Sbjct: 71  FIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTD 112

>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 = 60.3 bits (147), Expect = 1e-12
 Identities = 20/98 (20%), Positives = 41/98 (41%), Gaps = 4/98 (4%)

Query: 5   SRSRSRGRTET-GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRI-SRG 62
           S      R+    +P  T ++  L   VTE  +++ F     +++  L  EP      +G
Sbjct: 4   SHHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFR-GLNISAVRLPREPSNPERLKG 62

Query: 63  FAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKR 100
           F +   + ++     +  LN+  L  R I V+ + + +
Sbjct: 63  FGYAEFEDLDSLLSALS-LNEESLGNRRIRVDVADQAQ 99

>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 = 58.8 bits (143), Expect = 3e-12
 Identities = 19/90 (21%), Positives = 40/90 (44%), Gaps = 7/90 (7%)

Query: 10 RGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMD 69
          RG     + G+ ++V   +  +T  +L++ F + G+V   F+      +  R FAFVT  
Sbjct: 2  RGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFA 56

Query: 70 GVEDAERCIKYLNQSVLEGRYITVERSRRK 99
            + A+         +++G  + +  +  K
Sbjct: 57 DDKVAQSLCG--EDLIIKGISVHISNAEPK 84

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 58.9 bits (143), Expect = 3e-12
 Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 3/93 (3%)

Query: 7  SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
          S S G +     G+ +++ GL  R TE D+   FS         + + P  R   G A V
Sbjct: 3  SGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFS-PLNPMRVHIEIGPDGR-VTGEADV 60

Query: 67 TMDGVEDAERCIKYLNQSVLEGRYITVERSRRK 99
               EDA   +   +++ ++ RY+ +  +   
Sbjct: 61 EFATHEDAVAAMA-KDKANMQHRYVELFLNSTA 92

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

 Score = 58.1 bits (141), Expect = 5e-12
 Identities = 22/91 (24%), Positives = 36/91 (39%), Gaps = 6/91 (6%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           +++V+G    V    L ++F   G VAS  +      +    FA V M  V   E  +  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVM-----DKDKGVFAIVEMGDVGAREAVLS- 63

Query: 81  LNQSVLEGRYITVERSRRKRPRTPTPGHYLG 111
            +Q  L G  + V    +K  ++P      G
Sbjct: 64  QSQHSLGGHRLRVRPREQKEFQSPASKSPKG 94

>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 = 58.7 bits (142), Expect = 6e-12
 Identities = 11/88 (12%), Positives = 25/88 (28%), Gaps = 6/88 (6%)

Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
             +    L       ++++ FS+ G +    L            A V      +A +  +
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAFR 64

Query: 80  YLNQSVLEGRYITVERSRRKRPRTPTPG 107
           +L  S      + +E +           
Sbjct: 65  HLAYSKFHHVPLYLEWAPIGVFGAAPQK 92

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

 Score = 58.6 bits (142), Expect = 6e-12
 Identities = 13/78 (16%), Positives = 33/78 (42%), Gaps = 2/78 (2%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
           ++Y+ G  T  T  D+++    +G+V +  +      +  +G  FV  D +E A++ ++
Sbjct: 12 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE 70

Query: 80 YLNQSVLEGRYITVERSR 97
                 +   + +    
Sbjct: 71 -TPGQKYKETDLLILFKD 87

>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 = 57.8 bits (140), Expect = 1e-11
 Identities = 21/94 (22%), Positives = 39/94 (41%), Gaps = 4/94 (4%)

Query: 7  SRSRGRTETGNPGN-TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAF 65
          S S G+    NP +  + V G+     E D+   F    +V +  L+ +   R + G   
Sbjct: 3  SGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFH-GLRVDAVHLLKDHVGR-NNGNGL 60

Query: 66 VTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK 99
          V     +D    +K  N+ ++  RY+ V  +  +
Sbjct: 61 VKFLSPQDTFEALK-RNRMLMIQRYVEVSPATER 93

>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 = 57.9 bits (140), Expect = 2e-11
 Identities = 16/96 (16%), Positives = 30/96 (31%), Gaps = 1/96 (1%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
            S  +          G  +Y+ GL      + +   F K   V     +       + G 
Sbjct: 10  PSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGE 69

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK 99
            FV      D +  +   ++  +  R+I V    +K
Sbjct: 70  GFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKK 104

>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 = 56.8 bits (137), Expect = 5e-11
 Identities = 18/95 (18%), Positives = 36/95 (37%), Gaps = 1/95 (1%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
            +      +        + + GL    T+ ++ + FS    V +   +         G A
Sbjct: 28  QQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEA 87

Query: 65  FVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK 99
           FV     E AE+ +   ++  +  RYI V +S ++
Sbjct: 88  FVQFASQELAEKALG-KHKERIGHRYIEVFKSSQE 121

>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 = 57.9 bits (139), Expect = 5e-11
 Identities = 14/77 (18%), Positives = 34/77 (44%), Gaps = 2/77 (2%)

Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
            ++Y+ G  T  T  D+++    +G+V +  +      +  +G  FV  D +E A++ ++
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMR-RTLHKAFKGSIFVVFDSIESAKKFVE 168

Query: 80  YLNQSVLEGRYITVERS 96
              Q   +   + +   
Sbjct: 169 TPGQKY-KETDLLILFK 184

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 55.5 bits (134), Expect = 5e-11
 Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 8/78 (10%)

Query: 20 NTLYVTGL------STRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
          + + V  +           +  + K FSK GK+ + F   E     ++G+ F+       
Sbjct: 2  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAH 59

Query: 74 AERCIKYLNQSVLEGRYI 91
          A   +K  +   L+ ++ 
Sbjct: 60 AVDAVKNADGYKLDKQHT 77

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 55.7 bits (135), Expect = 5e-11
 Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 1/93 (1%)

Query: 11  GRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDG 70
           G + +  P  +L+V  L+  V +  L + F K         VV  +T +S+G+ FV    
Sbjct: 1   GSSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTD 60

Query: 71  VEDAERCIKYLN-QSVLEGRYITVERSRRKRPR 102
             + +R +        L  + + +  +  K  R
Sbjct: 61  ELEQKRALTECQGAVGLGSKPVRLSVAIPKASR 93

>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 = 54.7 bits (132), Expect = 1e-10
 Identities = 13/79 (16%), Positives = 34/79 (43%), Gaps = 6/79 (7%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFL-----VVEPRTRISRGFAFVTMDGVEDAER 76
          LYV  +   +TE  +   F+ + ++          V+  +    + FAF+    V++  +
Sbjct: 9  LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 77 CIKYLNQSVLEGRYITVER 95
           +   +  + +G+ + + R
Sbjct: 69 AMA-FDGIIFQGQSLKIRR 86

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 54.7 bits (132), Expect = 2e-10
 Identities = 14/79 (17%), Positives = 30/79 (37%), Gaps = 8/79 (10%)

Query: 19 GNTLYVTGL------STRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVE 72
           + + V  +           +  + K FSK GK+ + F   E     ++G+ F+      
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPA 72

Query: 73 DAERCIKYLNQSVLEGRYI 91
           A   +K  +   L+ ++ 
Sbjct: 73 HAVDAVKNADGYKLDKQHT 91

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 52.9 bits (127), Expect = 8e-10
 Identities = 15/89 (16%), Positives = 33/89 (37%), Gaps = 5/89 (5%)

Query: 14 ETGNPGNTLYVTGLSTRVTERDLEKHFSK---EGKVASCFLVVEPRTRISRGFAFVTMDG 70
          E  +    +   GL    T  D+   FS             ++    +  RG A + M+ 
Sbjct: 6  EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGK-RRGDALIEMES 64

Query: 71 VEDAERCIKYLNQSVLEGRYITVERSRRK 99
           +D ++ ++  ++  +  RY+ V     +
Sbjct: 65 EQDVQKALE-KHRMYMGQRYVEVYEINNE 92

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 52.5 bits (126), Expect = 1e-09
 Identities = 17/100 (17%), Positives = 29/100 (29%), Gaps = 3/100 (3%)

Query: 3   FRSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRG 62
                R    ++       + +  L    + +DL+    +     +        TR   G
Sbjct: 12  SGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETT---FSSVNTRDFDG 68

Query: 63  FAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPR 102
              +     E     ++ LN     G  ITVER     P 
Sbjct: 69  TGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPPPI 108

>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 = 52.2 bits (125), Expect = 2e-09
 Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 8/77 (10%)

Query: 8  RSRGRTETGNPGNTLYV--TGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAF 65
          R  G         +L V   GL   V+   L     K G V +  L++ P    ++ ++F
Sbjct: 14 RHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDA--LLMPP----NKPYSF 67

Query: 66 VTMDGVEDAERCIKYLN 82
                E+++R    LN
Sbjct: 68 ARYRTTEESKRAYVTLN 84

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 51.9 bits (124), Expect = 2e-09
 Identities = 17/105 (16%), Positives = 40/105 (38%), Gaps = 9/105 (8%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGL-STRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
                +   +    G  ++++ L  +  ++  + K     GK+ +  L+        +  
Sbjct: 11  EGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQ 64

Query: 64  AFVTMDGVEDAERCIKYL--NQSVLEGRYITVERSRRKRPRTPTP 106
           AF+ M+  EDA   + +        +GR + V+ S + +     P
Sbjct: 65  AFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVSGP 109

>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 = 51.7 bits (124), Expect = 2e-09
 Identities = 22/114 (19%), Positives = 36/114 (31%), Gaps = 7/114 (6%)

Query: 6   RSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAF 65
            S S G   +    N + V+GL    + +DL+ H  + G V    +          G   
Sbjct: 2   SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-------YRDGTGV 54

Query: 66  VTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIG 119
           V     ED    ++ L+ +            R K     +P +     S    G
Sbjct: 55  VEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSGPSSG 108

>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 = 52.5 bits (126), Expect = 2e-09
 Identities = 20/95 (21%), Positives = 37/95 (38%), Gaps = 3/95 (3%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFA 64
             S     T     G+ +++ GL  + TE D+   FS         + + P  R   G A
Sbjct: 32  RGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFS-PLNPVRVHIEIGPDGR-VTGEA 89

Query: 65  FVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK 99
            V     E+A   +   +++ ++ RYI +  +   
Sbjct: 90  DVEFATHEEAVAAMS-KDRANMQHRYIELFLNSTT 123

>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 = 51.5 bits (123), Expect = 4e-09
 Identities = 23/98 (23%), Positives = 38/98 (38%), Gaps = 5/98 (5%)

Query: 5  SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFS---KEGKVASCFLVVEPRTRISR 61
          S S        G  G  + + GL    +  D++   S       VA    +     R   
Sbjct: 3  SGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR-QS 61

Query: 62 GFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK 99
          G AFV ++  +D +  +K  ++  +  RYI V +S R 
Sbjct: 62 GEAFVELESEDDVKLALK-KDRESMGHRYIEVFKSHRT 98

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 49.9 bits (119), Expect = 1e-08
 Identities = 20/99 (20%), Positives = 35/99 (35%), Gaps = 6/99 (6%)

Query: 5   SRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKV----ASCFLVVEPRTRIS 60
             S    +  +      + + GL    T  ++   F +   +         V  P  R  
Sbjct: 9   GTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGR-P 67

Query: 61  RGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK 99
            G AFV     E A+  ++  ++ +L  RYI + RS   
Sbjct: 68  TGDAFVLFACEEYAQNALR-KHKDLLGKRYIELFRSTAA 105

>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 = 48.8 bits (116), Expect = 2e-08
 Identities = 19/91 (20%), Positives = 42/91 (46%), Gaps = 7/91 (7%)

Query: 11 GRTETGNPGNTLYVTGLSTRVTERDLEKH----FSKEGKVASCFLVVEPRTRISRGFAFV 66
          G + +   G  + V+ +  R++ ++L++     F++ GKV S  L         +  A V
Sbjct: 1  GSSGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTD---YQLKAVV 57

Query: 67 TMDGVEDAERCIKYLNQSVLEGRYITVERSR 97
           M+ ++DA   +  L++  +  + I V  + 
Sbjct: 58 QMENLQDAIGAVNSLHRYKIGSKKILVSLAT 88

>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 = 46.7 bits (111), Expect = 2e-07
 Identities = 22/118 (18%), Positives = 36/118 (30%), Gaps = 7/118 (5%)

Query: 6   RSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAF 65
             R R    +    N + V+GL    + +DL+ H  + G V    +          G   
Sbjct: 3   APRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-------YRDGTGV 55

Query: 66  VTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDR 123
           V     ED    ++ L+ +            R K     +P +      SR   R   
Sbjct: 56  VEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSRSRS 113

>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 Length = 136

 Score = 46.5 bits (110), Expect = 4e-07
 Identities = 21/99 (21%), Positives = 36/99 (36%), Gaps = 5/99 (5%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSK---EGKVASCFLVVEPRTRIS 60
           +    S      G  G  + + GL    +  D++   S        A    +     R  
Sbjct: 29  QMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGR-Q 87

Query: 61  RGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK 99
            G AFV +   +D +  +K  ++  +  RYI V +S R 
Sbjct: 88  SGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHRT 125

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 45.0 bits (106), Expect = 9e-07
 Identities = 12/85 (14%), Positives = 28/85 (32%), Gaps = 4/85 (4%)

Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVE--PRTRISRGFAFVTMDGVEDAERC 77
             ++V GL   + E ++   F + G +   +            +G+AF+        +  
Sbjct: 9   RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68

Query: 78  IKYLNQSVLEGRYITVERSRRKRPR 102
           I        +G+      S   + +
Sbjct: 69  ID--ACLEEDGKLYLCVSSPTIKDK 91

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 43.1 bits (101), Expect = 6e-06
 Identities = 17/100 (17%), Positives = 30/100 (30%), Gaps = 8/100 (8%)

Query: 5   SRSRSRGRTETGNPGNTL--YVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRG 62
           S +              L   V  L   VT   L + FSK G V          T+ ++ 
Sbjct: 12  SAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKII----TFTKNNQF 67

Query: 63  FAFVTMDGVEDAERCIKYLNQSVL--EGRYITVERSRRKR 100
            A +       A+     L+   +      + ++ S+   
Sbjct: 68  QALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS 107

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 41.8 bits (98), Expect = 1e-05
 Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 14/91 (15%)

Query: 17  NPGN-TLYVTGLSTRVTERDLEKHF------------SKEGKVASCFLVVEPRTRISRGF 63
           NP N +    GL + V++ ++++H+             K G+V     V +       G 
Sbjct: 12  NPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMN-VCDNLGDHLVGN 70

Query: 64  AFVTMDGVEDAERCIKYLNQSVLEGRYITVE 94
            +V     EDAE+ +  LN     G+ I  E
Sbjct: 71  VYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 18/84 (21%), Positives = 29/84 (34%), Gaps = 4/84 (4%)

Query: 19  GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
           G  + V GL   V +  L  +F    +  S    V    R       +T     DAER +
Sbjct: 8   GVAVEVRGLPPAVPDELLTLYFENRRR--SGGGPVLSWQR-LGCGGVLTFREPADAERVL 64

Query: 79  KYLNQSVLEGRYITVERSRRKRPR 102
                  L G  +++  +  + P 
Sbjct: 65  AQ-ADHELHGAQLSLRPAPPRAPA 87

>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 = 42.8 bits (100), Expect = 1e-05
 Identities = 18/100 (18%), Positives = 30/100 (30%), Gaps = 8/100 (8%)

Query: 5   SRSRSRGRTETGNPGNTL--YVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRG 62
           S +              L   V  L   VT   L + FSK G V          T+ ++ 
Sbjct: 30  SAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKII----TFTKNNQF 85

Query: 63  FAFVTMDGVEDAERCIKYLNQSVLEGRYIT--VERSRRKR 100
            A +       A+     L+   +     T  ++ S+   
Sbjct: 86  QALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS 125

>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 = 42.9 bits (100), Expect = 2e-05
 Identities = 38/173 (21%), Positives = 59/173 (34%)

Query: 15  TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDA 74
            G+   TL+V  ++   TE  L + F   G +    +V   R+   RG+AF+  +   D 
Sbjct: 98  QGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDM 157

Query: 75  ERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDRGRYRSGRDDYG 134
               K+ +   ++GR + V+  R +  +   P    G       G  D     SGRDD  
Sbjct: 158 HSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTS 217

Query: 135 YRRSPRRSPYRGGRDYSPRHSPPYGGRSRRERSRSVPRSPYGSPERKYARGSR 187
                        RD           RSR        R       R+ +R   
Sbjct: 218 RYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRD 270

>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 Length = 102

 Score = 40.6 bits (95), Expect = 2e-05
 Identities = 16/103 (15%), Positives = 38/103 (36%), Gaps = 9/103 (8%)

Query: 7   SRSRGRTETGNPGNTLYVTGL-STRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAF 65
           S S G+         +++      +     L +     G +++  ++           AF
Sbjct: 3   SGSSGQKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL------NKINEAF 56

Query: 66  VTMDGVEDAERCIKYL--NQSVLEGRYITVERSRRKRPRTPTP 106
           + M   EDA+  + Y     +++ G+ + V  S++ +     P
Sbjct: 57  IEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKSGP 99

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 41.7 bits (97), Expect = 4e-05
 Identities = 19/105 (18%), Positives = 30/105 (28%), Gaps = 15/105 (14%)

Query: 4   RSRSRSRGRTETGNPGNTLYVTGLSTRVT---------ERDLEKHFSKEGKVASCFLVVE 54
             R    G         TLYV G+   +          E  +   FS+ G +     V  
Sbjct: 119 DYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES 178

Query: 55  PRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK 99
                 +   FV      +AE   + ++   L          RR+
Sbjct: 179 ------KNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRRE 217

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 39.3 bits (91), Expect = 5e-05
 Identities = 16/81 (19%), Positives = 29/81 (35%), Gaps = 7/81 (8%)

Query: 15 TGNPGNT-LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
              G++ L +  L+ ++    L     + G + S          +++G A       E+
Sbjct: 2  AMAWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHP------YLNQGIALCKYTTREE 55

Query: 74 AERCIKYLNQSVLEGRYITVE 94
          A +    LN  VL    I  E
Sbjct: 56 ANKAQMALNNCVLANTTIFAE 76

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 38.1 bits (88), Expect = 3e-04
 Identities = 21/102 (20%), Positives = 35/102 (34%), Gaps = 10/102 (9%)

Query: 4   RSRSRSRGRTETGNPGNT---LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRIS 60
             R    G T+  + GN    L +      +T   L    +  GKV           + +
Sbjct: 7   GKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRI-----VIFKRN 61

Query: 61  RGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT--VERSRRKR 100
              A V  + V  A++    LN + +     T  +E +R  R
Sbjct: 62  GIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR 103

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	187
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.93
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.92
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.91
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.91
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.9
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.9
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.9
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.9
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.9
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.9
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.9
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.9
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.9
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.9
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.9
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.9
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.9
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.9
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.9
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.89
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.89
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.89
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.89
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.89
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.89
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.89
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.89
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.89
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.89
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.89
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.89
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.89
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.89
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.89
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.89
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.89
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.88
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.88
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.88
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.88
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.88
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.88
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.88
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.88
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.88
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.88
2div_A	99	TRNA selenocysteine associated protein; structural	99.88
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.88
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.88
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.88
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.88
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.88
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.87
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.87
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.87
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.87
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.87
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.87
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.87
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.87
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.87
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.87
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.87
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.86
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.86
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.86
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.86
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.86
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.86
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.86
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.86
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.86
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.86
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.86
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.86
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.86
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.86
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.86
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.86
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.86
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.86
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.86
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.86
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.86
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.86
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.86
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.85
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.85
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.85
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.85
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.85
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.85
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.85
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.85
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.85
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.85
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.85
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.85
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.85
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.85
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.84
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.84
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.84
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.84
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.84
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.84
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.84
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.84
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.84
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.84
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.84
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.84
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.74
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.84
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.83
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.83
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.83
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.83
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.83
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.83
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.83
1x5p_A	97	Negative elongation factor E; structure genomics,	99.83
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.83
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.83
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.83
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.83
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.83
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.83
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.82
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.82
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.82
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.82
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.82
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.82
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.82
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.82
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.82
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.81
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.81
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.81
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.81
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.81
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.81
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.8
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.8
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.8
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.8
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.8
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.8
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.8
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.79
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.79
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.79
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.79
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.79
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.79
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.79
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.78
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.78
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.78
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.78
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.77
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.77
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.77
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.77
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.76
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.76
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.76
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.76
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.76
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.75
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.74
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.74
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.74
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.74
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.73
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.73
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.72
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.72
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.72
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.71
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.71
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.71
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.71
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.71
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.7
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.7
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.69
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.67
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.67
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.66
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.66
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.66
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.65
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.65
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.64
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.63
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.62
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.62
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.62
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.61
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.6
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.57
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.51
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.49
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.41
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.26
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.15
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.87
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.29
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.22
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	98.19
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.18
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	98.03
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.95
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.77
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	97.49
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	97.17
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.78
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.59
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	95.29
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	93.89
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	93.08
4eyt_A	129	Telomerase associated protein P65; RNA, LA protein	92.09

>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=99.93  E-value=5.2e-25  Score=183.33  Aligned_cols=92  Identities=24%  Similarity=0.412  Sum_probs=84.3

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ...+.++|||+|||+.||+++|+++|.+||.|+.|.|+.+..+++++|||||+|.+.++|++||+.||+..|.|+.|.|+
T Consensus        98 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~  177 (437)
T 3pgw_S           98 QGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  177 (437)
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34566899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eccCCCCCCCCC
Q 029810           95 RSRRKRPRTPTP  106 (187)
Q Consensus        95 ~a~~~~~~~~~~  106 (187)
                      +++++......+
T Consensus       178 ~a~~~~~~~~~~  189 (437)
T 3pgw_S          178 VERGRTVKGWRP  189 (437)
T ss_pred             EeCCCCCCCCCC
Confidence            999776654433

>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=99.92  E-value=1.1e-24  Score=146.33  Aligned_cols=82  Identities=33%  Similarity=0.417  Sum_probs=78.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      -.+++|||+|||.++|+++|+++|++||+|..|.|+.+..++.++|||||+|.+.++|++||+.||+..|.|+.|.|++|
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~A   96 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA   96 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cC
Q 029810           97 RR   98 (187)
Q Consensus        97 ~~   98 (187)
                      +|
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            75

>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=99.91  E-value=4.7e-24  Score=154.44  Aligned_cols=88  Identities=27%  Similarity=0.412  Sum_probs=82.4

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      ....+.++|||+|||.++++++|+++|++||+|..|.|+.+..++.+++||||+|.+.++|++||+.|++..|.|+.|.|
T Consensus        34 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  113 (156)
T 1h2v_Z           34 KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRT  113 (156)
T ss_dssp             TTTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            44567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeccCCCC
Q 029810           94 ERSRRKRP  101 (187)
Q Consensus        94 ~~a~~~~~  101 (187)
                      +++++...
T Consensus       114 ~~a~~~~~  121 (156)
T 1h2v_Z          114 DWDAGFKE  121 (156)
T ss_dssp             EEESCCCT
T ss_pred             EECCCCCC
Confidence            99986543

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

Probab=99.91  E-value=1.4e-23  Score=141.71  Aligned_cols=93  Identities=27%  Similarity=0.393  Sum_probs=85.5

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ...+..+.++|||+|||.++++++|+++|++||.|..|.|+.+..++.+++||||+|.+.++|++||+.||+..|.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   87 (103)
T 2cq0_A            8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLIL   87 (103)
T ss_dssp             SCCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEE
Confidence            34456778999999999999999999999999999999999998899999999999999999999999999999999999


Q ss_pred             EEEeccCCCCCCC
Q 029810           92 TVERSRRKRPRTP  104 (187)
Q Consensus        92 ~v~~a~~~~~~~~  104 (187)
                      .|++++++....+
T Consensus        88 ~v~~a~~~~~~~~  100 (103)
T 2cq0_A           88 NVEWAKPSTNSGP  100 (103)
T ss_dssp             EEEESSCCCCSCC
T ss_pred             EEEECCCCCCCCC
Confidence            9999987765443

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

Probab=99.90  E-value=4.4e-23  Score=137.08  Aligned_cols=87  Identities=29%  Similarity=0.398  Sum_probs=81.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ..+.++|||+|||.++++++|+++|++||.|..|.|+.+..++.+++||||+|.+.++|++||+.||+..|.|+.|.|++
T Consensus         2 ~~~~~~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            2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGH   81 (95)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            35679999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 029810           96 SRRKRPR  102 (187)
Q Consensus        96 a~~~~~~  102 (187)
                      ++++...
T Consensus        82 a~~~~~~   88 (95)
T 2dnz_A           82 VTERLDG   88 (95)
T ss_dssp             SSCCCCC
T ss_pred             cccccCC
Confidence            9876543

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

Probab=99.90  E-value=3.2e-23  Score=141.75  Aligned_cols=84  Identities=24%  Similarity=0.296  Sum_probs=79.9

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+.+..|+.++|||||+|++.++|++||+.||+..|.|+.|.|++
T Consensus         3 ~~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            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL   82 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 029810           96 SRRK   99 (187)
Q Consensus        96 a~~~   99 (187)
                      +...
T Consensus        83 a~~~   86 (110)
T 3s8s_A           83 DIKG   86 (110)
T ss_dssp             CSTT
T ss_pred             CCCC
Confidence            8754

>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=99.90  E-value=4.3e-23  Score=141.96  Aligned_cols=92  Identities=24%  Similarity=0.391  Sum_probs=84.8

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      ..+..+.++|||+|||.++++++|+++|++||.|..|.|+.+..++.+++||||+|.+.++|++||+.||+..|.|+.|.
T Consensus        19 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   98 (115)
T 2cpz_A           19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK   98 (115)
T ss_dssp             CCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CcCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34456678999999999999999999999999999999999998999999999999999999999999999999999999


Q ss_pred             EEeccCCCCCCC
Q 029810           93 VERSRRKRPRTP  104 (187)
Q Consensus        93 v~~a~~~~~~~~  104 (187)
                      |++++++....+
T Consensus        99 V~~a~~~~~~~~  110 (115)
T 2cpz_A           99 VQLKRSKNDSKS  110 (115)
T ss_dssp             EECCCCSCCCCC
T ss_pred             EEEcCCCCcCCC
Confidence            999998766544

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

Probab=99.90  E-value=7.6e-23  Score=138.02  Aligned_cols=93  Identities=27%  Similarity=0.420  Sum_probs=84.2

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe
Q 029810           10 RGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGR   89 (187)
Q Consensus        10 ~~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~   89 (187)
                      .....+..+.++|||+|||+++++++|+++|++||.|..|.|+.+  ++.+++||||+|.+.++|++||+.||+..|.|+
T Consensus         6 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   83 (103)
T 2d9p_A            6 SGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATK   83 (103)
T ss_dssp             CCCCCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            344555678899999999999999999999999999999999987  788999999999999999999999999999999


Q ss_pred             EEEEEeccCCCCCCC
Q 029810           90 YITVERSRRKRPRTP  104 (187)
Q Consensus        90 ~l~v~~a~~~~~~~~  104 (187)
                      .|.|++++++..+..
T Consensus        84 ~l~V~~a~~~~~~~~   98 (103)
T 2d9p_A           84 PLYVALAQRKEERQS   98 (103)
T ss_dssp             BCEEEECSSCCCCCC
T ss_pred             EEEEEEecccccCCC
Confidence            999999998765443

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

Probab=99.90  E-value=2.7e-23  Score=140.22  Aligned_cols=91  Identities=30%  Similarity=0.436  Sum_probs=84.2

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .++..+.++|||+|||.++++++|+++|++||.|..|.|+.+..++.+++||||+|.+.++|++||+.||+..|.|+.|.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2dnm_A            7 GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELR   86 (103)
T ss_dssp             SSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCE
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            34566789999999999999999999999999999999999998999999999999999999999999999999999999


Q ss_pred             EEeccCCCCCC
Q 029810           93 VERSRRKRPRT  103 (187)
Q Consensus        93 v~~a~~~~~~~  103 (187)
                      |++++......
T Consensus        87 V~~a~~~~~~~   97 (103)
T 2dnm_A           87 VQVARYGRRDL   97 (103)
T ss_dssp             EEECSSCCSCC
T ss_pred             EEECCcCCCCC
Confidence            99998765443

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

Probab=99.90  E-value=1.8e-22  Score=138.82  Aligned_cols=93  Identities=27%  Similarity=0.419  Sum_probs=85.7

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe
Q 029810           10 RGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGR   89 (187)
Q Consensus        10 ~~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~   89 (187)
                      .....+..+.++|||+|||.++++++|+++|.+||.|..|.|+.+..++.+++||||+|.+.++|++||+.|++..|.|+
T Consensus         6 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   85 (115)
T 2dgo_A            6 SGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGR   85 (115)
T ss_dssp             CSSCCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTE
T ss_pred             CcCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            34455667889999999999999999999999999999999999988999999999999999999999999999999999


Q ss_pred             EEEEEeccCCCCC
Q 029810           90 YITVERSRRKRPR  102 (187)
Q Consensus        90 ~l~v~~a~~~~~~  102 (187)
                      .|.|++++++...
T Consensus        86 ~l~V~~a~~~~~~   98 (115)
T 2dgo_A           86 QIRTNWATRKPPA   98 (115)
T ss_dssp             ECEEEESSCCCCC
T ss_pred             EEEEEEccCCCCC
Confidence            9999999876543

>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=99.90  E-value=1.1e-22  Score=137.66  Aligned_cols=91  Identities=23%  Similarity=0.372  Sum_probs=83.0

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC---eE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG---RY   90 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g---~~   90 (187)
                      ....+.++|||+|||.++++++|+++|++||.|..|.|+.+. ++.+++||||+|.+.++|++||+.||+..|.+   +.
T Consensus        10 ~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~   88 (105)
T 2dnh_A           10 SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSS   88 (105)
T ss_dssp             CSCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCcc
Confidence            345678999999999999999999999999999999999887 78899999999999999999999999999988   99


Q ss_pred             EEEEeccCCCCCCCC
Q 029810           91 ITVERSRRKRPRTPT  105 (187)
Q Consensus        91 l~v~~a~~~~~~~~~  105 (187)
                      |.|++++++..+.+.
T Consensus        89 l~V~~a~~~~~~~~~  103 (105)
T 2dnh_A           89 LVVKFADTDKESGPS  103 (105)
T ss_dssp             CEEEESCSSCCCSCS
T ss_pred             EEEEECccCcccCCC
Confidence            999999987765443

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

Probab=99.90  E-value=3.2e-23  Score=139.62  Aligned_cols=91  Identities=31%  Similarity=0.449  Sum_probs=84.2

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .....+.++|||+|||.++++++|+++|++||.|..|.|+.+..++.+++||||+|.+.++|++||+.||+..|.|+.|.
T Consensus         6 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 2cqb_A            6 SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR   85 (102)
T ss_dssp             SCSCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            34556789999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEeccCCCCCC
Q 029810           93 VERSRRKRPRT  103 (187)
Q Consensus        93 v~~a~~~~~~~  103 (187)
                      |++++++....
T Consensus        86 V~~a~~~~~~~   96 (102)
T 2cqb_A           86 VNLAKPMRIKE   96 (102)
T ss_dssp             EEECCCCCCCC
T ss_pred             EEeCCCCCCCC
Confidence            99998776543

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

Probab=99.90  E-value=8.9e-23  Score=136.73  Aligned_cols=89  Identities=20%  Similarity=0.509  Sum_probs=82.7

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      .+..+.++|||+|||.++++++|+++|++||.|..|.|+.+..++.+++||||+|.+.++|++||+ |++..|.|+.|.|
T Consensus         5 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V   83 (99)
T 2dgs_A            5 SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEV   83 (99)
T ss_dssp             CCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEE
Confidence            345678999999999999999999999999999999999998899999999999999999999999 9999999999999


Q ss_pred             EeccCCCCCC
Q 029810           94 ERSRRKRPRT  103 (187)
Q Consensus        94 ~~a~~~~~~~  103 (187)
                      ++++++....
T Consensus        84 ~~a~~~~~~~   93 (99)
T 2dgs_A           84 KRAEPRDSKS   93 (99)
T ss_dssp             EECCCCCCCC
T ss_pred             EECCCCcccC
Confidence            9999776543

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

Probab=99.90  E-value=1.3e-22  Score=139.78  Aligned_cols=91  Identities=26%  Similarity=0.391  Sum_probs=83.0

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe
Q 029810           10 RGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGR   89 (187)
Q Consensus        10 ~~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~   89 (187)
                      ........+.++|||+|||+++++++|+++|++||.|..|.|+.+..++.+++||||+|.+.++|++||+.|++ .|.|+
T Consensus         8 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~   86 (116)
T 2cqd_A            8 MHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGR   86 (116)
T ss_dssp             CCCCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTE
T ss_pred             CCCCcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCE
Confidence            33455667789999999999999999999999999999999999998999999999999999999999999998 89999


Q ss_pred             EEEEEeccCCCC
Q 029810           90 YITVERSRRKRP  101 (187)
Q Consensus        90 ~l~v~~a~~~~~  101 (187)
                      .|.|+++.....
T Consensus        87 ~l~V~~a~~~~~   98 (116)
T 2cqd_A           87 KANVNLAYLGAK   98 (116)
T ss_dssp             ECEEEESTTTCC
T ss_pred             EEEEEEcccCCC
Confidence            999999986543

>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=99.90  E-value=7.5e-23  Score=137.03  Aligned_cols=88  Identities=31%  Similarity=0.412  Sum_probs=82.5

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ...+.++|||+|||+++++++|+++|++||.|..|.|+.+..++.+++||||+|.+.++|++||+.||+..|.|+.|.|+
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (99)
T 1whw_A            4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL   83 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            45677999999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eccCCCCC
Q 029810           95 RSRRKRPR  102 (187)
Q Consensus        95 ~a~~~~~~  102 (187)
                      +++++...
T Consensus        84 ~a~~~~~~   91 (99)
T 1whw_A           84 PSTIKKEA   91 (99)
T ss_dssp             ECCCCSTT
T ss_pred             EcCCCccc
Confidence            99877554

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

Probab=99.90  E-value=5.4e-23  Score=138.47  Aligned_cols=90  Identities=31%  Similarity=0.554  Sum_probs=83.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .....+.++|||+|||.++++++|+++|++||.|..|.|+.+..++.+++||||+|.+.++|++||+.||+..|.|+.|.
T Consensus         6 ~~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 1x5s_A            6 SGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIR   85 (102)
T ss_dssp             CCCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            44566789999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EEeccCCCCC
Q 029810           93 VERSRRKRPR  102 (187)
Q Consensus        93 v~~a~~~~~~  102 (187)
                      |++++++...
T Consensus        86 v~~a~~~~~~   95 (102)
T 1x5s_A           86 VDQAGKSSDN   95 (102)
T ss_dssp             EEEEECCCCC
T ss_pred             EEECCCCCCC
Confidence            9999876543

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

Probab=99.90  E-value=9.2e-23  Score=138.42  Aligned_cols=93  Identities=22%  Similarity=0.358  Sum_probs=85.1

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeec-CCCCCcceEEEEEecCHHHHHHHHHHh-CCCccC
Q 029810           10 RGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVE-PRTRISRGFAFVTMDGVEDAERCIKYL-NQSVLE   87 (187)
Q Consensus        10 ~~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~-~~~~~~~g~afV~f~~~~~a~~ai~~l-~g~~i~   87 (187)
                      ........+.++|||+|||.++++++|+++|++||.|..|.|+.+ ..++.+++||||+|.+.++|++||+.| |+..|.
T Consensus         6 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~   85 (107)
T 2cph_A            6 SGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLY   85 (107)
T ss_dssp             CCSSCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSS
T ss_pred             CcccccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeEC
Confidence            334556678899999999999999999999999999999999988 778999999999999999999999999 999999


Q ss_pred             CeEEEEEeccCCCCC
Q 029810           88 GRYITVERSRRKRPR  102 (187)
Q Consensus        88 g~~l~v~~a~~~~~~  102 (187)
                      |+.|.|++++++...
T Consensus        86 g~~l~v~~a~~~~~~  100 (107)
T 2cph_A           86 GRRLVLEWADSEVTV  100 (107)
T ss_dssp             SCBCEEEECCCCCCC
T ss_pred             CCEEEEEeCCCCCCC
Confidence            999999999877554

>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=99.90  E-value=8.4e-23  Score=138.23  Aligned_cols=90  Identities=28%  Similarity=0.388  Sum_probs=83.9

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ...+..+.++|||+|||+++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+.|++..|.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (105)
T 1x5u_A            8 PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI   87 (105)
T ss_dssp             CCCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBC
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            34556778999999999999999999999999999999999998899999999999999999999999999999999999


Q ss_pred             EEEeccCCCC
Q 029810           92 TVERSRRKRP  101 (187)
Q Consensus        92 ~v~~a~~~~~  101 (187)
                      .|++++++..
T Consensus        88 ~v~~a~~~~~   97 (105)
T 1x5u_A           88 RVNKASAHNK   97 (105)
T ss_dssp             EEEETTTTSC
T ss_pred             EEEECCCCCc
Confidence            9999987654

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

Probab=99.90  E-value=1.5e-22  Score=135.85  Aligned_cols=89  Identities=21%  Similarity=0.331  Sum_probs=82.3

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ...+..+.++|||+|||.++++++|+++|++||.|..|.|+.+. ++.+++||||+|.+.++|++||+.|++..|.|+.|
T Consensus        10 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   88 (100)
T 2do4_A           10 RYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENII   88 (100)
T ss_dssp             CCSSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEE
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            34556678999999999999999999999999999999999988 89999999999999999999999999999999999


Q ss_pred             EEEeccCCCC
Q 029810           92 TVERSRRKRP  101 (187)
Q Consensus        92 ~v~~a~~~~~  101 (187)
                      .|++++++..
T Consensus        89 ~v~~a~~~~~   98 (100)
T 2do4_A           89 KVAISNSGPS   98 (100)
T ss_dssp             EEEECCCCSC
T ss_pred             EEEECCCCCC
Confidence            9999987654

>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=99.89  E-value=1.4e-22  Score=138.36  Aligned_cols=93  Identities=24%  Similarity=0.380  Sum_probs=85.4

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC------CC
Q 029810           11 GRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLN------QS   84 (187)
Q Consensus        11 ~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~------g~   84 (187)
                      ....+..+.++|||+|||+++++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|++||+.|+      +.
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~   86 (111)
T 1x4h_A            7 GLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGL   86 (111)
T ss_dssp             CCCCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCE
T ss_pred             CCCCcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCc
Confidence            344566778999999999999999999999999999999999999999999999999999999999999999      99


Q ss_pred             ccCCeEEEEEeccCCCCCC
Q 029810           85 VLEGRYITVERSRRKRPRT  103 (187)
Q Consensus        85 ~i~g~~l~v~~a~~~~~~~  103 (187)
                      .|+|+.|.|.++.++....
T Consensus        87 ~~~g~~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           87 KLDGRQLKVDLAVTRDEAA  105 (111)
T ss_dssp             ESSSCEEEEECCCCCCCCC
T ss_pred             EEcCEEEEEEECCCCccCC
Confidence            9999999999998775543

>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=99.89  E-value=5.7e-23  Score=134.32  Aligned_cols=84  Identities=26%  Similarity=0.365  Sum_probs=77.2

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ..+.++|||+|||.++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++|++.||+..|.|+.|.|++
T Consensus         3 ~~~~~~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            3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   82 (87)
T ss_dssp             ---CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEe
Confidence            45678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 029810           96 SRRK   99 (187)
Q Consensus        96 a~~~   99 (187)
                      ++++
T Consensus        83 a~~k   86 (87)
T 3bs9_A           83 ATRK   86 (87)
T ss_dssp             EC--
T ss_pred             cCCC
Confidence            9865

>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=99.89  E-value=3.5e-23  Score=144.61  Aligned_cols=89  Identities=26%  Similarity=0.446  Sum_probs=82.6

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      ....+.++|||+|||+++++++|+++|++||.|..|.|+.+..++.+++||||+|.+.++|++||+.||+..|+|+.|.|
T Consensus        17 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   96 (126)
T 3ex7_B           17 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   96 (126)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            44556789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EeccCCCCC
Q 029810           94 ERSRRKRPR  102 (187)
Q Consensus        94 ~~a~~~~~~  102 (187)
                      ++++++...
T Consensus        97 ~~a~~~~~~  105 (126)
T 3ex7_B           97 DWCFVRGPP  105 (126)
T ss_dssp             EESEESSSC
T ss_pred             EEecCCCCC
Confidence            999876543

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

Probab=99.89  E-value=1.4e-22  Score=143.86  Aligned_cols=89  Identities=26%  Similarity=0.337  Sum_probs=83.1

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      ++..+.++|||+|||.++++++|+++|+.||+|..|.|+.+..++.++|||||+|.+.++|++||+.||+..|.|+.|.|
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  116 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            44566789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeccCCCCC
Q 029810           94 ERSRRKRPR  102 (187)
Q Consensus        94 ~~a~~~~~~  102 (187)
                      ++++++..+
T Consensus       117 ~~a~~~~~~  125 (139)
T 1u6f_A          117 ALAASGHQR  125 (139)
T ss_dssp             EESSCCCCC
T ss_pred             EECCCCCCC
Confidence            999876544

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

Probab=99.89  E-value=1.1e-22  Score=135.06  Aligned_cols=89  Identities=39%  Similarity=0.543  Sum_probs=82.9

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe
Q 029810           10 RGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGR   89 (187)
Q Consensus        10 ~~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~   89 (187)
                      .....+..+.++|||+|||.++++++|+++|++||.|..|.|+.+..++.+++||||+|.+.++|++||+.||+..|.|+
T Consensus         6 ~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   85 (95)
T 2cqc_A            6 SGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR   85 (95)
T ss_dssp             CCCCCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            34455677889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEeccC
Q 029810           90 YITVERSRR   98 (187)
Q Consensus        90 ~l~v~~a~~   98 (187)
                      .|.|++++.
T Consensus        86 ~l~v~~a~~   94 (95)
T 2cqc_A           86 RIRVSGPSS   94 (95)
T ss_dssp             EEEEECCSC
T ss_pred             EEEEEecCC
Confidence            999999874

>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=99.89  E-value=1.4e-22  Score=139.83  Aligned_cols=85  Identities=31%  Similarity=0.558  Sum_probs=79.7

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      +.++.++|||+|||.++++++|+++|++||.|..|.|+.+. ++.++|||||+|.+.++|++||+.|++..|.|+.|.|+
T Consensus         3 e~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~   81 (116)
T 2fy1_A            3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVE   81 (116)
T ss_dssp             TTCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999987 89999999999999999999999999999999999999


Q ss_pred             eccCCC
Q 029810           95 RSRRKR  100 (187)
Q Consensus        95 ~a~~~~  100 (187)
                      +++++.
T Consensus        82 ~a~~~~   87 (116)
T 2fy1_A           82 QAKKPS   87 (116)
T ss_dssp             ECCCSS
T ss_pred             ECCCCC
Confidence            998654

>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=99.89  E-value=5e-23  Score=144.64  Aligned_cols=93  Identities=42%  Similarity=0.557  Sum_probs=85.6

Q ss_pred             CCCCCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 029810            8 RSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE   87 (187)
Q Consensus         8 r~~~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~   87 (187)
                      +......+..+.++|||+|||.++++++|+++|++||+|..|.|+.+..++.++|||||+|.+.++|++||+.|++..|+
T Consensus        35 ~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~  114 (129)
T 2kxn_B           35 RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD  114 (129)
T ss_dssp             CCCCCSSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSS
T ss_pred             CCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            33445566778899999999999999999999999999999999999989999999999999999999999999999999


Q ss_pred             CeEEEEEeccCCC
Q 029810           88 GRYITVERSRRKR  100 (187)
Q Consensus        88 g~~l~v~~a~~~~  100 (187)
                      |+.|.|++++++.
T Consensus       115 g~~l~V~~a~~~~  127 (129)
T 2kxn_B          115 GRRIRVDFSITKR  127 (129)
T ss_dssp             SSCCEESCCSSSS
T ss_pred             CEEEEEEEecCCC
Confidence            9999999998764

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

Probab=99.89  E-value=7.2e-23  Score=136.32  Aligned_cols=86  Identities=23%  Similarity=0.404  Sum_probs=80.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEE-EEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASC-FLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~-~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      .+.++|||+|||.++++++|+++|++||.|..| .|+.+..++.+++||||+|.+.++|++||+.||+..|.|+.|.|++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            467999999999999999999999999999999 9999988999999999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 029810           96 SRRKRPR  102 (187)
Q Consensus        96 a~~~~~~  102 (187)
                      +.++...
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            9876543

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

Probab=99.89  E-value=1.1e-22  Score=137.78  Aligned_cols=87  Identities=26%  Similarity=0.454  Sum_probs=81.5

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ...++++|||+|||.++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+.|++..|.|+.|.|+
T Consensus        19 ~~~~~~~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           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            34566899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 029810           95 RSRRKRP  101 (187)
Q Consensus        95 ~a~~~~~  101 (187)
                      +++++..
T Consensus        99 ~a~~~~~  105 (106)
T 1p27_B           99 WCFVRGP  105 (106)
T ss_dssp             ESEESSC
T ss_pred             eecCCCC
Confidence            9987643

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

Probab=99.89  E-value=2.5e-22  Score=135.49  Aligned_cols=90  Identities=22%  Similarity=0.393  Sum_probs=82.4

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE
Q 029810           11 GRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY   90 (187)
Q Consensus        11 ~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~   90 (187)
                      ....+..+.++|||+|||.++++++|+++|++|| |..|.|+.+..++.++|||||+|.+.++|++|| .|++..|.|+.
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~   84 (103)
T 2dng_A            7 GKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRS   84 (103)
T ss_dssp             CCCCCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEE
T ss_pred             CCCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeE
Confidence            3455667789999999999999999999999996 999999999999999999999999999999999 79999999999


Q ss_pred             EEEEeccCCCCC
Q 029810           91 ITVERSRRKRPR  102 (187)
Q Consensus        91 l~v~~a~~~~~~  102 (187)
                      |.|++++++...
T Consensus        85 l~V~~a~~~~~~   96 (103)
T 2dng_A           85 LRVDIAEGRKQD   96 (103)
T ss_dssp             CEEEECCCCCCC
T ss_pred             EEEEEecCCCCC
Confidence            999999876543

>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=99.89  E-value=4.9e-22  Score=134.01  Aligned_cols=94  Identities=30%  Similarity=0.486  Sum_probs=83.5

Q ss_pred             CCCCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 029810            9 SRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG   88 (187)
Q Consensus         9 ~~~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g   88 (187)
                      +....+...+.++|||+|||+++++++|+++|++||.|..|.|+.+..  .+++||||+|.+.++|++||+.|++..|+|
T Consensus         5 ~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   82 (103)
T 2cq3_A            5 SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEG   82 (103)
T ss_dssp             CCCCSCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            344556677889999999999999999999999999999999998764  378999999999999999999999999999


Q ss_pred             eEEEEEeccCCCCCCC
Q 029810           89 RYITVERSRRKRPRTP  104 (187)
Q Consensus        89 ~~l~v~~a~~~~~~~~  104 (187)
                      +.|.|++++++.....
T Consensus        83 ~~l~v~~a~~~~~~~~   98 (103)
T 2cq3_A           83 RKIEVNNATARVMTNS   98 (103)
T ss_dssp             EECEEEECCSSCCCCC
T ss_pred             EEEEEEEcccCCCCCC
Confidence            9999999998765443

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

Probab=99.89  E-value=1.5e-22  Score=135.32  Aligned_cols=87  Identities=28%  Similarity=0.450  Sum_probs=80.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCC---CCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPR---TRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~---~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.+..   |+.+++||||+|.+.++|++||+.||+..|.|+.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            4678999999999999999999999999999999998876   6688999999999999999999999999999999999


Q ss_pred             EeccCCCCCC
Q 029810           94 ERSRRKRPRT  103 (187)
Q Consensus        94 ~~a~~~~~~~  103 (187)
                      ++++++....
T Consensus        83 ~~a~~~~~~~   92 (98)
T 2cpf_A           83 RISERATKPA   92 (98)
T ss_dssp             ECSSCSSCCC
T ss_pred             EEccCCCCCC
Confidence            9998765543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.89  E-value=1.5e-23  Score=138.64  Aligned_cols=83  Identities=24%  Similarity=0.352  Sum_probs=76.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCC-ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC-CCccCCeEEEEEec
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEG-KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLN-QSVLEGRYITVERS   96 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G-~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~-g~~i~g~~l~v~~a   96 (187)
                      +++|||+|||.++|+++|+++|++|| +|..|.|+.++.|+.++|||||+|.+.++|++||+.|+ +..|.|+.|.|+++
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            47999999999999999999999999 89999999999999999999999999999999999775 56799999999999


Q ss_pred             cCCCC
Q 029810           97 RRKRP  101 (187)
Q Consensus        97 ~~~~~  101 (187)
                      .+++.
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            87654

>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=99.89  E-value=1.9e-22  Score=130.66  Aligned_cols=82  Identities=22%  Similarity=0.369  Sum_probs=78.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccC
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR   98 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   98 (187)
                      +++|||+|||.++++++|+++|++||.|..+.|+.+..++.++|||||+|.+.++|++|++.||+..|.|+.|.|+++++
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            36899999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             CC
Q 029810           99 KR  100 (187)
Q Consensus        99 ~~  100 (187)
                      ++
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

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

Probab=99.89  E-value=2.2e-22  Score=133.45  Aligned_cols=86  Identities=30%  Similarity=0.439  Sum_probs=80.5

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ......+.++|||+|||.++++++|+++|++||.|..|.|+.+..++.+++||||+|.+.++|++||+.||+..|.|+.|
T Consensus         9 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   88 (94)
T 2e5h_A            9 SGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVI   88 (94)
T ss_dssp             CCSCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEE
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEE
Confidence            34455678999999999999999999999999999999999998889999999999999999999999999999999999


Q ss_pred             EEEecc
Q 029810           92 TVERSR   97 (187)
Q Consensus        92 ~v~~a~   97 (187)
                      .|++++
T Consensus        89 ~v~~ak   94 (94)
T 2e5h_A           89 KASIAI   94 (94)
T ss_dssp             EEEECC
T ss_pred             EEEecC
Confidence            999985

>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=99.89  E-value=1.6e-22  Score=137.00  Aligned_cols=91  Identities=20%  Similarity=0.260  Sum_probs=83.4

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc---CC
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVL---EG   88 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i---~g   88 (187)
                      ...+..+.++|||+|||.++++++|+++|++||.|..|.|+.+..++.+++||||+|.+.++|++||+.||+..|   .+
T Consensus         6 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g   85 (106)
T 2dgp_A            6 SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMN   85 (106)
T ss_dssp             CSCCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCS
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCC
Confidence            344566789999999999999999999999999999999999998999999999999999999999999999987   88


Q ss_pred             eEEEEEeccCCCCC
Q 029810           89 RYITVERSRRKRPR  102 (187)
Q Consensus        89 ~~l~v~~a~~~~~~  102 (187)
                      +.|.|+++.++...
T Consensus        86 ~~l~v~~a~~~~~~   99 (106)
T 2dgp_A           86 RPIQVKPADSESRG   99 (106)
T ss_dssp             SCCEEEECCCCSCC
T ss_pred             ceEEEEECCccccc
Confidence            99999999876543

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

Probab=99.89  E-value=2.6e-22  Score=137.60  Aligned_cols=90  Identities=23%  Similarity=0.410  Sum_probs=83.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCcee--------EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVA--------SCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS   84 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~--------~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~   84 (187)
                      ..+..+.++|||+|||.++++++|+++|++||.|.        .|.|+.+..++.++|||||+|.+.++|++||+.||+.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   88 (113)
T 2cpe_A            9 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   88 (113)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCC
Confidence            34566789999999999999999999999999999        6999999889999999999999999999999999999


Q ss_pred             ccCCeEEEEEeccCCCCC
Q 029810           85 VLEGRYITVERSRRKRPR  102 (187)
Q Consensus        85 ~i~g~~l~v~~a~~~~~~  102 (187)
                      .|.|+.|.|++++++...
T Consensus        89 ~~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           89 DFQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             EETTEECEEECSSCCCCS
T ss_pred             ccCCCEEEEEECCCCCCC
Confidence            999999999999876543

>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=99.88  E-value=1.7e-22  Score=131.45  Aligned_cols=83  Identities=33%  Similarity=0.479  Sum_probs=78.8

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ...+.++|||+|||+++++++|+++|++||.|..|.|+.+..++.+++||||+|.+.++|++|++.||+..|.|+.|.|+
T Consensus         3 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   82 (85)
T 3mdf_A            3 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   82 (85)
T ss_dssp             CCCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34577999999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             ecc
Q 029810           95 RSR   97 (187)
Q Consensus        95 ~a~   97 (187)
                      +++
T Consensus        83 ~ak   85 (85)
T 3mdf_A           83 LAK   85 (85)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            975

>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=99.88  E-value=3.5e-23  Score=136.49  Aligned_cols=84  Identities=20%  Similarity=0.298  Sum_probs=72.8

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCC--ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEG--KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G--~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      .+|||+|||+++++++|+++|++||  .|..|.|+.+..++.++|||||+|.+.++|++||+.||+..|.|+.|.|+++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5799999999999999999999999  99999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCCC
Q 029810           98 RKRPRT  103 (187)
Q Consensus        98 ~~~~~~  103 (187)
                      +.....
T Consensus        82 ~~~~~~   87 (90)
T 3p5t_L           82 KLEHHH   87 (90)
T ss_dssp             ------
T ss_pred             CCcccc
Confidence            765543

>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=99.88  E-value=3.2e-22  Score=135.25  Aligned_cols=87  Identities=20%  Similarity=0.354  Sum_probs=80.4

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCC-CCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRT-RISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~-~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ..+..+.++|||+|||+++++++|+++|.+|| |..|.|+.+..+ +.++|||||+|.+.++|++|| .|++..|.|+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   86 (104)
T 1wi8_A            9 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRI   86 (104)
T ss_dssp             CCCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEE
Confidence            44556779999999999999999999999999 999999999887 899999999999999999999 899999999999


Q ss_pred             EEEeccCCCC
Q 029810           92 TVERSRRKRP  101 (187)
Q Consensus        92 ~v~~a~~~~~  101 (187)
                      .|++++++..
T Consensus        87 ~V~~a~~~~~   96 (104)
T 1wi8_A           87 RVDVADQAQD   96 (104)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEccCCCC
Confidence            9999987654

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

Probab=99.88  E-value=1.8e-21  Score=133.53  Aligned_cols=89  Identities=27%  Similarity=0.385  Sum_probs=81.5

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ...+..+.++|||+|||.++++++|+++|.+||.|..|.|+.+. ++.+++||||+|.+.++|++||+.||+..|.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   86 (114)
T 2do0_A            8 ALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPM   86 (114)
T ss_dssp             CCCCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEE
Confidence            34556778999999999999999999999999999999999887 58899999999999999999999999999999999


Q ss_pred             EEEeccCCCC
Q 029810           92 TVERSRRKRP  101 (187)
Q Consensus        92 ~v~~a~~~~~  101 (187)
                      .|++++....
T Consensus        87 ~v~~a~~~~~   96 (114)
T 2do0_A           87 HVKMDERALP   96 (114)
T ss_dssp             EEEECSCCCC
T ss_pred             EEEEcccCCC
Confidence            9999875543

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

Probab=99.88  E-value=2.5e-22  Score=135.96  Aligned_cols=90  Identities=24%  Similarity=0.404  Sum_probs=83.3

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ...+..+.++|||+|||+++++++|+++|.+||+|..|.|+.+..++.+++||||+|.+.++|++||+. ++..|+|+.|
T Consensus         9 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l   87 (105)
T 2dh8_A            9 NNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNI   87 (105)
T ss_dssp             CCCCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEE
T ss_pred             CcCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEE
Confidence            344567789999999999999999999999999999999999988999999999999999999999998 9999999999


Q ss_pred             EEEeccCCCCC
Q 029810           92 TVERSRRKRPR  102 (187)
Q Consensus        92 ~v~~a~~~~~~  102 (187)
                      .|++++++...
T Consensus        88 ~V~~a~~~~~~   98 (105)
T 2dh8_A           88 DPKPCTPRGMQ   98 (105)
T ss_dssp             BCCCSCCSSCC
T ss_pred             EEEEccCCCCC
Confidence            99999877554

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

Probab=99.88  E-value=4e-22  Score=134.63  Aligned_cols=89  Identities=21%  Similarity=0.349  Sum_probs=82.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhc-CCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCc-cCCeE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSK-EGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSV-LEGRY   90 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~-~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~-i~g~~   90 (187)
                      ..+..+.++|||+|||+++++++|+++|.+ ||.|..|.|+.+. ++.+++||||+|.+.++|++||+.|++.. |+|+.
T Consensus         3 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~   81 (104)
T 2dhg_A            3 SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKP   81 (104)
T ss_dssp             CCCSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSC
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEe
Confidence            445677899999999999999999999999 9999999999998 89999999999999999999999999999 99999


Q ss_pred             EEEEeccCCCCC
Q 029810           91 ITVERSRRKRPR  102 (187)
Q Consensus        91 l~v~~a~~~~~~  102 (187)
                      |.|+++.++...
T Consensus        82 l~v~~a~~~~~~   93 (104)
T 2dhg_A           82 VRLSVAIPKASR   93 (104)
T ss_dssp             CCCCBCCCCCSC
T ss_pred             EEEEEccCCCcC
Confidence            999999876543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.88  E-value=1.1e-22  Score=135.40  Aligned_cols=84  Identities=20%  Similarity=0.347  Sum_probs=76.9

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCc--eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC----ccCC
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGK--VASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS----VLEG   88 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~--i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~----~i~g   88 (187)
                      ....-++|||+|||+++|+++|+++|++||.  |..|.|+.++.|+.++|||||+|.+.++|++||+.||+.    .|+|
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            3445589999999999999999999999995  678999999999999999999999999999999999997    4899


Q ss_pred             eEEEEEeccC
Q 029810           89 RYITVERSRR   98 (187)
Q Consensus        89 ~~l~v~~a~~   98 (187)
                      +.|.|++|+.
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999999874

>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=99.88  E-value=3.6e-22  Score=133.08  Aligned_cols=84  Identities=23%  Similarity=0.412  Sum_probs=79.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ++++|||+|||.++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+.|++..|+|+.|.|++++
T Consensus         1 P~~~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            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            46899999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 029810           98 RKRP  101 (187)
Q Consensus        98 ~~~~  101 (187)
                      ++..
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            7643

>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=99.88  E-value=1.2e-21  Score=132.07  Aligned_cols=89  Identities=26%  Similarity=0.362  Sum_probs=80.3

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ...+..+.++|||+|||+++++++|+++|++||.|..|.|+.+..+  +++||||+|.+.++|++||+.|++..|.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   85 (103)
T 2cqi_A            8 MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEV   85 (103)
T ss_dssp             CCCCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeE
Confidence            3455677899999999999999999999999999999999988543  58999999999999999999999999999999


Q ss_pred             EEEeccCCCCC
Q 029810           92 TVERSRRKRPR  102 (187)
Q Consensus        92 ~v~~a~~~~~~  102 (187)
                      .|++++++...
T Consensus        86 ~V~~a~~~~~~   96 (103)
T 2cqi_A           86 KVNWATTPSSQ   96 (103)
T ss_dssp             EEEECCCTTCC
T ss_pred             EEEECCCCccc
Confidence            99999876543

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

Probab=99.88  E-value=5.2e-22  Score=133.03  Aligned_cols=85  Identities=24%  Similarity=0.341  Sum_probs=80.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeE--------EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVAS--------CFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS   84 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~--------~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~   84 (187)
                      ..+..+.++|||+|||.++++++|+++|++||.|..        |.|+.+..++.++|||||+|.+.++|++||+.||+.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A            7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            456677899999999999999999999999999999        999999999999999999999999999999999999


Q ss_pred             ccCCeEEEEEecc
Q 029810           85 VLEGRYITVERSR   97 (187)
Q Consensus        85 ~i~g~~l~v~~a~   97 (187)
                      .|.|+.|.|++|+
T Consensus        87 ~~~g~~l~V~~A~   99 (99)
T 2la6_A           87 EFSGNPIKVSFAT   99 (99)
T ss_dssp             BSSSSBCEEEECC
T ss_pred             EeCCcEEEEEecC
Confidence            9999999999974

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

Probab=99.88  E-value=3.3e-22  Score=133.89  Aligned_cols=86  Identities=20%  Similarity=0.380  Sum_probs=80.9

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCcee-EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE--
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVA-SCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY--   90 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~-~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~--   90 (187)
                      ....+.++|||+|||+++++++|+++|++||.|. .|.|+.+..++.+++||||+|.+.++|++||+.||+..|.|+.  
T Consensus         4 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~   83 (99)
T 2div_A            4 GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPA   83 (99)
T ss_dssp             CCCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSC
T ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcc
Confidence            4456789999999999999999999999999999 9999999999999999999999999999999999999999999  


Q ss_pred             --EEEEeccCC
Q 029810           91 --ITVERSRRK   99 (187)
Q Consensus        91 --l~v~~a~~~   99 (187)
                        |.|+++++.
T Consensus        84 ~~l~v~~a~~~   94 (99)
T 2div_A           84 KRFKLNYATYS   94 (99)
T ss_dssp             EECCEEETTCC
T ss_pred             eeEEEeecCCC
Confidence              999998865

>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=99.88  E-value=4.6e-22  Score=136.96  Aligned_cols=83  Identities=28%  Similarity=0.518  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ..++|||+|||+++++++|+++|++||.|..|.|+.+.  +.++|||||+|.+.++|++||+.|++..|+|+.|.|+++.
T Consensus         4 ~~~~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            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            45789999999999999999999999999999999886  4478999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 029810           98 RKRPR  102 (187)
Q Consensus        98 ~~~~~  102 (187)
                      ++..+
T Consensus        82 ~~~~~   86 (115)
T 4f25_A           82 SRKER   86 (115)
T ss_dssp             CCCC-
T ss_pred             Ccccc
Confidence            76543

>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=99.88  E-value=5.3e-22  Score=135.24  Aligned_cols=88  Identities=27%  Similarity=0.394  Sum_probs=82.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      +....+.++|||+|||..+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+.|++..|.|+.|.
T Consensus        20 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~   99 (108)
T 2jrs_A           20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMK   99 (108)
T ss_dssp             CCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            44566778999999999999999999999999999999999998999999999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 029810           93 VERSRRKR  100 (187)
Q Consensus        93 v~~a~~~~  100 (187)
                      |++++++.
T Consensus       100 V~~a~~k~  107 (108)
T 2jrs_A          100 VGHVTERT  107 (108)
T ss_dssp             EECSCSSC
T ss_pred             EEEcccCC
Confidence            99998653

>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=99.88  E-value=5.6e-22  Score=132.22  Aligned_cols=86  Identities=21%  Similarity=0.317  Sum_probs=78.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHH----HHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLE----KHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG   88 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~----~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g   88 (187)
                      ..+..+.++|||+|||+++++++|+    ++|++||+|..|.|+.+..+   ++||||+|.+.++|++||+.||+..|.|
T Consensus         3 s~~~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~g   79 (96)
T 2dgx_A            3 SGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGS   79 (96)
T ss_dssp             CCCCSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            3455677899999999999999999    99999999999999988765   7899999999999999999999999999


Q ss_pred             eEEEEEeccCCCC
Q 029810           89 RYITVERSRRKRP  101 (187)
Q Consensus        89 ~~l~v~~a~~~~~  101 (187)
                      +.|.|+++++...
T Consensus        80 r~l~V~~a~~~~~   92 (96)
T 2dgx_A           80 KKILVSLATGASG   92 (96)
T ss_dssp             EEEEEEECCCSSC
T ss_pred             eEEEEEEcCCCCC
Confidence            9999999987644

>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=99.88  E-value=1.3e-21  Score=133.24  Aligned_cols=86  Identities=28%  Similarity=0.353  Sum_probs=77.4

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      ..+..+.++|||+|||.++++++|+++|++||.|..|.|+.+   +.+++||||+|.+.++|++||+.||+..|+|+.|.
T Consensus        16 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   92 (109)
T 1x4a_A           16 GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLR   92 (109)
T ss_dssp             CCCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            445567799999999999999999999999999999998654   45689999999999999999999999999999999


Q ss_pred             EEeccCCCC
Q 029810           93 VERSRRKRP  101 (187)
Q Consensus        93 v~~a~~~~~  101 (187)
                      |++++++..
T Consensus        93 V~~a~~~~~  101 (109)
T 1x4a_A           93 VEFPRSGRG  101 (109)
T ss_dssp             EECCCCCCC
T ss_pred             EEEcccCCC
Confidence            999987644

>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=99.88  E-value=3.8e-22  Score=136.11  Aligned_cols=88  Identities=25%  Similarity=0.412  Sum_probs=81.9

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      ....+.++|||+|||.++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||..|++..|.|+.|.|
T Consensus        21 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  100 (110)
T 1oo0_B           21 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV  100 (110)
T ss_dssp             CCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            34456789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EeccCCCC
Q 029810           94 ERSRRKRP  101 (187)
Q Consensus        94 ~~a~~~~~  101 (187)
                      ++++++..
T Consensus       101 ~~a~~~~~  108 (110)
T 1oo0_B          101 DWCFVKGP  108 (110)
T ss_dssp             EESEESSC
T ss_pred             EEcccCCC
Confidence            99987643

>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=99.87  E-value=1.8e-21  Score=132.45  Aligned_cols=83  Identities=22%  Similarity=0.343  Sum_probs=75.5

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--
Q 029810           11 GRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG--   88 (187)
Q Consensus        11 ~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g--   88 (187)
                      ...++....++|||+|||+++++++|+++|.+||+|..|.|+.+       +||||+|++.++|++||+.||+..|.|  
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~   79 (108)
T 1x4c_A            7 GGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHE   79 (108)
T ss_dssp             SSCCCCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTT
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCc
Confidence            34455677899999999999999999999999999999999865       699999999999999999999999999  


Q ss_pred             ---eEEEEEeccCCC
Q 029810           89 ---RYITVERSRRKR  100 (187)
Q Consensus        89 ---~~l~v~~a~~~~  100 (187)
                         +.|.|++++++.
T Consensus        80 ~~~~~i~V~~a~~~~   94 (108)
T 1x4c_A           80 GETAYIRVKVDGPRS   94 (108)
T ss_dssp             SCEEEEEEEESSCCS
T ss_pred             CcceEEEEEeCCCCC
Confidence               999999998753

>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=99.87  E-value=6.7e-22  Score=134.19  Aligned_cols=84  Identities=23%  Similarity=0.307  Sum_probs=79.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      ..+..+.++|||+|||+.+++++|+++|.+||.|..|.|+.+. ++.+++||||+|.+.++|++||+.|++..|.|+.|.
T Consensus        23 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  101 (107)
T 3ulh_A           23 GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMN  101 (107)
T ss_dssp             -CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            4556778999999999999999999999999999999999998 899999999999999999999999999999999999


Q ss_pred             EEecc
Q 029810           93 VERSR   97 (187)
Q Consensus        93 v~~a~   97 (187)
                      |++++
T Consensus       102 V~~a~  106 (107)
T 3ulh_A          102 IQLVT  106 (107)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99985

>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=99.87  E-value=2.9e-21  Score=130.23  Aligned_cols=90  Identities=26%  Similarity=0.415  Sum_probs=81.9

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE
Q 029810           11 GRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY   90 (187)
Q Consensus        11 ~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~   90 (187)
                      ....+..+.++|||+|||+++++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|++||.  +++.|+|+.
T Consensus         7 ~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~   84 (103)
T 2cqg_A            7 GVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRW   84 (103)
T ss_dssp             SCSCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEE
T ss_pred             CCCCccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeE
Confidence            345566778999999999999999999999999999999999999899999999999999999999999  467899999


Q ss_pred             EEEEeccCCCCC
Q 029810           91 ITVERSRRKRPR  102 (187)
Q Consensus        91 l~v~~a~~~~~~  102 (187)
                      |.|+++.++...
T Consensus        85 l~v~~a~~~~~~   96 (103)
T 2cqg_A           85 CDCKLPNSKQSQ   96 (103)
T ss_dssp             EEEECCCTTCCC
T ss_pred             EEEEecCCCCcC
Confidence            999999876543

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

Probab=99.87  E-value=1.3e-22  Score=136.36  Aligned_cols=83  Identities=24%  Similarity=0.357  Sum_probs=78.9

Q ss_pred             CCCCeEEEcCCCC------CCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC-e
Q 029810           17 NPGNTLYVTGLST------RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG-R   89 (187)
Q Consensus        17 ~~~~~l~V~~Lp~------~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g-~   89 (187)
                      ..+++|||+|||.      ++++++|+++|++||.|..|.|+.+..|+.++|||||+|.+.++|++||+.||+..|.| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            4568999999999      99999999999999999999999999999999999999999999999999999999999 9


Q ss_pred             EEEEEeccCC
Q 029810           90 YITVERSRRK   99 (187)
Q Consensus        90 ~l~v~~a~~~   99 (187)
                      .|.|.++.+.
T Consensus        84 ~l~V~~a~~~   93 (100)
T 3ns6_A           84 RLFLYTMKDV   93 (100)
T ss_dssp             BCEEEESHHH
T ss_pred             EEEEEECchh
Confidence            9999998754

>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=99.87  E-value=6.2e-22  Score=129.56  Aligned_cols=83  Identities=23%  Similarity=0.355  Sum_probs=77.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCC-cceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRI-SRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~-~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ..++|||+|||.++++++|+++|++||.|..|.|+.+..++. ++|||||+|.+.++|++|++.||+..|+|+.|.|+++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            468999999999999999999999999999999998887665 7899999999999999999999999999999999999


Q ss_pred             cCCC
Q 029810           97 RRKR  100 (187)
Q Consensus        97 ~~~~  100 (187)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

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

Probab=99.87  E-value=6.2e-22  Score=136.69  Aligned_cols=85  Identities=26%  Similarity=0.421  Sum_probs=79.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      ..+..+.++|||+|||.++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+.||+..|+|+.|.
T Consensus        34 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  113 (118)
T 2khc_A           34 QIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLK  113 (118)
T ss_dssp             SCCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34556779999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEecc
Q 029810           93 VERSR   97 (187)
Q Consensus        93 v~~a~   97 (187)
                      |++++
T Consensus       114 V~~ak  118 (118)
T 2khc_A          114 VQLKK  118 (118)
T ss_dssp             EEEC-
T ss_pred             EEecC
Confidence            99974

>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=99.87  E-value=5.2e-22  Score=132.65  Aligned_cols=86  Identities=12%  Similarity=0.135  Sum_probs=79.7

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      ......++|||+|||+++++++|+++|.+||.|..+.++.+..++.+++||||+|.+.++|++||+.||+..|.|+.|.|
T Consensus        10 ~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V   89 (98)
T 2cqp_A           10 SGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKL   89 (98)
T ss_dssp             CCCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            34556789999999999999999999999999998888888889999999999999999999999999999999999999


Q ss_pred             EeccCC
Q 029810           94 ERSRRK   99 (187)
Q Consensus        94 ~~a~~~   99 (187)
                      +++...
T Consensus        90 ~~a~~~   95 (98)
T 2cqp_A           90 VLGSGP   95 (98)
T ss_dssp             EESSCS
T ss_pred             EEcCCC
Confidence            998743

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

Probab=99.87  E-value=1.5e-21  Score=128.90  Aligned_cols=85  Identities=26%  Similarity=0.328  Sum_probs=78.5

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      +..+.++|||+|||.++++++|+++|++||.|..|.|+.+  ++.+++||||+|.+.++|++||+.|++..|.|+.|.|+
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   81 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVR   81 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            4567899999999999999999999999999999999874  68889999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 029810           95 RSRRKRP  101 (187)
Q Consensus        95 ~a~~~~~  101 (187)
                      ++++...
T Consensus        82 ~a~~~~~   88 (92)
T 2dgv_A           82 IDRNASG   88 (92)
T ss_dssp             ECSCCSS
T ss_pred             EcCCCCC
Confidence            9986543

>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=99.87  E-value=3.5e-21  Score=129.93  Aligned_cols=81  Identities=27%  Similarity=0.390  Sum_probs=74.2

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      ....+.++|||+|||+++++++|+++|.+||.|..|.|+        ++||||+|.+.++|++||+.||+..|.|+.|.|
T Consensus         6 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   77 (103)
T 2dgu_A            6 SGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEI   77 (103)
T ss_dssp             CCCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEE
Confidence            345677999999999999999999999999999999886        459999999999999999999999999999999


Q ss_pred             EeccCCCCC
Q 029810           94 ERSRRKRPR  102 (187)
Q Consensus        94 ~~a~~~~~~  102 (187)
                      ++++++...
T Consensus        78 ~~a~~~~~~   86 (103)
T 2dgu_A           78 VFAKPPDQK   86 (103)
T ss_dssp             EECCCCCCC
T ss_pred             EEcCCCccc
Confidence            999876554

>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=99.87  E-value=8.3e-22  Score=130.88  Aligned_cols=85  Identities=25%  Similarity=0.337  Sum_probs=78.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      ..+..+.++|||+|||+.+++++|+++|++||+|..|.|+.+.. +.+++||||+|.+.++|++||+.||+..|.|+.|.
T Consensus        10 ~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (95)
T 2ywk_A           10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPIN   88 (95)
T ss_dssp             --CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEE
Confidence            44566779999999999999999999999999999999999875 88899999999999999999999999999999999


Q ss_pred             EEeccC
Q 029810           93 VERSRR   98 (187)
Q Consensus        93 v~~a~~   98 (187)
                      |++++.
T Consensus        89 V~~a~~   94 (95)
T 2ywk_A           89 VSGPSS   94 (95)
T ss_dssp             EECCCC
T ss_pred             EEEcCC
Confidence            999863

>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=99.87  E-value=1.8e-21  Score=127.27  Aligned_cols=83  Identities=28%  Similarity=0.574  Sum_probs=76.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .++..+.++|||+|||+++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+ +++..|+|+.|.
T Consensus         5 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~   83 (87)
T 3s7r_A            5 SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVID   83 (87)
T ss_dssp             --CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEE
Confidence            3456778999999999999999999999999999999999999999999999999999999999997 688899999999


Q ss_pred             EEec
Q 029810           93 VERS   96 (187)
Q Consensus        93 v~~a   96 (187)
                      |++|
T Consensus        84 v~~A   87 (87)
T 3s7r_A           84 PKKA   87 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9875

>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=99.86  E-value=3.9e-22  Score=132.50  Aligned_cols=84  Identities=12%  Similarity=0.160  Sum_probs=76.1

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      ....+.++|||+|||+++++++|+++|++||.|..+.++.+..++.+++||||+|.+.++|++||+.||+..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v   89 (95)
T 2ek1_A           10 SGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKL   89 (95)
T ss_dssp             -----CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEE
Confidence            34455689999999999999999999999999999989988889999999999999999999999999999999999999


Q ss_pred             Eecc
Q 029810           94 ERSR   97 (187)
Q Consensus        94 ~~a~   97 (187)
                      +++.
T Consensus        90 ~~a~   93 (95)
T 2ek1_A           90 SGPS   93 (95)
T ss_dssp             ECCC
T ss_pred             Eecc
Confidence            9976

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

Probab=99.86  E-value=2.9e-21  Score=134.55  Aligned_cols=91  Identities=21%  Similarity=0.256  Sum_probs=83.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .....+.++|||+|||..+++++|+++|++||.|..|.|+.+. ++.++|||||+|.+.++|++||+.|++..|.|+.|.
T Consensus        29 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  107 (124)
T 2kt5_A           29 GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMD  107 (124)
T ss_dssp             CCCCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            3456777899999999999999999999999999999999988 889999999999999999999999999999999999


Q ss_pred             EEeccCCCCCCC
Q 029810           93 VERSRRKRPRTP  104 (187)
Q Consensus        93 v~~a~~~~~~~~  104 (187)
                      |++|.+.....+
T Consensus       108 V~~a~~~~~~~~  119 (124)
T 2kt5_A          108 IQLVASQIDLEH  119 (124)
T ss_dssp             EEEECCTTCCCC
T ss_pred             EEEeCCCCCCCC
Confidence            999987665544

>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=99.86  E-value=1.4e-21  Score=131.56  Aligned_cols=84  Identities=14%  Similarity=0.252  Sum_probs=74.3

Q ss_pred             CCCCCCCCCeEEEcCCCC-CCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC--ccCC
Q 029810           12 RTETGNPGNTLYVTGLST-RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS--VLEG   88 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~-~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~--~i~g   88 (187)
                      .....++.++|||+|||+ .+++++|+++|++||.|..|.|+.+      ++||||+|++.++|++||+.|++.  .|.|
T Consensus         8 ~~~~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~G   81 (102)
T 1x4d_A            8 QKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFG   81 (102)
T ss_dssp             CCCCCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             CCCCCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECC
Confidence            344566889999999999 9999999999999999999999764      479999999999999999999864  5999


Q ss_pred             eEEEEEeccCCCC
Q 029810           89 RYITVERSRRKRP  101 (187)
Q Consensus        89 ~~l~v~~a~~~~~  101 (187)
                      +.|.|++++....
T Consensus        82 r~l~V~~a~~~~~   94 (102)
T 1x4d_A           82 KPVRVHLSQKYKR   94 (102)
T ss_dssp             EECEEEEECCCTT
T ss_pred             cEEEEEECCCCCC
Confidence            9999999986543

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

Probab=99.86  E-value=3.3e-21  Score=129.64  Aligned_cols=87  Identities=28%  Similarity=0.480  Sum_probs=78.2

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ......+.++|||+|||.++++++|+++|+.|+   .|.++.+..++.+++||||+|.+.++|++||+.||+..|.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   84 (102)
T 2fc8_A            8 PNARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKV   84 (102)
T ss_dssp             TSSSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            345567789999999999999999999999874   67778888889999999999999999999999999999999999


Q ss_pred             EEEeccCCCC
Q 029810           92 TVERSRRKRP  101 (187)
Q Consensus        92 ~v~~a~~~~~  101 (187)
                      .|++++++..
T Consensus        85 ~V~~a~~~~~   94 (102)
T 2fc8_A           85 TLDWAKPKGE   94 (102)
T ss_dssp             EEEECCCCCS
T ss_pred             EEEEecCCCC
Confidence            9999987644

>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=99.86  E-value=1.5e-22  Score=138.98  Aligned_cols=83  Identities=29%  Similarity=0.436  Sum_probs=78.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ..++|||+|||.++++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|++|| .||+..|.|+.|.|++++
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~  102 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecC
Confidence            3479999999999999999999999999999999999999999999999999999999999 899999999999999998


Q ss_pred             CCCC
Q 029810           98 RKRP  101 (187)
Q Consensus        98 ~~~~  101 (187)
                      ++..
T Consensus       103 ~~~~  106 (114)
T 2cq4_A          103 AEKN  106 (114)
T ss_dssp             HHHH
T ss_pred             CCcc
Confidence            6543

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

Probab=99.86  E-value=4.1e-21  Score=126.61  Aligned_cols=84  Identities=24%  Similarity=0.397  Sum_probs=78.4

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      .+....++|||+|||+++++++|+++|++| .|..|.|+.+ .++.++|||||+|.+.++|++||+ ||+..|.|+.|.|
T Consensus         5 ~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v   81 (91)
T 2dgw_A            5 SSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEV   81 (91)
T ss_dssp             CCCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEE
T ss_pred             CCCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEE
Confidence            445677999999999999999999999999 9999999998 789999999999999999999999 9999999999999


Q ss_pred             EeccCCC
Q 029810           94 ERSRRKR  100 (187)
Q Consensus        94 ~~a~~~~  100 (187)
                      .+++++.
T Consensus        82 ~~a~~~~   88 (91)
T 2dgw_A           82 FREKSGP   88 (91)
T ss_dssp             EEESSCC
T ss_pred             EECCcCC
Confidence            9998764

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

Probab=99.86  E-value=6.3e-22  Score=136.31  Aligned_cols=85  Identities=25%  Similarity=0.525  Sum_probs=79.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      .+.++|||+|||+++++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|++||+. ++..|+|+.|.|+++
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEEC
Confidence            4458999999999999999999999999999999999998999999999999999999999996 999999999999999


Q ss_pred             cCCCCC
Q 029810           97 RRKRPR  102 (187)
Q Consensus        97 ~~~~~~  102 (187)
                      +++...
T Consensus       104 ~~~~~~  109 (116)
T 1x4b_A          104 VAREES  109 (116)
T ss_dssp             SSCCCC
T ss_pred             CCCccC
Confidence            877543

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

Probab=99.86  E-value=3.6e-21  Score=129.28  Aligned_cols=87  Identities=26%  Similarity=0.404  Sum_probs=76.8

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE
Q 029810           11 GRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY   90 (187)
Q Consensus        11 ~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~   90 (187)
                      ...+...+.++|||+|||.++++++|+++|.+||.|   .|+.+ .++.+++||||+|.+.++|++||+.||+..|.|+.
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   82 (101)
T 2fc9_A            7 GNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRA   82 (101)
T ss_dssp             CCCCCSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEE
T ss_pred             CCccCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeE
Confidence            344566778999999999999999999999999987   45555 57888999999999999999999999999999999


Q ss_pred             EEEEeccCCCC
Q 029810           91 ITVERSRRKRP  101 (187)
Q Consensus        91 l~v~~a~~~~~  101 (187)
                      |.|++++++..
T Consensus        83 l~v~~a~~~~~   93 (101)
T 2fc9_A           83 IRLELQGPRGS   93 (101)
T ss_dssp             EEEEECSSCCC
T ss_pred             EEEEEcCCCCC
Confidence            99999987643

>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=99.86  E-value=5.6e-21  Score=128.55  Aligned_cols=87  Identities=23%  Similarity=0.309  Sum_probs=76.8

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC--CCccC
Q 029810           10 RGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLN--QSVLE   87 (187)
Q Consensus        10 ~~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~--g~~i~   87 (187)
                      +.......+.++|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|++.++|++||+.|+  +..|.
T Consensus         6 ~~~~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~   79 (101)
T 2cq1_A            6 SGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLR   79 (101)
T ss_dssp             CCCCCCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEET
T ss_pred             CCCCccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceEC
Confidence            444566678899999999999999999999999999999988754      6899999999999999999875  67899


Q ss_pred             CeEEEEEeccCCCCC
Q 029810           88 GRYITVERSRRKRPR  102 (187)
Q Consensus        88 g~~l~v~~a~~~~~~  102 (187)
                      |+.|.|++++.+...
T Consensus        80 Gr~l~V~~a~~~~~~   94 (101)
T 2cq1_A           80 NQPIYIQYSNHKELK   94 (101)
T ss_dssp             TEECEEEECSCSSCC
T ss_pred             CcEEEEEEcCcccCc
Confidence            999999999876554

>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=99.86  E-value=2.1e-21  Score=141.75  Aligned_cols=86  Identities=26%  Similarity=0.416  Sum_probs=80.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ..+.++|||+|||+.+++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|++||+.||+..|.|+.|.|.+
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 029810           96 SRRKRP  101 (187)
Q Consensus        96 a~~~~~  101 (187)
                      +.++..
T Consensus       149 a~~~~~  154 (165)
T 1rk8_A          149 CFVKGP  154 (165)
T ss_dssp             SEECC-
T ss_pred             ecCCCC
Confidence            987654

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

Probab=99.86  E-value=4.2e-21  Score=126.37  Aligned_cols=80  Identities=28%  Similarity=0.475  Sum_probs=74.1

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      +..+.++|||+|||.++++++|+++|++||.|..|.|+        ++||||+|.+.++|++||+.||+..|.|+.|.|+
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   75 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVE   75 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEE
Confidence            45677999999999999999999999999999999987        5699999999999999999999999999999999


Q ss_pred             eccCCCCC
Q 029810           95 RSRRKRPR  102 (187)
Q Consensus        95 ~a~~~~~~  102 (187)
                      +++++...
T Consensus        76 ~a~~~~~~   83 (90)
T 2dnq_A           76 ASKNKSKA   83 (90)
T ss_dssp             CSSCCCCC
T ss_pred             ECCCCCCC
Confidence            99876554

>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=99.86  E-value=2.2e-21  Score=127.25  Aligned_cols=81  Identities=25%  Similarity=0.458  Sum_probs=77.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ..++|||+|||.++++++|+++|++||.|..|.|+.+..++.+++||||+|.+.++|++|+ .|++..|.|+.|.|++++
T Consensus         5 ~~~~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            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            3579999999999999999999999999999999999889999999999999999999999 899999999999999997


Q ss_pred             CC
Q 029810           98 RK   99 (187)
Q Consensus        98 ~~   99 (187)
                      +.
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>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=99.86  E-value=5.9e-22  Score=133.75  Aligned_cols=86  Identities=24%  Similarity=0.395  Sum_probs=80.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ..+.++|||+|||..+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+.|++..|.|+.|.|++
T Consensus         5 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   84 (104)
T 1p1t_A            5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEE
T ss_pred             CCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 029810           96 SRRKRP  101 (187)
Q Consensus        96 a~~~~~  101 (187)
                      +.++..
T Consensus        85 a~~~~~   90 (104)
T 1p1t_A           85 AASEKN   90 (104)
T ss_dssp             TTCTTH
T ss_pred             CCCccc
Confidence            987643

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

Probab=99.86  E-value=5e-21  Score=126.49  Aligned_cols=82  Identities=28%  Similarity=0.495  Sum_probs=74.7

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .....+.++|||+|||+++++++|+++|++||.|..|.|+        ++||||+|.+.++|++||+.||+..|.|+.|.
T Consensus         4 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   75 (92)
T 2dgt_A            4 GSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMH   75 (92)
T ss_dssp             SCCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Confidence            3456678999999999999999999999999999999987        34999999999999999999999999999999


Q ss_pred             EEeccCCCCC
Q 029810           93 VERSRRKRPR  102 (187)
Q Consensus        93 v~~a~~~~~~  102 (187)
                      |++++++...
T Consensus        76 V~~a~~~~~~   85 (92)
T 2dgt_A           76 VQLSTSRLRT   85 (92)
T ss_dssp             EEESSCCCSC
T ss_pred             EEEccCCCCC
Confidence            9999876554

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

Probab=99.86  E-value=1.4e-21  Score=141.46  Aligned_cols=82  Identities=21%  Similarity=0.300  Sum_probs=77.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCC--ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEG--KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G--~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ..++|||+|||+++++++|+++|++||  .|..|.|+.+..++.++|||||+|.+.++|++||+.||+..|.|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            458999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 029810           96 SRRK   99 (187)
Q Consensus        96 a~~~   99 (187)
                      +.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            8753

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

Probab=99.86  E-value=1.4e-21  Score=131.94  Aligned_cols=83  Identities=25%  Similarity=0.369  Sum_probs=74.5

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC--CccCCeEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQ--SVLEGRYI   91 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g--~~i~g~~l   91 (187)
                      ....+.++|||+|||+++++++|+++|++||+|..|.|+.+      +|||||+|++.++|++||+.|++  ..|.|+.|
T Consensus        11 ~~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l   84 (105)
T 1sjq_A           11 GSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPI   84 (105)
T ss_dssp             -CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            35667899999999999999999999999999999999864      68999999999999999998864  68999999


Q ss_pred             EEEeccCCCCC
Q 029810           92 TVERSRRKRPR  102 (187)
Q Consensus        92 ~v~~a~~~~~~  102 (187)
                      .|++++++...
T Consensus        85 ~V~~A~~~~~~   95 (105)
T 1sjq_A           85 YIQFSNHKELK   95 (105)
T ss_dssp             CBCCCSSSSCC
T ss_pred             EEEEcCCCCCC
Confidence            99999876554

>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=99.86  E-value=3.2e-21  Score=131.91  Aligned_cols=87  Identities=26%  Similarity=0.328  Sum_probs=78.6

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHH---HHhhcCCceeEEEEeecCCCC---CcceEEEEEecCHHHHHHHHHHhCCCccC
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLE---KHFSKEGKVASCFLVVEPRTR---ISRGFAFVTMDGVEDAERCIKYLNQSVLE   87 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~---~~f~~~G~i~~~~i~~~~~~~---~~~g~afV~f~~~~~a~~ai~~l~g~~i~   87 (187)
                      ......++|||+|||+++++++|+   ++|++||+|..|.|+.+..++   .++|||||+|++.++|++||+.||+..|+
T Consensus        10 ~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   89 (111)
T 2cpi_A           10 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD   89 (111)
T ss_dssp             CCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             ccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEEC
Confidence            345567899999999999999999   999999999999998887644   45599999999999999999999999999


Q ss_pred             CeEEEEEeccCCC
Q 029810           88 GRYITVERSRRKR  100 (187)
Q Consensus        88 g~~l~v~~a~~~~  100 (187)
                      |+.|.|++++++.
T Consensus        90 gr~l~V~~a~~k~  102 (111)
T 2cpi_A           90 GRTLKASLGTTKY  102 (111)
T ss_dssp             TEEEEEESCCCCS
T ss_pred             CEEEEEEeccccc
Confidence            9999999998765

>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=99.86  E-value=6.4e-22  Score=135.99  Aligned_cols=92  Identities=30%  Similarity=0.411  Sum_probs=77.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      ..+..+.++|||+|||.++++++|+++|.+||.|..+.+..+..++.++|||||+|.+.++|++||+.|++..|.|+.|.
T Consensus        19 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   98 (115)
T 2cpx_A           19 YNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILV   98 (115)
T ss_dssp             CCCCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCE
T ss_pred             cCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            34456789999999999999999999999999984332222222678899999999999999999999999999999999


Q ss_pred             EEeccCCCCCCC
Q 029810           93 VERSRRKRPRTP  104 (187)
Q Consensus        93 v~~a~~~~~~~~  104 (187)
                      |++++++....+
T Consensus        99 v~~a~~~~~~~~  110 (115)
T 2cpx_A           99 IEFGKNKKQRSS  110 (115)
T ss_dssp             EEECCCCSCCCC
T ss_pred             EEEccCCCCCCC
Confidence            999997765443

>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=99.86  E-value=6.1e-21  Score=127.28  Aligned_cols=83  Identities=19%  Similarity=0.331  Sum_probs=75.2

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC--CeE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE--GRY   90 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~--g~~   90 (187)
                      .....+.++|||+|||.++++++|+++|++||.|..|.|+.+      ++||||+|.+.++|++||+.||+..|.  |+.
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~   84 (97)
T 1why_A           11 YGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRR   84 (97)
T ss_dssp             CCCCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCB
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcE
Confidence            445567799999999999999999999999999999998753      679999999999999999999999999  999


Q ss_pred             EEEEeccCCCC
Q 029810           91 ITVERSRRKRP  101 (187)
Q Consensus        91 l~v~~a~~~~~  101 (187)
                      |.|++++++..
T Consensus        85 l~V~~a~~~~~   95 (97)
T 1why_A           85 LRVDFAKSGPS   95 (97)
T ss_dssp             CEEEECCCCCC
T ss_pred             EEEEECCCCCC
Confidence            99999987643

>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=99.86  E-value=4.3e-21  Score=129.76  Aligned_cols=89  Identities=25%  Similarity=0.310  Sum_probs=79.7

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe
Q 029810           11 GRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVAS-CFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGR   89 (187)
Q Consensus        11 ~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~-~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~   89 (187)
                      ...++....++|||+|||+++++++|+++|.+||.|.. |.|+.+ .++.++|||||+|.+.++|++||+. ++..|.++
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr   84 (104)
T 1wg5_A            7 GNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHR   84 (104)
T ss_dssp             CCCSSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSS
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCc
Confidence            34455677899999999999999999999999999987 888877 7899999999999999999999996 99999999


Q ss_pred             EEEEEeccCCCC
Q 029810           90 YITVERSRRKRP  101 (187)
Q Consensus        90 ~l~v~~a~~~~~  101 (187)
                      .|.|.++..+..
T Consensus        85 ~i~v~~~~~~~~   96 (104)
T 1wg5_A           85 YIEIFKSSRAEV   96 (104)
T ss_dssp             CCEEEEECTTTS
T ss_pred             EEEEEECCHHHH
Confidence            999999876543

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

Probab=99.86  E-value=8.1e-22  Score=138.74  Aligned_cols=89  Identities=19%  Similarity=0.396  Sum_probs=81.7

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeE--EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC----cc
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVAS--CFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS----VL   86 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~--~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~----~i   86 (187)
                      .....+.++|||+|||+++++++|+++|.+||.|..  |.|+.+..++.++|||||+|.+. +|++||..||+.    .|
T Consensus        17 ~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~   95 (131)
T 2m2b_A           17 PSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTI   95 (131)
T ss_dssp             CCCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCG
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccC
Confidence            344567889999999999999999999999999976  99999999999999999999999 999999999999    99


Q ss_pred             CCeEEEEEeccCCCCC
Q 029810           87 EGRYITVERSRRKRPR  102 (187)
Q Consensus        87 ~g~~l~v~~a~~~~~~  102 (187)
                      +|+.|.|+++++....
T Consensus        96 ~gr~l~V~~a~~~~~~  111 (131)
T 2m2b_A           96 DGKTINVEFAKGSKRD  111 (131)
T ss_dssp             GGCCCCCEECCCSCCC
T ss_pred             CCEEEEEEECCCCCCC
Confidence            9999999999876443

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

Probab=99.86  E-value=3.9e-21  Score=128.51  Aligned_cols=81  Identities=19%  Similarity=0.281  Sum_probs=73.0

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCc--cCCeEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSV--LEGRYI   91 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~--i~g~~l   91 (187)
                      ...+++.+|||+|||..+++++|.++|++||.|..|.|+..      +|||||+|++.++|++||+.|++..  |.|++|
T Consensus        16 ~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i   89 (100)
T 3r27_A           16 HKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPA   89 (100)
T ss_dssp             -CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEE
T ss_pred             ccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEE
Confidence            45568899999999999999999999999999999998743      6899999999999999999999875  789999


Q ss_pred             EEEeccCCC
Q 029810           92 TVERSRRKR  100 (187)
Q Consensus        92 ~v~~a~~~~  100 (187)
                      .|++++.+.
T Consensus        90 ~V~~S~~k~   98 (100)
T 3r27_A           90 FVNYSTSQK   98 (100)
T ss_dssp             EEEECSCSC
T ss_pred             EEEeccccc
Confidence            999998764

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

Probab=99.86  E-value=2.6e-21  Score=132.01  Aligned_cols=88  Identities=26%  Similarity=0.506  Sum_probs=76.6

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .++..+.++|||+|||.++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+.+ +..|+|+.|.
T Consensus        19 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~   97 (109)
T 2rs2_A           19 SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTID   97 (109)
T ss_dssp             -------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEE
Confidence            345667899999999999999999999999999999999999989999999999999999999999966 5899999999


Q ss_pred             EEeccCCCC
Q 029810           93 VERSRRKRP  101 (187)
Q Consensus        93 v~~a~~~~~  101 (187)
                      |+++.++..
T Consensus        98 V~~a~~~~~  106 (109)
T 2rs2_A           98 PKVAFPRRA  106 (109)
T ss_dssp             EEECCCCCC
T ss_pred             EEEccCCCC
Confidence            999987654

>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=99.85  E-value=4.6e-21  Score=138.76  Aligned_cols=89  Identities=31%  Similarity=0.488  Sum_probs=82.6

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      ......++|||+|||+++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+.||+..|.|+.|.|
T Consensus        65 ~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  144 (158)
T 2kn4_A           65 MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV  144 (158)
T ss_dssp             CCCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34456799999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EeccCCCCC
Q 029810           94 ERSRRKRPR  102 (187)
Q Consensus        94 ~~a~~~~~~  102 (187)
                      .+++++...
T Consensus       145 ~~a~~~~~~  153 (158)
T 2kn4_A          145 QMARYGRPP  153 (158)
T ss_dssp             EEECCSSCC
T ss_pred             EECCCCCCC
Confidence            999876543

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

Probab=99.85  E-value=5.1e-22  Score=129.32  Aligned_cols=82  Identities=23%  Similarity=0.398  Sum_probs=76.6

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+.||+..|.|+.|+|.+
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A            2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            45779999999999999999999999999999999999988999999999999999999999999999999999888776


Q ss_pred             cc
Q 029810           96 SR   97 (187)
Q Consensus        96 a~   97 (187)
                      +.
T Consensus        82 ~~   83 (85)
T 1x4e_A           82 PS   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.85  E-value=6.1e-21  Score=129.06  Aligned_cols=84  Identities=20%  Similarity=0.334  Sum_probs=74.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC--ccCCeE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS--VLEGRY   90 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~--~i~g~~   90 (187)
                      .....+.++|||+|||+.+++++|+++|++||.|..|.|+.+      ++||||+|++.++|++||+.|++.  .|.|+.
T Consensus         9 ~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~   82 (104)
T 1wex_A            9 HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQ   82 (104)
T ss_dssp             CCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSB
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEE
Confidence            345567899999999999999999999999999999988753      689999999999999999988754  599999


Q ss_pred             EEEEeccCCCCC
Q 029810           91 ITVERSRRKRPR  102 (187)
Q Consensus        91 l~v~~a~~~~~~  102 (187)
                      |.|++++.+...
T Consensus        83 l~V~~a~~~~~~   94 (104)
T 1wex_A           83 AFFNYSTSKRIT   94 (104)
T ss_dssp             CEEEECSSSSCC
T ss_pred             EEEEEccCcccc
Confidence            999999876554

>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=99.85  E-value=9.6e-22  Score=150.80  Aligned_cols=82  Identities=20%  Similarity=0.302  Sum_probs=77.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCC--ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEG--KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G--~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ..++|||+||++++++++|+++|++||  .|+.|.|+.+..+++++|||||+|.+.++|++||+.||+..|.|+.|.|++
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            567899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 029810           96 SRRK   99 (187)
Q Consensus        96 a~~~   99 (187)
                      ++++
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8753

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

Probab=99.85  E-value=9.4e-22  Score=139.18  Aligned_cols=90  Identities=31%  Similarity=0.488  Sum_probs=82.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      ..+..+.++|||+|||+++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+.|++..|.|+.|.
T Consensus        41 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~  120 (135)
T 2lea_A           41 PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELR  120 (135)
T ss_dssp             CSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34456678999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EEeccCCCCC
Q 029810           93 VERSRRKRPR  102 (187)
Q Consensus        93 v~~a~~~~~~  102 (187)
                      |++++++...
T Consensus       121 V~~a~~~~~~  130 (135)
T 2lea_A          121 VQMARYGRPP  130 (135)
T ss_dssp             EEECCCCCCC
T ss_pred             EEECCCCCCC
Confidence            9999876543

>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=99.85  E-value=5.4e-21  Score=128.94  Aligned_cols=84  Identities=21%  Similarity=0.294  Sum_probs=76.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .......++|||+|||+++++++|+++|++||.| .|.|+.+. +++++|||||+|++.++|++||+ +|+..|.++.|.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (102)
T 1wez_A            9 SFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVE   85 (102)
T ss_dssp             SCCCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEE
Confidence            3455677899999999999999999999999954 99999987 89999999999999999999996 899999999999


Q ss_pred             EEeccCC
Q 029810           93 VERSRRK   99 (187)
Q Consensus        93 v~~a~~~   99 (187)
                      |.++...
T Consensus        86 V~~~~~~   92 (102)
T 1wez_A           86 LFLNSTA   92 (102)
T ss_dssp             EEEECCC
T ss_pred             EEECCCC
Confidence            9998754

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

Probab=99.85  E-value=7.8e-21  Score=125.07  Aligned_cols=80  Identities=29%  Similarity=0.495  Sum_probs=73.6

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      ....+.++|||+|||+++++++|+++|++||.|..|.|+        ++||||+|.+.++|++||+.||+..|+|+.|.|
T Consensus         4 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   75 (90)
T 2dnp_A            4 GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINV   75 (90)
T ss_dssp             CSSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            455678999999999999999999999999999999987        349999999999999999999999999999999


Q ss_pred             EeccCCCC
Q 029810           94 ERSRRKRP  101 (187)
Q Consensus        94 ~~a~~~~~  101 (187)
                      ++++++..
T Consensus        76 ~~a~~~~~   83 (90)
T 2dnp_A           76 ELSTKGQK   83 (90)
T ss_dssp             EESCCCCC
T ss_pred             EECCCCCC
Confidence            99987644

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

Probab=99.85  E-value=2.2e-21  Score=131.10  Aligned_cols=82  Identities=16%  Similarity=0.289  Sum_probs=76.4

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ...+..+|||+|||+++|+++|+++|++||+|..|.|+.+.. +.++|||||+|.+.++|++||. +++..|+|+.|.|.
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~   84 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLIL   84 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            345668999999999999999999999999999999999887 8999999999999999999999 99999999999999


Q ss_pred             eccC
Q 029810           95 RSRR   98 (187)
Q Consensus        95 ~a~~   98 (187)
                      ++..
T Consensus        85 ~~~~   88 (103)
T 1s79_A           85 FKDD   88 (103)
T ss_dssp             EHHH
T ss_pred             EchH
Confidence            8764

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

Probab=99.85  E-value=8.4e-21  Score=134.50  Aligned_cols=85  Identities=32%  Similarity=0.457  Sum_probs=79.1

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ......+.++|||+|||..+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+.||+..|.|+.|
T Consensus        56 ~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  135 (140)
T 2ku7_A           56 SGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI  135 (140)
T ss_dssp             SCSSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEE
T ss_pred             CCCCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            34456678999999999999999999999999999999999998899999999999999999999999999999999999


Q ss_pred             EEEec
Q 029810           92 TVERS   96 (187)
Q Consensus        92 ~v~~a   96 (187)
                      .|++|
T Consensus       136 ~v~~A  140 (140)
T 2ku7_A          136 RVNLA  140 (140)
T ss_dssp             EEEC-
T ss_pred             EEEeC
Confidence            99985

>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=4e-21  Score=130.76  Aligned_cols=86  Identities=19%  Similarity=0.261  Sum_probs=79.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCc-eeEEEEe-ecCCCCCcceEEEEEecCHHHHHHHHHHhC--CCccCCeEEE
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGK-VASCFLV-VEPRTRISRGFAFVTMDGVEDAERCIKYLN--QSVLEGRYIT   92 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~-i~~~~i~-~~~~~~~~~g~afV~f~~~~~a~~ai~~l~--g~~i~g~~l~   92 (187)
                      .+.++|||+|||+++++++|+++|.+||. |..|.|+ .+..++.++|||||+|.+.++|++||+.|+  +..|.|+.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            45789999999999999999999999998 9999998 788888999999999999999999999996  5899999999


Q ss_pred             EEeccCCCCC
Q 029810           93 VERSRRKRPR  102 (187)
Q Consensus        93 v~~a~~~~~~  102 (187)
                      |++++++...
T Consensus        86 V~~a~~~~~~   95 (109)
T 2dis_A           86 VDWAEPEIDV   95 (109)
T ss_dssp             EEESCSSCST
T ss_pred             EEEcCCCCCc
Confidence            9999877553

>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=99.85  E-value=1.8e-20  Score=128.55  Aligned_cols=85  Identities=22%  Similarity=0.350  Sum_probs=78.3

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc-------
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVL-------   86 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i-------   86 (187)
                      ....+.++|||+|||.++++++|+++|.+||.|..|.|+.+. ++.+++||||+|.+.++|++||+.||+..|       
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~   98 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVS   98 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCcccc
Confidence            445677999999999999999999999999999999999988 899999999999999999999999999999       


Q ss_pred             -CCeEEEEEeccCC
Q 029810           87 -EGRYITVERSRRK   99 (187)
Q Consensus        87 -~g~~l~v~~a~~~   99 (187)
                       .++.|.|.++.+.
T Consensus        99 ~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           99 APTEPLLCKFSGPS  112 (114)
T ss_dssp             CCSSCBEEEECCCS
T ss_pred             CCCCceeEEccCCC
Confidence             5788999998753

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

Probab=99.85  E-value=7.6e-21  Score=132.31  Aligned_cols=82  Identities=22%  Similarity=0.434  Sum_probs=77.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      +.++|||+|||.++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++|| .|++..|.|+.|.|++++
T Consensus        35 ~~~~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           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            3589999999999999999999999999999999999889999999999999999999999 699999999999999998


Q ss_pred             CCC
Q 029810           98 RKR  100 (187)
Q Consensus        98 ~~~  100 (187)
                      +..
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.85  E-value=9.7e-21  Score=130.70  Aligned_cols=84  Identities=26%  Similarity=0.375  Sum_probs=75.2

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC--CccCCeEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQ--SVLEGRYI   91 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g--~~i~g~~l   91 (187)
                      ....++++|||+|||+++++++|+++|++||.|..|.|+.+      +|||||+|++.++|++||+.|++  ..|.|+.|
T Consensus        26 ~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l   99 (119)
T 2ad9_A           26 SAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPI   99 (119)
T ss_dssp             SCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEE
Confidence            34567899999999999999999999999999999999865      68999999999999999998874  68999999


Q ss_pred             EEEeccCCCCCC
Q 029810           92 TVERSRRKRPRT  103 (187)
Q Consensus        92 ~v~~a~~~~~~~  103 (187)
                      .|++++.+....
T Consensus       100 ~V~~a~~k~~~~  111 (119)
T 2ad9_A          100 YIQFSNHKELKT  111 (119)
T ss_dssp             EEEECSSSSCCC
T ss_pred             EEEEccCCCCCc
Confidence            999998776543

>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=99.85  E-value=1.6e-21  Score=135.92  Aligned_cols=85  Identities=18%  Similarity=0.290  Sum_probs=77.8

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      .+..+.++|||+|||+++++++|+++|..||.|..+.++.+..++.++|||||+|.+.++|++||+ ||+..|+|+.|.|
T Consensus        20 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   98 (124)
T 1wel_A           20 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQV   98 (124)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEE
Confidence            345667999999999999999999999999999987777777789999999999999999999999 9999999999999


Q ss_pred             EeccCC
Q 029810           94 ERSRRK   99 (187)
Q Consensus        94 ~~a~~~   99 (187)
                      .++..+
T Consensus        99 ~~a~~~  104 (124)
T 1wel_A           99 HPITKK  104 (124)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            998754

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

Probab=99.84  E-value=6.5e-21  Score=129.98  Aligned_cols=86  Identities=31%  Similarity=0.511  Sum_probs=78.6

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ......+.++|||+|||.++++++|+++|++||.|..|.|+.+.  +.++|||||+|.+.++|++|++.|++..|+|+.|
T Consensus        22 ~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   99 (109)
T 2err_A           22 NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKI   99 (109)
T ss_dssp             CCSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEEC
T ss_pred             CccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34556678999999999999999999999999999999998875  3478999999999999999999999999999999


Q ss_pred             EEEeccCC
Q 029810           92 TVERSRRK   99 (187)
Q Consensus        92 ~v~~a~~~   99 (187)
                      .|++++++
T Consensus       100 ~V~~a~~~  107 (109)
T 2err_A          100 EVNNATAR  107 (109)
T ss_dssp             EEEECCCS
T ss_pred             EEEECCCC
Confidence            99999865

>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=2.4e-21  Score=123.22  Aligned_cols=75  Identities=25%  Similarity=0.500  Sum_probs=72.1

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        21 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      +|||+|||+++++++|+++|++||+|..|.|+.+..++.++|||||+|.+.++|++|++ |++..|+|+.|.|++|
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-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            58999999999999999999999999999999998889999999999999999999998 9999999999999875

>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=99.84  E-value=1.7e-20  Score=125.51  Aligned_cols=84  Identities=25%  Similarity=0.391  Sum_probs=75.8

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ......+.++|||+|||+++++++|+++|++||.|..|.|+.+      ++||||+|.+.++|++||+.|++..|.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l   81 (99)
T 2cpj_A            8 GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQL   81 (99)
T ss_dssp             CSCCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCC
T ss_pred             CCCcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceE
Confidence            3345567789999999999999999999999999999998744      6799999999999999999999999999999


Q ss_pred             EEEeccCCCC
Q 029810           92 TVERSRRKRP  101 (187)
Q Consensus        92 ~v~~a~~~~~  101 (187)
                      .|++++++..
T Consensus        82 ~v~~a~~~~~   91 (99)
T 2cpj_A           82 RVRFACHSAS   91 (99)
T ss_dssp             EEEESSCCSC
T ss_pred             EEEEcCCCCC
Confidence            9999987644

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

Probab=99.84  E-value=3.4e-20  Score=124.07  Aligned_cols=81  Identities=32%  Similarity=0.427  Sum_probs=73.4

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcC--CceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKE--GKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY   90 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~--G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~   90 (187)
                      .....+.++|||+|||+++++++|+++|++|  |.|..|.+.        ++||||+|.+.++|++||+.||+..|.|+.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (99)
T 2cpd_A            9 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSP   80 (99)
T ss_dssp             CSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEE
T ss_pred             ccccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            3445677999999999999999999999999  899998875        569999999999999999999999999999


Q ss_pred             EEEEeccCCCC
Q 029810           91 ITVERSRRKRP  101 (187)
Q Consensus        91 l~v~~a~~~~~  101 (187)
                      |.|++++++..
T Consensus        81 l~v~~a~~~~~   91 (99)
T 2cpd_A           81 IEVTLAKPVDK   91 (99)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCCC
Confidence            99999987643

>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=99.84  E-value=3e-21  Score=132.63  Aligned_cols=87  Identities=15%  Similarity=0.183  Sum_probs=79.5

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCce-eEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKV-ASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY   90 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i-~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~   90 (187)
                      ......+.++|||+|||+++++++|+++|+.||.| ..|.|+.+. ++.++|||||+|.+.++|++||+. |+..|.|+.
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~   85 (114)
T 2cpy_A            8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGRE   85 (114)
T ss_dssp             CCSCCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEE
T ss_pred             CCCCCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeE
Confidence            34456678999999999999999999999999999 889999888 899999999999999999999996 999999999


Q ss_pred             EEEEeccCCC
Q 029810           91 ITVERSRRKR  100 (187)
Q Consensus        91 l~v~~a~~~~  100 (187)
                      |.|.++.++.
T Consensus        86 i~v~~a~~~~   95 (114)
T 2cpy_A           86 AFVHVVTLED   95 (114)
T ss_dssp             EEEEEECHHH
T ss_pred             EEEEECCHHH
Confidence            9999998654

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

Probab=99.84  E-value=1.6e-20  Score=125.28  Aligned_cols=83  Identities=22%  Similarity=0.261  Sum_probs=73.7

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      ..+....++|||+|||+++++++|+++|++||.|. +.++.+    .+++||||+|.+.++|++||+.||+..|.|+.|.
T Consensus        13 ~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   87 (97)
T 2e5j_A           13 GEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLR   87 (97)
T ss_dssp             CSSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            34456689999999999999999999999999997 666644    4578999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 029810           93 VERSRRKR  100 (187)
Q Consensus        93 v~~a~~~~  100 (187)
                      |++++++.
T Consensus        88 V~~a~~~~   95 (97)
T 2e5j_A           88 VALARQQR   95 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEEcCCCC
Confidence            99998764

>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=99.84  E-value=2.1e-21  Score=130.36  Aligned_cols=84  Identities=21%  Similarity=0.372  Sum_probs=74.7

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEP-RTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~-~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      ......++|||+|||.++++++|+++|++|| |..|.|+.+. .++.++|||||+|.+.++|++|| .|++..|+|+.|.
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~   91 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIR   91 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEE
Confidence            4456789999999999999999999999999 9999999888 68999999999999999999999 7999999999999


Q ss_pred             EEeccCC
Q 029810           93 VERSRRK   99 (187)
Q Consensus        93 v~~a~~~   99 (187)
                      |++++++
T Consensus        92 V~~a~~~   98 (100)
T 2j76_E           92 VDVADQA   98 (100)
T ss_dssp             CEECCCS
T ss_pred             EEeccCC
Confidence            9999865

>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=99.84  E-value=1.9e-20  Score=127.54  Aligned_cols=82  Identities=21%  Similarity=0.388  Sum_probs=75.3

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      .....++|||+|||..+++++|+++|++||.|..|.|+.+      ++||||+|.+.++|++||+.|++..|.|+.|.|.
T Consensus        21 ~~~~~~~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           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY   94 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            3456789999999999999999999999999999999865      6799999999999999999999999999999999


Q ss_pred             eccCCCCC
Q 029810           95 RSRRKRPR  102 (187)
Q Consensus        95 ~a~~~~~~  102 (187)
                      +++++...
T Consensus        95 ~a~~~~~~  102 (109)
T 1x4g_A           95 WGKESPDM  102 (109)
T ss_dssp             CCCCCCSS
T ss_pred             ecCCCCCC
Confidence            99876544

>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=99.84  E-value=2e-20  Score=127.56  Aligned_cols=81  Identities=27%  Similarity=0.498  Sum_probs=73.2

Q ss_pred             CCCCCCCCeEEEcCCCCC-CcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           13 TETGNPGNTLYVTGLSTR-VTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~-~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      .++....++|||+|||++ +++++|+++|++||.|..|.|        +++||||+|++.++|++||+.|++..|+|+.|
T Consensus        21 ~~~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   92 (110)
T 1wf1_A           21 NDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTL   92 (110)
T ss_dssp             CCCTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            445556789999999999 999999999999999999988        36899999999999999999999999999999


Q ss_pred             EEEeccCCCC
Q 029810           92 TVERSRRKRP  101 (187)
Q Consensus        92 ~v~~a~~~~~  101 (187)
                      .|++++....
T Consensus        93 ~V~~a~~~~~  102 (110)
T 1wf1_A           93 DINMAGEPKP  102 (110)
T ss_dssp             CEEESCCCCS
T ss_pred             EEEECCCCCC
Confidence            9999985433

>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=99.84  E-value=1.8e-21  Score=133.99  Aligned_cols=77  Identities=21%  Similarity=0.296  Sum_probs=65.6

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE----
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY----   90 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~----   90 (187)
                      +....++|||+|||+++++++|+++|++||+|..|.|+.+       +||||+|++.++|++||+.||+..|+|+.    
T Consensus        12 ~~r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~   84 (115)
T 3beg_B           12 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA   84 (115)
T ss_dssp             -----CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeE
Confidence            3456799999999999999999999999999999999754       79999999999999999999999999988    


Q ss_pred             -EEEEeccC
Q 029810           91 -ITVERSRR   98 (187)
Q Consensus        91 -l~v~~a~~   98 (187)
                       |.|+.+.+
T Consensus        85 ~i~v~~~~~   93 (115)
T 3beg_B           85 YIRVKVDGP   93 (115)
T ss_dssp             BCEEEECC-
T ss_pred             EEEeccCCC
Confidence             66666543

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

Probab=99.84  E-value=1.1e-20  Score=130.61  Aligned_cols=85  Identities=24%  Similarity=0.359  Sum_probs=78.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCc---eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGK---VASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGR   89 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~---i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~   89 (187)
                      .++....++|||+|||+++++++|+++|+.||.   |..|.|+.+.. ++++|||||+|.+.++|++||+ ||+..|+|+
T Consensus        11 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr   88 (118)
T 2db1_A           11 GPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHR   88 (118)
T ss_dssp             SSCBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCe
Confidence            345567899999999999999999999999998   89999999876 8999999999999999999999 999999999


Q ss_pred             EEEEEeccCC
Q 029810           90 YITVERSRRK   99 (187)
Q Consensus        90 ~l~v~~a~~~   99 (187)
                      .|.|.++..+
T Consensus        89 ~i~V~~a~~~   98 (118)
T 2db1_A           89 YIEVFKSHRT   98 (118)
T ss_dssp             EEEEEEECHH
T ss_pred             EEEEEECCHH
Confidence            9999998754

>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=99.84  E-value=1.8e-20  Score=121.90  Aligned_cols=80  Identities=29%  Similarity=0.449  Sum_probs=73.0

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh-CCCccCCeE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL-NQSVLEGRY   90 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l-~g~~i~g~~   90 (187)
                      ..++..+.++|||+|||.++++++|+++|++||.|..|.|+.+      ++||||+|.+.++|++|++.| ++..|.|+.
T Consensus         5 ~~~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~   78 (85)
T 2ytc_A            5 SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRR   78 (85)
T ss_dssp             CCCSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEE
T ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCE
Confidence            3445567899999999999999999999999999999999864      689999999999999999998 999999999


Q ss_pred             EEEEecc
Q 029810           91 ITVERSR   97 (187)
Q Consensus        91 l~v~~a~   97 (187)
                      |.|++++
T Consensus        79 l~v~~ak   85 (85)
T 2ytc_A           79 LNVKWGR   85 (85)
T ss_dssp             CCEEECC
T ss_pred             EEEEecC
Confidence            9999975

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

Probab=99.74  E-value=1.5e-22  Score=139.45  Aligned_cols=87  Identities=24%  Similarity=0.357  Sum_probs=81.0

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeE--------EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVAS--------CFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVL   86 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~--------~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i   86 (187)
                      +..+.++|||+|||.++++++|+++|++||.|..        |.|+.+..++.++|||||+|.+.++|++||+.||+..|
T Consensus         3 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   82 (116)
T 2lcw_A            3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   82 (116)
Confidence            4567799999999999999999999999999998        88998888899999999999999999999999999999


Q ss_pred             CCeEEEEEeccCCCC
Q 029810           87 EGRYITVERSRRKRP  101 (187)
Q Consensus        87 ~g~~l~v~~a~~~~~  101 (187)
                      .|+.|.|++++++..
T Consensus        83 ~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           83 SGNPIKVSFATRRAD   97 (116)
Confidence            999999999987643

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

Probab=99.84  E-value=1.2e-20  Score=127.79  Aligned_cols=83  Identities=17%  Similarity=0.206  Sum_probs=75.8

Q ss_pred             CCCCCCeEEEcCCCCCC------cHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 029810           15 TGNPGNTLYVTGLSTRV------TERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG   88 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~------t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g   88 (187)
                      +....++|||+|||+.+      ++++|+++|++||.|..|.|+  ..++.++|||||+|.+.++|++||..|||..|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g   88 (105)
T 2nlw_A           11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK   88 (105)
T ss_dssp             CCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECST
T ss_pred             CCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCC
Confidence            34457899999999999      889999999999999999887  4678899999999999999999999999999999


Q ss_pred             e-EEEEEeccCC
Q 029810           89 R-YITVERSRRK   99 (187)
Q Consensus        89 ~-~l~v~~a~~~   99 (187)
                      + .|.|+++...
T Consensus        89 ~~~l~V~~a~~~  100 (105)
T 2nlw_A           89 QHTFRVNLFTDF  100 (105)
T ss_dssp             TCEEEEECSCCC
T ss_pred             CceEEEEEcchH
Confidence            8 9999998754

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

Probab=99.83  E-value=3.8e-21  Score=122.77  Aligned_cols=76  Identities=26%  Similarity=0.496  Sum_probs=73.0

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ++|||+|||.++++++|+++|++||+|..+.|+.+..++.++|||||+|.+.++|++|++.++ ..|+|+.|.|++|
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-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            579999999999999999999999999999999998889999999999999999999999999 9999999999986

>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=99.83  E-value=1.4e-21  Score=128.61  Aligned_cols=82  Identities=28%  Similarity=0.440  Sum_probs=73.9

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccCC
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK   99 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   99 (187)
                      ++|||+|||.++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.+ |++|+..||+..|.|+.|.|++|.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            58999999999999999999999999999999999989999999999999999 99999999999999999999999876


Q ss_pred             CCC
Q 029810          100 RPR  102 (187)
Q Consensus       100 ~~~  102 (187)
                      ...
T Consensus        81 ~~~   83 (90)
T 2ki2_A           81 KSL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            543

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

Probab=99.83  E-value=1.2e-20  Score=125.65  Aligned_cols=79  Identities=22%  Similarity=0.348  Sum_probs=71.5

Q ss_pred             CCCCCCeEEEcCCCC-CCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           15 TGNPGNTLYVTGLST-RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~-~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      ...+.++|||+|||+ ++++++|+++|++||.|..|.|.        ++||||+|.+.++|++||+.|++..|.|+.|.|
T Consensus         6 ~~~~~~~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            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLIL   77 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCE
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            456789999999998 99999999999999999999985        679999999999999999999999999999999


Q ss_pred             EeccCCCC
Q 029810           94 ERSRRKRP  101 (187)
Q Consensus        94 ~~a~~~~~  101 (187)
                      ++++++..
T Consensus        78 ~~a~~~~~   85 (96)
T 2kvi_A           78 EVSSSNAR   85 (96)
T ss_dssp             EEEECCCC
T ss_pred             EEcCcCCC
Confidence            99987644

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

Probab=99.83  E-value=1.9e-21  Score=130.66  Aligned_cols=85  Identities=21%  Similarity=0.334  Sum_probs=76.2

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ...+.++|||+|||.++++++|+++|.+||.|.. .++.+..++.++|||||+|.+.++|++||+ |++..|.|+.|.|+
T Consensus        13 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~   90 (101)
T 1fj7_A           13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   90 (101)
T ss_dssp             TCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEE
Confidence            3456789999999999999999999999999887 566666678889999999999999999999 99999999999999


Q ss_pred             eccCCCC
Q 029810           95 RSRRKRP  101 (187)
Q Consensus        95 ~a~~~~~  101 (187)
                      +++++..
T Consensus        91 ~a~~~~~   97 (101)
T 1fj7_A           91 KPKGRDG   97 (101)
T ss_dssp             CCSCCCC
T ss_pred             EcCCCCC
Confidence            9987643

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

Probab=99.83  E-value=9.7e-21  Score=129.44  Aligned_cols=81  Identities=16%  Similarity=0.128  Sum_probs=72.2

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCC-ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEG-KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G-~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      .....++|||+|||+++++++|+++|++|| +|..+.|+..    .++|||||+|++.++|++||+.||+..|+|+.|.|
T Consensus        24 ~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V   99 (111)
T 2jvr_A           24 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITV   99 (111)
T ss_dssp             -CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            345678999999999999999999999999 8999988532    35899999999999999999999999999999999


Q ss_pred             EeccCC
Q 029810           94 ERSRRK   99 (187)
Q Consensus        94 ~~a~~~   99 (187)
                      ++++..
T Consensus       100 ~~a~~~  105 (111)
T 2jvr_A          100 ERDDNP  105 (111)
T ss_dssp             EESCC-
T ss_pred             EECCCC
Confidence            998754

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

Probab=99.83  E-value=2.7e-20  Score=130.20  Aligned_cols=84  Identities=14%  Similarity=0.282  Sum_probs=74.9

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHH----HHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLE----KHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGR   89 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~----~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~   89 (187)
                      .+..++++|||+|||+.+++++|+    ++|++||.|..|.+..   ++.++|||||+|.+.++|++||..|||..|.|+
T Consensus        24 ~~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr  100 (127)
T 2a3j_A           24 PHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGN  100 (127)
T ss_dssp             CCCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCC
Confidence            445678999999999999999876    6999999999987753   567899999999999999999999999999999


Q ss_pred             EEEEEeccCCC
Q 029810           90 YITVERSRRKR  100 (187)
Q Consensus        90 ~l~v~~a~~~~  100 (187)
                      .|.|++++.+.
T Consensus       101 ~l~V~~a~~~~  111 (127)
T 2a3j_A          101 PLVITFSETPQ  111 (127)
T ss_dssp             CCEEEECCCCC
T ss_pred             EEEEEEccCcc
Confidence            99999998654

>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=99.83  E-value=1.3e-20  Score=133.32  Aligned_cols=84  Identities=23%  Similarity=0.343  Sum_probs=78.0

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCc---eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGK---VASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY   90 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~---i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~   90 (187)
                      ++....++|||+|||+++|+++|+++|++||.   |..|.|+.+.. ++++|||||+|++.++|++||+ ||+..|+|+.
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~  116 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRY  116 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEE
Confidence            45567899999999999999999999999999   88999999887 9999999999999999999999 9999999999


Q ss_pred             EEEEeccCC
Q 029810           91 ITVERSRRK   99 (187)
Q Consensus        91 l~v~~a~~~   99 (187)
                      |.|.++.++
T Consensus       117 i~V~~a~~~  125 (136)
T 2hgl_A          117 IEVFKSHRT  125 (136)
T ss_dssp             EEEEECCHH
T ss_pred             EEEEECChH
Confidence            999998654

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

Probab=99.83  E-value=1.4e-19  Score=120.67  Aligned_cols=84  Identities=29%  Similarity=0.363  Sum_probs=74.4

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           12 RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        12 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ......+.++|||+||  ++++++|+++|.+||+|..|.|.      .+++||||+|.+.++|++||+.|++..|.|+.|
T Consensus         8 ~~~~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   79 (97)
T 1x5p_A            8 ERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQL   79 (97)
T ss_dssp             CCCCCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEE
T ss_pred             ccCCCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            3445667899999996  89999999999999999999884      347899999999999999999999999999999


Q ss_pred             EEEeccCCCCCC
Q 029810           92 TVERSRRKRPRT  103 (187)
Q Consensus        92 ~v~~a~~~~~~~  103 (187)
                      .|++++++....
T Consensus        80 ~v~~a~~~~~~~   91 (97)
T 1x5p_A           80 KVNIARKQPMLD   91 (97)
T ss_dssp             EEECCSSCCCCC
T ss_pred             EEEECCCCCCCC
Confidence            999998775543

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

Probab=99.83  E-value=2.7e-20  Score=126.70  Aligned_cols=81  Identities=22%  Similarity=0.347  Sum_probs=72.8

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .....+.++|||+|||.++++++|+++|++||.|..|.|+        +|||||+|.+.++|++|++.|++..|+|+.|.
T Consensus        25 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   96 (108)
T 2jvo_A           25 QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLE   96 (108)
T ss_dssp             ---CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             cCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            4556778999999999999999999999999999999987        57999999999999999999999999999999


Q ss_pred             EEeccCCCC
Q 029810           93 VERSRRKRP  101 (187)
Q Consensus        93 v~~a~~~~~  101 (187)
                      |++++++..
T Consensus        97 V~~a~~~~~  105 (108)
T 2jvo_A           97 VVYSKLPAK  105 (108)
T ss_dssp             EESCSCCC-
T ss_pred             EEEecCCCC
Confidence            999987643

>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=99.83  E-value=2e-20  Score=123.83  Aligned_cols=81  Identities=32%  Similarity=0.418  Sum_probs=71.3

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCc-eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC-CccCCeEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGK-VASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQ-SVLEGRYIT   92 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~-i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g-~~i~g~~l~   92 (187)
                      ...+.++|||+|||.++++++|+++|++||. |..+.+.       +++||||+|.+.++|++||+.||+ ..|+|+.|.
T Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~   76 (93)
T 2cqh_A            4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIME   76 (93)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEE
Confidence            4456789999999999999999999999999 5555553       367999999999999999999999 999999999


Q ss_pred             EEeccCCCCC
Q 029810           93 VERSRRKRPR  102 (187)
Q Consensus        93 v~~a~~~~~~  102 (187)
                      |++++++..+
T Consensus        77 v~~a~~~~~~   86 (93)
T 2cqh_A           77 VDYSVSKKLR   86 (93)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEccCcccc
Confidence            9999876543

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

Probab=99.83  E-value=2.4e-20  Score=125.21  Aligned_cols=76  Identities=30%  Similarity=0.470  Sum_probs=71.8

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccCC
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK   99 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   99 (187)
                      ++|||+|||+++++++|+++|++||+|..|.|+.+     +++||||+|.+.++|++||+.|++..|.|+.|.|++++++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            58999999999999999999999999999999876     4789999999999999999999999999999999999876


Q ss_pred             C
Q 029810          100 R  100 (187)
Q Consensus       100 ~  100 (187)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

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

Probab=99.83  E-value=2e-20  Score=138.16  Aligned_cols=85  Identities=21%  Similarity=0.280  Sum_probs=79.3

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ...++++|||+|||+.+++++|+++|++||+|..|.|+.+. ++.++|||||+|.+.++|++||+.|++..|+|+.|.|+
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~  162 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34557899999999999999999999999999999999888 88999999999999999999999999999999999999


Q ss_pred             eccCCC
Q 029810           95 RSRRKR  100 (187)
Q Consensus        95 ~a~~~~  100 (187)
                      ++....
T Consensus       163 ~a~~~~  168 (177)
T 2f3j_A          163 LVASQI  168 (177)
T ss_dssp             EESSGG
T ss_pred             EecCCC
Confidence            998654

>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=99.83  E-value=1.6e-20  Score=128.23  Aligned_cols=82  Identities=20%  Similarity=0.281  Sum_probs=72.7

Q ss_pred             CCCCCCeEEEcCCCCC-CcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC--CccCCeEE
Q 029810           15 TGNPGNTLYVTGLSTR-VTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQ--SVLEGRYI   91 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~-~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g--~~i~g~~l   91 (187)
                      ...++++|||+|||++ +++++|+++|++||.|..|.|+.      .++||||+|++.++|++||+.|++  ..|.|+.|
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   94 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            3567899999999998 99999999999999999999873      268999999999999999998864  56999999


Q ss_pred             EEEeccCCCCC
Q 029810           92 TVERSRRKRPR  102 (187)
Q Consensus        92 ~v~~a~~~~~~  102 (187)
                      .|++++.+...
T Consensus        95 ~V~~a~~~~~~  105 (112)
T 1x4f_A           95 KVDLSEKYKKL  105 (112)
T ss_dssp             EEEEECSCSSS
T ss_pred             EEEECcccccc
Confidence            99999876544

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

Probab=99.83  E-value=3.3e-20  Score=120.33  Aligned_cols=74  Identities=20%  Similarity=0.271  Sum_probs=69.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ...-|||+||++.+|+++|+++|.+||+|..+.+..      ++|||||+|.+.++|++|++.||+..|.|++|.|++|.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            467899999999999999999999999999999865      48999999999999999999999999999999999984

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

Probab=99.82  E-value=2.5e-20  Score=125.15  Aligned_cols=79  Identities=23%  Similarity=0.308  Sum_probs=72.1

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      .....++|||+|||.++++++|+++|++||.|..|.|..      +++||||+|.+.++|++||..||+..|+|+.|.|+
T Consensus        23 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   96 (101)
T 2la4_A           23 APPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTG   96 (101)
T ss_dssp             SCSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCC
T ss_pred             CCCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            344578999999999999999999999999999999872      37899999999999999999999999999999999


Q ss_pred             eccCC
Q 029810           95 RSRRK   99 (187)
Q Consensus        95 ~a~~~   99 (187)
                      +++++
T Consensus        97 ~a~~~  101 (101)
T 2la4_A           97 WGKER  101 (101)
T ss_dssp             BCCCC
T ss_pred             eccCC
Confidence            98753

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

Probab=99.82  E-value=7.9e-20  Score=121.21  Aligned_cols=81  Identities=26%  Similarity=0.376  Sum_probs=71.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ....++|||+|||+++++++|+++|.+||.|..|  +.+..++.   ||||+|.+.++|++||+ |++..|+|+.|.|++
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~   78 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRP   78 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEE
Confidence            3456899999999999999999999999999987  55655554   99999999999999999 999999999999998


Q ss_pred             ccCCCCC
Q 029810           96 SRRKRPR  102 (187)
Q Consensus        96 a~~~~~~  102 (187)
                      +..+...
T Consensus        79 a~~~~~~   85 (94)
T 2e5g_A           79 REQKEFQ   85 (94)
T ss_dssp             SCCSCCC
T ss_pred             CCcCCCC
Confidence            8765443

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

Probab=99.82  E-value=2.7e-20  Score=123.80  Aligned_cols=83  Identities=20%  Similarity=0.344  Sum_probs=74.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .....+.++|||+|||..+++++|+++|.+||.|..+     ..++.++|||||+|.+.++|++||+.|++..|.|+.|.
T Consensus        10 ~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   84 (96)
T 1fjc_A           10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVS   84 (96)
T ss_dssp             TSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            3445677999999999999999999999999988766     23577899999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 029810           93 VERSRRKR  100 (187)
Q Consensus        93 v~~a~~~~  100 (187)
                      |+++.++.
T Consensus        85 v~~a~~~~   92 (96)
T 1fjc_A           85 LYYTGEKG   92 (96)
T ss_dssp             EEECSSSC
T ss_pred             EEEcCCCC
Confidence            99998654

>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=99.82  E-value=9.5e-20  Score=121.66  Aligned_cols=79  Identities=20%  Similarity=0.339  Sum_probs=71.6

Q ss_pred             CCCCCCCCeEEEcCCCC-CCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           13 TETGNPGNTLYVTGLST-RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~-~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      .....+.++|||+|||. ++++++|+++|++||.|..|.|.        +|||||+|.+.++|++||+.|++..|.|+.|
T Consensus        16 ~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   87 (97)
T 2xnq_A           16 PRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKL   87 (97)
T ss_dssp             ---CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEEC
T ss_pred             cCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34566789999999998 99999999999999999999884        6799999999999999999999999999999


Q ss_pred             EEEeccCC
Q 029810           92 TVERSRRK   99 (187)
Q Consensus        92 ~v~~a~~~   99 (187)
                      .|++++++
T Consensus        88 ~V~~a~~~   95 (97)
T 2xnq_A           88 ILEVSSSN   95 (97)
T ss_dssp             EEEECCCC
T ss_pred             EEEecCCC
Confidence            99998764

>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=99.82  E-value=1.8e-20  Score=124.83  Aligned_cols=83  Identities=18%  Similarity=0.384  Sum_probs=74.8

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHH----HHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLE----KHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY   90 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~----~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~   90 (187)
                      +..+.++|||+|||.++++++|+    ++|++||.|..|.|+.   ++.++|||||+|.+.++|++|++.||+..|.|+.
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   80 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcE
Confidence            45678999999999999999999    9999999999998873   4567899999999999999999999999999999


Q ss_pred             EEEEeccCCC
Q 029810           91 ITVERSRRKR  100 (187)
Q Consensus        91 l~v~~a~~~~  100 (187)
                      |.|++++++.
T Consensus        81 l~v~~a~~~~   90 (97)
T 1nu4_A           81 MRIQYAKTDS   90 (97)
T ss_dssp             CEEEECSSCC
T ss_pred             EEEEEccCCC
Confidence            9999998754

>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=99.82  E-value=6.6e-20  Score=125.90  Aligned_cols=83  Identities=22%  Similarity=0.333  Sum_probs=75.8

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      +..++++|||+|||.++++++|+++|++||.|..|.|+.+   +.++|||||+|.+.++|++||+.||+..|.|+.|.|.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   80 (115)
T 3lqv_A            4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVL   80 (115)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            4567799999999999999999999999999999999865   3448999999999999999999999999999999999


Q ss_pred             eccCCC
Q 029810           95 RSRRKR  100 (187)
Q Consensus        95 ~a~~~~  100 (187)
                      ++.++.
T Consensus        81 ~a~~~~   86 (115)
T 3lqv_A           81 YYNANR   86 (115)
T ss_dssp             ECCHHH
T ss_pred             EecCCh
Confidence            998643

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

Probab=99.82  E-value=1.6e-20  Score=121.21  Aligned_cols=73  Identities=19%  Similarity=0.277  Sum_probs=67.6

Q ss_pred             CCeEEEcCCCCCC------cHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe-EE
Q 029810           19 GNTLYVTGLSTRV------TERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGR-YI   91 (187)
Q Consensus        19 ~~~l~V~~Lp~~~------t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~-~l   91 (187)
                      +++|||+|||..+      ++++|+++|++||.|..|.|+  ..++.++|||||+|.+.++|++||+.|||..|.|+ .|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            4789999999999      789999999999999999887  46788999999999999999999999999999999 88


Q ss_pred             EE
Q 029810           92 TV   93 (187)
Q Consensus        92 ~v   93 (187)
                      .|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            76

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

Probab=99.82  E-value=4e-20  Score=126.05  Aligned_cols=81  Identities=17%  Similarity=0.255  Sum_probs=73.9

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      .....+|||+|||+++++++|+++|+.| .|..|.|+.+.. ++++|||||+|.+.++|++|| .||+..|+|+.|.|..
T Consensus        13 ~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~   89 (109)
T 2dnn_A           13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSP   89 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEE
Confidence            3445799999999999999999999999 899999998875 889999999999999999999 5999999999999988


Q ss_pred             ccCC
Q 029810           96 SRRK   99 (187)
Q Consensus        96 a~~~   99 (187)
                      +..+
T Consensus        90 a~~~   93 (109)
T 2dnn_A           90 ATER   93 (109)
T ss_dssp             CCHH
T ss_pred             CCcc
Confidence            8643

>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=99.82  E-value=1.4e-20  Score=127.84  Aligned_cols=85  Identities=18%  Similarity=0.241  Sum_probs=78.4

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCc---eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGK---VASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGR   89 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~---i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~   89 (187)
                      .++....++|||+|||+++++++|+++|..||.   |..|.|+.+.. +.++|||||+|.+.++|++||+ |++..|+|+
T Consensus         5 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr   82 (107)
T 2lmi_A            5 EEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQR   82 (107)
T ss_dssp             CCCCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSS
T ss_pred             cCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCe
Confidence            345677899999999999999999999999998   89999998887 8999999999999999999999 999999999


Q ss_pred             EEEEEeccCC
Q 029810           90 YITVERSRRK   99 (187)
Q Consensus        90 ~l~v~~a~~~   99 (187)
                      .|.|.++.++
T Consensus        83 ~i~V~~a~~~   92 (107)
T 2lmi_A           83 YVEVYEINNE   92 (107)
T ss_dssp             CCCCEECCHH
T ss_pred             EEEEEECCHH
Confidence            9999998754

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

Probab=99.81  E-value=1.2e-19  Score=137.37  Aligned_cols=85  Identities=33%  Similarity=0.462  Sum_probs=78.0

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      +..+.++|||+|||+++++++|+++|++||+|..|.|+.+..++.++|||||+|.+.++|++||+.|++..+.|+.|.|.
T Consensus        11 p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~   90 (213)
T 4f02_A           11 PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIM   90 (213)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccc
Confidence            45577899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCC
Q 029810           95 RSRRK   99 (187)
Q Consensus        95 ~a~~~   99 (187)
                      ++...
T Consensus        91 ~~~~~   95 (213)
T 4f02_A           91 WSQRD   95 (213)
T ss_dssp             ECCCC
T ss_pred             ccccc
Confidence            88654

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

Probab=99.81  E-value=1.1e-19  Score=120.87  Aligned_cols=83  Identities=18%  Similarity=0.193  Sum_probs=74.4

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEE-EEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASC-FLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~-~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      .+.....++|||+|||+++++++|+++|.+||.|..| .|+.+..++    .|||+|.+.++|++||+.||+..|.|+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   84 (96)
T 2e44_A            9 VPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTL   84 (96)
T ss_dssp             CCCCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBC
T ss_pred             CCCCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            3445567999999999999999999999999999999 577776543    49999999999999999999999999999


Q ss_pred             EEEeccCC
Q 029810           92 TVERSRRK   99 (187)
Q Consensus        92 ~v~~a~~~   99 (187)
                      .|+++.++
T Consensus        85 ~V~~a~~~   92 (96)
T 2e44_A           85 KVAYIPDE   92 (96)
T ss_dssp             EEEECCCC
T ss_pred             EEEEcCcc
Confidence            99999876

>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=1.3e-20  Score=119.73  Aligned_cols=75  Identities=23%  Similarity=0.360  Sum_probs=71.5

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        21 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      +|||+|||.++++++|+++|++||+|..|.|+.+..++.++|||||+|.+.++|++||+ +++..|.|+.|.|++|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            59999999999999999999999999999999998899999999999999999999999 5889999999999875

>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=99.81  E-value=9.6e-21  Score=134.41  Aligned_cols=84  Identities=20%  Similarity=0.264  Sum_probs=74.2

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      ......++|||+|||+++|+++|+++|++|| |+.|.|+.+.. ++++|||||+|++.++|++|| .+|+..|.++.|.|
T Consensus        41 ~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V  117 (139)
T 2hgn_A           41 VQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIEL  117 (139)
T ss_dssp             ----CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEE
Confidence            3456678999999999999999999999999 67999998876 899999999999999999999 69999999999999


Q ss_pred             EeccCCC
Q 029810           94 ERSRRKR  100 (187)
Q Consensus        94 ~~a~~~~  100 (187)
                      .++.+..
T Consensus       118 ~~a~~~~  124 (139)
T 2hgn_A          118 FLNSTTG  124 (139)
T ss_dssp             EECCCSC
T ss_pred             EECCCCC
Confidence            9987653

>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=99.81  E-value=1e-19  Score=124.50  Aligned_cols=84  Identities=17%  Similarity=0.216  Sum_probs=73.2

Q ss_pred             CCCCCCCeEEE--cCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc-----
Q 029810           14 ETGNPGNTLYV--TGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVL-----   86 (187)
Q Consensus        14 ~~~~~~~~l~V--~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i-----   86 (187)
                      ....++.+|||  +||++++++++|+++|++||+|..|.|+.+      +|||||+|++.++|++|++.|||.+|     
T Consensus        20 ~~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg   93 (114)
T 2cq2_A           20 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLG   93 (114)
T ss_dssp             CCSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTS
T ss_pred             CCCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccC
Confidence            34567889999  779999999999999999999999887632      68999999999999999999999988     


Q ss_pred             CCeEEEEEeccCCCCCC
Q 029810           87 EGRYITVERSRRKRPRT  103 (187)
Q Consensus        87 ~g~~l~v~~a~~~~~~~  103 (187)
                      .+..|.|.+++..+...
T Consensus        94 ~g~~l~v~~a~~~p~~~  110 (114)
T 2cq2_A           94 QKITLYLNFVEKVQWSG  110 (114)
T ss_dssp             CEEECEEEEESCCCCSS
T ss_pred             CCcEEEEEecccCcccC
Confidence            68899999998655433

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

Probab=99.81  E-value=3.7e-19  Score=134.21  Aligned_cols=89  Identities=21%  Similarity=0.403  Sum_probs=82.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ...++|||+|||.++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++|++.||+..|.|+.|.|.++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCC
Q 029810           97 RRKRPRTPT  105 (187)
Q Consensus        97 ~~~~~~~~~  105 (187)
                      .++....+.
T Consensus       203 ~~~~~~~~~  211 (216)
T 2qfj_A          203 VTPPMPLLT  211 (216)
T ss_dssp             SSCSSTTSC
T ss_pred             cCCCCCCCC
Confidence            987554443

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

Probab=99.80  E-value=4e-20  Score=124.36  Aligned_cols=85  Identities=24%  Similarity=0.463  Sum_probs=77.5

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      ++....++|||+|||.++++++|+++|++||.|..|.|+.+. ++.++|||||+|.+.++|++||+  ++..|+|+.|.|
T Consensus         4 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v   80 (102)
T 2xs2_A            4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKL   80 (102)
T ss_dssp             CCEEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEE
Confidence            344566899999999999999999999999999999999998 89999999999999999999999  899999999999


Q ss_pred             EeccCCCC
Q 029810           94 ERSRRKRP  101 (187)
Q Consensus        94 ~~a~~~~~  101 (187)
                      .++.++..
T Consensus        81 ~~a~~~~~   88 (102)
T 2xs2_A           81 GPAIRKQN   88 (102)
T ss_dssp             EEEEECC-
T ss_pred             EECCcCcc
Confidence            99886543

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

Probab=99.80  E-value=5.5e-19  Score=127.73  Aligned_cols=84  Identities=21%  Similarity=0.371  Sum_probs=79.8

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      ....+.++|||+|||..+++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|++|+..||+..|+|+.|.|
T Consensus        82 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  161 (166)
T 3md3_A           82 SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI  161 (166)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Confidence            45567789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             Eecc
Q 029810           94 ERSR   97 (187)
Q Consensus        94 ~~a~   97 (187)
                      .+|+
T Consensus       162 ~~a~  165 (166)
T 3md3_A          162 NWAA  165 (166)
T ss_dssp             EESC
T ss_pred             EecC
Confidence            9986

>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=99.80  E-value=3.5e-20  Score=132.09  Aligned_cols=88  Identities=28%  Similarity=0.432  Sum_probs=75.1

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEE------EEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASC------FLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE   87 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~------~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~   87 (187)
                      .+..++++|||+|||+++++++|+++|.+||.|..+      .+.. ..++.++|||||+|.+.++|++||..||+..|.
T Consensus        40 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~  118 (143)
T 3egn_A           40 EPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRL-MKEGRMKGQAFIGLPNEKAAAKALKEANGYVLF  118 (143)
T ss_dssp             CCCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEE-EEETTTEEEEEEECSSHHHHHHHHHHHTTBEET
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEe-ccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeC
Confidence            446678999999999999999999999999988764      1111 135778999999999999999999999999999


Q ss_pred             CeEEEEEeccCCCCC
Q 029810           88 GRYITVERSRRKRPR  102 (187)
Q Consensus        88 g~~l~v~~a~~~~~~  102 (187)
                      |+.|.|+++++...+
T Consensus       119 g~~l~V~~a~~~~~~  133 (143)
T 3egn_A          119 GKPMVVQFARSARPK  133 (143)
T ss_dssp             TEECEEEECCCSCC-
T ss_pred             CcEEEEEECCCCCCc
Confidence            999999999876443

>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=99.80  E-value=1.8e-19  Score=123.20  Aligned_cols=77  Identities=14%  Similarity=0.141  Sum_probs=70.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ..++|||+|||..+++++|+++|++||.|..|.|+.      .++||||+|.+.++|++||+.||+..|.|+.|.|+|+.
T Consensus         9 ~~~~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            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            467999999999999999999999999999998864      36799999999999999999999999999999999997


Q ss_pred             CCC
Q 029810           98 RKR  100 (187)
Q Consensus        98 ~~~  100 (187)
                      ...
T Consensus        83 ~~~   85 (111)
T 1whx_A           83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            643

>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=99.80  E-value=2.6e-19  Score=128.59  Aligned_cols=82  Identities=26%  Similarity=0.406  Sum_probs=75.6

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .....+.++|||+|||+++++++|+++|++||.|..|.|+.+     ++|||||+|.+.++|++||..||+..|.|+.|.
T Consensus        67 ~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  141 (150)
T 2i2y_A           67 RDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVR  141 (150)
T ss_dssp             SSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            445567899999999999999999999999999999999866     478999999999999999999999999999999


Q ss_pred             EEeccCC
Q 029810           93 VERSRRK   99 (187)
Q Consensus        93 v~~a~~~   99 (187)
                      |++++++
T Consensus       142 v~~a~~~  148 (150)
T 2i2y_A          142 VELSNGE  148 (150)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCC
Confidence            9999865

>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=99.80  E-value=8.1e-20  Score=127.45  Aligned_cols=84  Identities=24%  Similarity=0.336  Sum_probs=74.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCcee--EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVA--SCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY   90 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~--~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~   90 (187)
                      ..+....++|||+|||+++++++|+++|++| .|.  .|.|+.+.. +.++|||||+|++.++|++||+ +++..|+|+.
T Consensus        36 ~~~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~  112 (126)
T 2hgm_A           36 SADSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRY  112 (126)
T ss_dssp             TTCSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEE
Confidence            3445667899999999999999999999999 666  899998877 8999999999999999999999 5779999999


Q ss_pred             EEEEeccCC
Q 029810           91 ITVERSRRK   99 (187)
Q Consensus        91 l~v~~a~~~   99 (187)
                      |.|..+..+
T Consensus       113 I~V~~a~~~  121 (126)
T 2hgm_A          113 IEVFKSSQE  121 (126)
T ss_dssp             CCCEEECHH
T ss_pred             EEEEECCHH
Confidence            999988654

>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=99.80  E-value=4.7e-19  Score=128.52  Aligned_cols=84  Identities=27%  Similarity=0.427  Sum_probs=79.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      +.++|||+|||.++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++|++.|++..|.|+.|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            57899999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 029810           98 RKRP  101 (187)
Q Consensus        98 ~~~~  101 (187)
                      +...
T Consensus        82 ~~~~   85 (168)
T 1b7f_A           82 PGGE   85 (168)
T ss_dssp             CCSS
T ss_pred             CCcc
Confidence            6543

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

Probab=99.79  E-value=7.1e-20  Score=127.36  Aligned_cols=82  Identities=21%  Similarity=0.274  Sum_probs=74.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCce----eEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKV----ASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i----~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      .....+|||+|||+++|+++|+++|++||.|    ..|.|+.+ .+++++|||||+|++.++|++||+. |+..|.++.|
T Consensus        20 ~~~~~~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           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYI   97 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEE
Confidence            3567899999999999999999999999975    68999888 4899999999999999999999995 9999999999


Q ss_pred             EEEeccCC
Q 029810           92 TVERSRRK   99 (187)
Q Consensus        92 ~v~~a~~~   99 (187)
                      .|..+.++
T Consensus        98 ~V~~a~~~  105 (123)
T 2dha_A           98 ELFRSTAA  105 (123)
T ss_dssp             CCEEECHH
T ss_pred             EEEECCHH
Confidence            99988653

>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=99.79  E-value=7.8e-19  Score=127.04  Aligned_cols=82  Identities=30%  Similarity=0.417  Sum_probs=78.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccC
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR   98 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   98 (187)
                      .++|||+|||.++++++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|++|++.|++..|.|+.|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            58999999999999999999999999999999999988999999999999999999999999999999999999999886


Q ss_pred             CC
Q 029810           99 KR  100 (187)
Q Consensus        99 ~~  100 (187)
                      ..
T Consensus        82 ~~   83 (167)
T 1fxl_A           82 SS   83 (167)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>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=99.79  E-value=4.8e-19  Score=116.01  Aligned_cols=76  Identities=17%  Similarity=0.292  Sum_probs=70.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ..++|||+|||+++++++|+++|++| .|..+.|.      .++|||||+|.+.++|++|++.||+..|.|+.|.|+++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            46899999999999999999999999 99999884      458899999999999999999999999999999999987


Q ss_pred             CCC
Q 029810           98 RKR  100 (187)
Q Consensus        98 ~~~  100 (187)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            543

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

Probab=99.79  E-value=1.1e-18  Score=129.97  Aligned_cols=85  Identities=20%  Similarity=0.372  Sum_probs=80.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      .+.++|||+|||..+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++|++.||+..|+|+.|.|.++
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            56799999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 029810           97 RRKRP  101 (187)
Q Consensus        97 ~~~~~  101 (187)
                      +++..
T Consensus       192 ~~~~~  196 (198)
T 2yh0_A          192 SVGAK  196 (198)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87644

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

Probab=99.79  E-value=1.8e-18  Score=120.14  Aligned_cols=80  Identities=20%  Similarity=0.205  Sum_probs=69.5

Q ss_pred             CCCCCCe--EEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceE-EEEEecCHHHHHHHHHHhCCCccCC--e
Q 029810           15 TGNPGNT--LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF-AFVTMDGVEDAERCIKYLNQSVLEG--R   89 (187)
Q Consensus        15 ~~~~~~~--l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~-afV~f~~~~~a~~ai~~l~g~~i~g--~   89 (187)
                      +..++++  |||+||++.+++++|.++|++||.|..|.|+..      .|| |||+|++.++|++|++.|||..|.|  .
T Consensus        19 ~~~ps~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~   92 (124)
T 2e5i_A           19 PSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCC   92 (124)
T ss_dssp             CCCCCSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBS
T ss_pred             CCCCCcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCe
Confidence            3344554  578999999999999999999999999998642      276 9999999999999999999999987  5


Q ss_pred             EEEEEeccCCC
Q 029810           90 YITVERSRRKR  100 (187)
Q Consensus        90 ~l~v~~a~~~~  100 (187)
                      .|.|++|+++.
T Consensus        93 ~l~V~~Ak~~~  103 (124)
T 2e5i_A           93 TLKIEYARPTR  103 (124)
T ss_dssp             EEEEECCSCSC
T ss_pred             EEEEEEecCCc
Confidence            89999998764

>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=99.79  E-value=7.4e-19  Score=127.23  Aligned_cols=80  Identities=19%  Similarity=0.127  Sum_probs=71.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--eEEEEE
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG--RYITVE   94 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g--~~l~v~   94 (187)
                      ....+|||+||++.+++++|+++|++||+|..|.|+...    .++||||+|++.++|++|++.|||..|.+  +.|.|+
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~  119 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            334578999999999999999999999999999987432    46899999999999999999999999965  999999


Q ss_pred             eccCCC
Q 029810           95 RSRRKR  100 (187)
Q Consensus        95 ~a~~~~  100 (187)
                      |++++.
T Consensus       120 ~Ak~~~  125 (164)
T 1sjr_A          120 FSKLTS  125 (164)
T ss_dssp             ECSSSS
T ss_pred             EecCCc
Confidence            998763

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

Probab=99.79  E-value=1.1e-18  Score=121.94  Aligned_cols=79  Identities=20%  Similarity=0.178  Sum_probs=70.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceE-EEEEecCHHHHHHHHHHhCCCccCC--eEEEE
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF-AFVTMDGVEDAERCIKYLNQSVLEG--RYITV   93 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~-afV~f~~~~~a~~ai~~l~g~~i~g--~~l~v   93 (187)
                      ..-..|||+||++.+|+++|.++|++||+|..|.|+...     ++| |||+|.+.++|++|++.|||..|.+  ..|+|
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI  100 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  100 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEE
Confidence            344577799999999999999999999999999887542     577 9999999999999999999999988  89999


Q ss_pred             EeccCCC
Q 029810           94 ERSRRKR  100 (187)
Q Consensus        94 ~~a~~~~  100 (187)
                      ++++++.
T Consensus       101 ~~ak~~~  107 (130)
T 3zzy_A          101 DFSKLTS  107 (130)
T ss_dssp             EECSCSS
T ss_pred             EecCCCc
Confidence            9998763

>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=99.78  E-value=8.1e-19  Score=130.44  Aligned_cols=86  Identities=21%  Similarity=0.370  Sum_probs=75.9

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ..+.++|||+|||.++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||.. ++..|+|+.|.|.+
T Consensus       101 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~  179 (196)
T 1l3k_A          101 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRK  179 (196)
T ss_dssp             --CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEE
T ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEe
Confidence            34568999999999999999999999999999999999988999999999999999999999985 89999999999999


Q ss_pred             ccCCCCC
Q 029810           96 SRRKRPR  102 (187)
Q Consensus        96 a~~~~~~  102 (187)
                      +.++...
T Consensus       180 a~~k~~~  186 (196)
T 1l3k_A          180 ALSKQEM  186 (196)
T ss_dssp             CC-----
T ss_pred             cCChhHh
Confidence            9887654

>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=99.78  E-value=1.1e-18  Score=129.73  Aligned_cols=87  Identities=28%  Similarity=0.553  Sum_probs=78.8

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      ..+..+.++|||+|||+++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+ +++..|.|+.|.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~l~   85 (196)
T 1l3k_A            7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVE   85 (196)
T ss_dssp             -CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHh-cCCCEECCEEee
Confidence            3455678999999999999999999999999999999999999999999999999999999999998 489999999999


Q ss_pred             EEeccCCC
Q 029810           93 VERSRRKR  100 (187)
Q Consensus        93 v~~a~~~~  100 (187)
                      |.++....
T Consensus        86 v~~~~~~~   93 (196)
T 1l3k_A           86 PKRAVSRE   93 (196)
T ss_dssp             EEECCC--
T ss_pred             eecccCcc
Confidence            99987654

>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=99.78  E-value=1.8e-18  Score=126.01  Aligned_cols=81  Identities=21%  Similarity=0.370  Sum_probs=77.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ....++|||+|||..+++++|+++|++||.|..+.|+.+..++.++|||||+|.+.++|++|++.||+..|+|+.|.|++
T Consensus        91 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  170 (172)
T 2g4b_A           91 LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  170 (172)
T ss_dssp             CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEe
Confidence            44578999999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             c
Q 029810           96 S   96 (187)
Q Consensus        96 a   96 (187)
                      |
T Consensus       171 A  171 (172)
T 2g4b_A          171 A  171 (172)
T ss_dssp             C
T ss_pred             C
Confidence            7

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=3e-18  Score=112.18  Aligned_cols=76  Identities=26%  Similarity=0.282  Sum_probs=67.0

Q ss_pred             CCCCCe-EEEcCCCCCCcHHH----HHHHhhcCC-ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe
Q 029810           16 GNPGNT-LYVTGLSTRVTERD----LEKHFSKEG-KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGR   89 (187)
Q Consensus        16 ~~~~~~-l~V~~Lp~~~t~~~----L~~~f~~~G-~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~   89 (187)
                      .++..+ |||+|||+.+++++    |.++|++|| +|..|       ++   |+|||+|.+.++|++|++.|+|..|.|+
T Consensus         5 ~~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            5 SSGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGN   74 (96)
T ss_dssp             CCCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCc
Confidence            345566 99999999999987    558999995 99988       23   8999999999999999999999999999


Q ss_pred             EEEEEeccCCCC
Q 029810           90 YITVERSRRKRP  101 (187)
Q Consensus        90 ~l~v~~a~~~~~  101 (187)
                      +|.|.+|+.+..
T Consensus        75 ~i~v~~A~~~sd   86 (96)
T 2diu_A           75 RIIVSFTPKNRE   86 (96)
T ss_dssp             CCEEESSCCSCC
T ss_pred             eEEEEecCCCcc
Confidence            999999987654

>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=99.77  E-value=1.5e-18  Score=114.00  Aligned_cols=80  Identities=23%  Similarity=0.384  Sum_probs=62.8

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCc--cCCeE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSV--LEGRY   90 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~--i~g~~   90 (187)
                      .....+.++|||+|||+++++++|+++|++||.|..|.|+.+     ++|||||+|++.++|++    |++..  +.+..
T Consensus         5 ~~~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~   75 (89)
T 3d2w_A            5 HHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGIS   75 (89)
T ss_dssp             ------CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEE
Confidence            445678899999999999999999999999999999999864     58999999999999883    45554  56999


Q ss_pred             EEEEeccCCCC
Q 029810           91 ITVERSRRKRP  101 (187)
Q Consensus        91 l~v~~a~~~~~  101 (187)
                      |.|.++.++..
T Consensus        76 v~v~~a~~k~~   86 (89)
T 3d2w_A           76 VHISNAEPKHN   86 (89)
T ss_dssp             EEEEECC----
T ss_pred             EEEEEcCCCCc
Confidence            99999987643

>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=9.6e-19  Score=120.86  Aligned_cols=78  Identities=13%  Similarity=0.209  Sum_probs=71.3

Q ss_pred             CeEEEcCC----CCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecC----HHH----HHHHHH--HhCCCc
Q 029810           20 NTLYVTGL----STRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDG----VED----AERCIK--YLNQSV   85 (187)
Q Consensus        20 ~~l~V~~L----p~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~----~~~----a~~ai~--~l~g~~   85 (187)
                      +.|||+||    |+.+++++|+++|+.||+|..|.++.|+.|+.++|||||+|.+    +++    |.+||.  .|++..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            78999999    9999999999999999999999999999999999999999996    333    788888  789999


Q ss_pred             cCCeEEEEEecc
Q 029810           86 LEGRYITVERSR   97 (187)
Q Consensus        86 i~g~~l~v~~a~   97 (187)
                      |+|..|.|++..
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999864

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

Probab=99.77  E-value=1.5e-18  Score=119.09  Aligned_cols=80  Identities=15%  Similarity=0.251  Sum_probs=68.3

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCC---CCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRT---RISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~---~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      .....++|||+|||+++++++|+++|++||+|. +.++.+..+   +.++|||||+|++.++|++||+.|+  .++|+.|
T Consensus         4 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~   80 (114)
T 2dnl_A            4 GSSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLY   80 (114)
T ss_dssp             SSSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEE
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEE
Confidence            345678999999999999999999999999999 888877766   7889999999999999999999884  3666666


Q ss_pred             EEEecc
Q 029810           92 TVERSR   97 (187)
Q Consensus        92 ~v~~a~   97 (187)
                      .+..+.
T Consensus        81 ~~~~~~   86 (114)
T 2dnl_A           81 LCVSSP   86 (114)
T ss_dssp             EEECCS
T ss_pred             EeccCC
Confidence            665543

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

Probab=99.76  E-value=2.3e-18  Score=130.34  Aligned_cols=81  Identities=27%  Similarity=0.499  Sum_probs=75.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ...+|||+|||+.+++++|+++|++||.|..|.|+.+.  +.++|||||+|.+.++|++||+.|||..|+|+.|.|++++
T Consensus       102 ~~~~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          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK  179 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45789999999999999999999999999999999885  4468999999999999999999999999999999999998


Q ss_pred             CCC
Q 029810           98 RKR  100 (187)
Q Consensus        98 ~~~  100 (187)
                      ++.
T Consensus       180 ~~~  182 (213)
T 4f02_A          180 SRK  182 (213)
T ss_dssp             CHH
T ss_pred             CCc
Confidence            654

>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=99.76  E-value=6.9e-19  Score=115.20  Aligned_cols=79  Identities=23%  Similarity=0.349  Sum_probs=66.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.+     ++|||||+|.+.++|++|+..  ...+.+..|.|.++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEec
Confidence            45799999999999999999999999999999998754     478999999999999865331  34568999999999


Q ss_pred             cCCCCC
Q 029810           97 RRKRPR  102 (187)
Q Consensus        97 ~~~~~~  102 (187)
                      +++...
T Consensus        76 ~~~~~~   81 (88)
T 1wf0_A           76 EPKHNS   81 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.76  E-value=9.9e-19  Score=126.80  Aligned_cols=81  Identities=26%  Similarity=0.486  Sum_probs=77.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      +..+|||+|||.++++++|+++|++||.|..+.|+.+..++.++|||||+|.+.++|++|++ +++..|+|+.|.|.++.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            45799999999999999999999999999999999998899999999999999999999998 89999999999999998


Q ss_pred             CC
Q 029810           98 RK   99 (187)
Q Consensus        98 ~~   99 (187)
                      ++
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.76  E-value=2.6e-18  Score=129.61  Aligned_cols=79  Identities=23%  Similarity=0.276  Sum_probs=72.8

Q ss_pred             CCCCeEEEcCCC-CCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           17 NPGNTLYVTGLS-TRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        17 ~~~~~l~V~~Lp-~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      .++++|||+||| +.+++++|+++|++||.|..|.|+.+.     +|||||+|.+.++|++||+.|||..|.|+.|.|.+
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   76 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCV   76 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            467899999999 799999999999999999999998653     68999999999999999999999999999999999


Q ss_pred             ccCCC
Q 029810           96 SRRKR  100 (187)
Q Consensus        96 a~~~~  100 (187)
                      ++.+.
T Consensus        77 s~~~~   81 (205)
T 3tyt_A           77 SKQPA   81 (205)
T ss_dssp             CSCSC
T ss_pred             ccCCc
Confidence            97543

>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=99.76  E-value=8.2e-18  Score=121.94  Aligned_cols=81  Identities=30%  Similarity=0.445  Sum_probs=76.6

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--eEEEE
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG--RYITV   93 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g--~~l~v   93 (187)
                      ..+.++|||+|||..+++++|+++|++||.|..+.|+.+..++.++|||||+|.+.++|++|++.||+..|.|  ++|.|
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V  165 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV  165 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEE
Confidence            4567899999999999999999999999999999999998889999999999999999999999999999988  99999


Q ss_pred             Eec
Q 029810           94 ERS   96 (187)
Q Consensus        94 ~~a   96 (187)
                      .+|
T Consensus       166 ~~A  168 (168)
T 1b7f_A          166 RLA  168 (168)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>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=4.6e-18  Score=128.14  Aligned_cols=83  Identities=25%  Similarity=0.348  Sum_probs=75.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      .+.++|||+|||.++++++|+++|++||.|..|.|+.+..++.+++||||+|.+.++|++||+.|++..|.|+.|.|.++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            34589999999999999999999999999999999999888999999999999999999999999999999999999887


Q ss_pred             cCC
Q 029810           97 RRK   99 (187)
Q Consensus        97 ~~~   99 (187)
                      ...
T Consensus       106 ~~~  108 (216)
T 2qfj_A          106 SNI  108 (216)
T ss_dssp             SCC
T ss_pred             CCc
Confidence            654

>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=99.74  E-value=3.2e-18  Score=111.50  Aligned_cols=73  Identities=19%  Similarity=0.456  Sum_probs=66.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcC----C-------ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKE----G-------KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS   84 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~----G-------~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~   84 (187)
                      ..+.++|||+|||+++++++|+++|++|    |       .|..+.+..+      ++||||+|.+.++|++|+ .||+.
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~   75 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGI   75 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCC
Confidence            3456899999999999999999999999    8       8999988754      689999999999999999 89999


Q ss_pred             ccCCeEEEEEe
Q 029810           85 VLEGRYITVER   95 (187)
Q Consensus        85 ~i~g~~l~v~~   95 (187)
                      .|.|+.|.|+.
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

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

Probab=99.74  E-value=1.1e-17  Score=120.89  Aligned_cols=81  Identities=22%  Similarity=0.378  Sum_probs=74.4

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccCC
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK   99 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   99 (187)
                      .+|||+|||.++++++|+++|++||.|..|.|+.+.. +.++|||||+|.+.++|++|++.|++..|.|+.|.|.++.+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC--CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC-CCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            4899999999999999999999999999999998864 668999999999999999999999999999999999998765


Q ss_pred             CC
Q 029810          100 RP  101 (187)
Q Consensus       100 ~~  101 (187)
                      ..
T Consensus        80 ~~   81 (166)
T 3md3_A           80 QQ   81 (166)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.74  E-value=1.2e-17  Score=120.82  Aligned_cols=81  Identities=35%  Similarity=0.526  Sum_probs=75.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE--EEE
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY--ITV   93 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~--l~v   93 (187)
                      .....+|||+|||..+++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|++|++.||+..|.|+.  |.|
T Consensus        85 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v  164 (167)
T 1fxl_A           85 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV  164 (167)
T ss_dssp             GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEE
Confidence            346689999999999999999999999999999999999888999999999999999999999999999999964  888


Q ss_pred             Eec
Q 029810           94 ERS   96 (187)
Q Consensus        94 ~~a   96 (187)
                      .||
T Consensus       165 ~~A  167 (167)
T 1fxl_A          165 KFA  167 (167)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            875

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

Probab=99.74  E-value=2e-17  Score=111.92  Aligned_cols=82  Identities=20%  Similarity=0.255  Sum_probs=72.8

Q ss_pred             CCCCeEEEcCCCC-----CCcHHHHHHHhhcCCceeEEEEeecCCC-CCcceEEEEEecCHHHHHHHHHHhCCCccCCeE
Q 029810           17 NPGNTLYVTGLST-----RVTERDLEKHFSKEGKVASCFLVVEPRT-RISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY   90 (187)
Q Consensus        17 ~~~~~l~V~~Lp~-----~~t~~~L~~~f~~~G~i~~~~i~~~~~~-~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~   90 (187)
                      .++.+|+|.||..     +.++++|+++|++||.|..|.|+.+..+ +.++|||||+|.+.++|++|++.|||..|.|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            5678999999963     2368999999999999999999987653 678999999999999999999999999999999


Q ss_pred             EEEEeccC
Q 029810           91 ITVERSRR   98 (187)
Q Consensus        91 l~v~~a~~   98 (187)
                      |.|.++..
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

>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=99.73  E-value=1.8e-17  Score=120.75  Aligned_cols=84  Identities=18%  Similarity=0.232  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCC--CcceEEEEEecCHHHHHHHHHHhCCCccC---CeEEE
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTR--ISRGFAFVTMDGVEDAERCIKYLNQSVLE---GRYIT   92 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~--~~~g~afV~f~~~~~a~~ai~~l~g~~i~---g~~l~   92 (187)
                      +.++|||+|||+++++++|+++|++||+|..|.|+.+..++  .++|||||+|.+.++|++|++.|++..+.   +..|.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            46799999999999999999999999999999999998876  88999999999999999999999998775   57788


Q ss_pred             EEeccCCCC
Q 029810           93 VERSRRKRP  101 (187)
Q Consensus        93 v~~a~~~~~  101 (187)
                      |.++.....
T Consensus        82 ~~~~~~~~~   90 (175)
T 3nmr_A           82 MKPADSEKN   90 (175)
T ss_dssp             EEECGGGCC
T ss_pred             Ecccccccc
Confidence            888775543

>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=99.73  E-value=2e-17  Score=120.52  Aligned_cols=82  Identities=27%  Similarity=0.406  Sum_probs=74.4

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC---CeEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE---GRYI   91 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~---g~~l   91 (187)
                      ...+..+|||+|||..+++++|+++|++||.|..+.|+.+. ++.++|||||+|.+.++|++|++.||+..|.   ++.|
T Consensus        91 ~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l  169 (175)
T 3nmr_A           91 NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPM  169 (175)
T ss_dssp             SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCC
T ss_pred             ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCe
Confidence            34467899999999999999999999999999999999886 5888999999999999999999999998776   4899


Q ss_pred             EEEecc
Q 029810           92 TVERSR   97 (187)
Q Consensus        92 ~v~~a~   97 (187)
                      .|.||.
T Consensus       170 ~V~~ad  175 (175)
T 3nmr_A          170 VVKFAD  175 (175)
T ss_dssp             EEEECC
T ss_pred             EEEecC
Confidence            999873

>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=99.72  E-value=2.9e-17  Score=128.91  Aligned_cols=84  Identities=18%  Similarity=0.373  Sum_probs=76.3

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHH----HHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLE----KHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGR   89 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~----~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~   89 (187)
                      .+..+.++|||+|||.++++++|+    ++|++||.|..|.|+.   ++.++|||||+|.+.++|++||+.||+..|.|+
T Consensus         4 ~~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   80 (282)
T 3pgw_A            4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK   80 (282)
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCc
Confidence            356778999999999999999966    8999999999998875   577899999999999999999999999999999


Q ss_pred             EEEEEeccCCC
Q 029810           90 YITVERSRRKR  100 (187)
Q Consensus        90 ~l~v~~a~~~~  100 (187)
                      .|.|++++...
T Consensus        81 ~l~v~~a~~~~   91 (282)
T 3pgw_A           81 PMRIQYAKTDS   91 (282)
T ss_pred             EEEEEEeccCc
Confidence            99999997654

>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=99.72  E-value=1.6e-17  Score=121.42  Aligned_cols=80  Identities=21%  Similarity=0.349  Sum_probs=73.0

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ...+.++|||+|||..+++++|+++|++||.|..+     ..++.++|||||+|.+.++|++|+..||+..|.|+.|.|.
T Consensus        95 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  169 (175)
T 1fje_B           95 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY  169 (175)
T ss_dssp             TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEE
T ss_pred             ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999988766     4567889999999999999999999999999999999999


Q ss_pred             eccCC
Q 029810           95 RSRRK   99 (187)
Q Consensus        95 ~a~~~   99 (187)
                      +++++
T Consensus       170 ~a~~k  174 (175)
T 1fje_B          170 YTGEK  174 (175)
T ss_dssp             ECSSC
T ss_pred             ecCCC
Confidence            99865

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

Probab=99.72  E-value=1.4e-17  Score=127.76  Aligned_cols=81  Identities=22%  Similarity=0.304  Sum_probs=71.1

Q ss_pred             CCCCCCeEEEcCCCCCC---------cHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCc
Q 029810           15 TGNPGNTLYVTGLSTRV---------TERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSV   85 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~---------t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~   85 (187)
                      .....++|||+||+..+         ++++|+++|++||+|..|.|+.+      +|||||+|.+.++|+.|+++|++..
T Consensus       130 ~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~  203 (240)
T 3u1l_A          130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQT  203 (240)
T ss_dssp             -CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             cccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCE
Confidence            35567999999999998         79999999999999999999853      7899999999999999999999999


Q ss_pred             c------------CCeEEEEEeccCCCC
Q 029810           86 L------------EGRYITVERSRRKRP  101 (187)
Q Consensus        86 i------------~g~~l~v~~a~~~~~  101 (187)
                      |            .|..|.|.||+..+.
T Consensus       204 l~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          204 LLLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             EeccccccccccCCCCEEEEEEccCCCC
Confidence            9            899999999986543

>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=99.71  E-value=4.8e-17  Score=124.38  Aligned_cols=82  Identities=26%  Similarity=0.329  Sum_probs=75.4

Q ss_pred             CCCCCCCeEEEcCCCC-CCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           14 ETGNPGNTLYVTGLST-RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~-~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .+..++++|||+|||. ++++++|+++|++||.|..|.|+.+.     ++||||+|.+.++|++||+.|++..|.|+.|.
T Consensus        29 ~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~  103 (229)
T 2adc_A           29 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIR  103 (229)
T ss_dssp             GGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            4456789999999999 99999999999999999999998764     67999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 029810           93 VERSRRKR  100 (187)
Q Consensus        93 v~~a~~~~  100 (187)
                      |.+++.+.
T Consensus       104 v~~a~~~~  111 (229)
T 2adc_A          104 ITLSKHQN  111 (229)
T ss_dssp             EECCSCCC
T ss_pred             EEEecCcc
Confidence            99998654

>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=99.71  E-value=2.5e-16  Score=107.64  Aligned_cols=84  Identities=21%  Similarity=0.301  Sum_probs=71.2

Q ss_pred             CCCCCCCeEEEcCCCCCCc-----------HHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 029810           14 ETGNPGNTLYVTGLSTRVT-----------ERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLN   82 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t-----------~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~   82 (187)
                      ....++.+|+|.||....+           +++|+++|++||.|..|.| .+.   .++|||||+|.+.++|++||+.||
T Consensus        10 ~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~ln   85 (112)
T 2dit_A           10 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLD   85 (112)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcC
Confidence            3456789999999954332           5899999999999999966 443   268999999999999999999999


Q ss_pred             CCccCCeEEEEEeccCCCC
Q 029810           83 QSVLEGRYITVERSRRKRP  101 (187)
Q Consensus        83 g~~i~g~~l~v~~a~~~~~  101 (187)
                      +..|+|+.|.|.++.++..
T Consensus        86 g~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           86 GRWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             TCEETTEECEEEECCSCCC
T ss_pred             CCEECCcEEEEEEeCCCCC
Confidence            9999999999999986543

>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=99.71  E-value=1.6e-17  Score=120.31  Aligned_cols=80  Identities=28%  Similarity=0.514  Sum_probs=73.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      +.++|||+|||.++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+.  +..|+|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            468999999999999999999999999999999999988999999999999999999999994  568999999998876


Q ss_pred             CC
Q 029810           98 RK   99 (187)
Q Consensus        98 ~~   99 (187)
                      ++
T Consensus        80 ~~   81 (167)
T 2cjk_A           80 PR   81 (167)
T ss_dssp             CH
T ss_pred             ch
Confidence            43

>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=99.71  E-value=7.4e-17  Score=120.51  Aligned_cols=78  Identities=17%  Similarity=0.301  Sum_probs=71.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccC
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR   98 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   98 (187)
                      .++|||+|||+++++++|+++|++||.|..|.|+.+. ++.++|||||+|++.++|++||+.+ +..|+|+.|.|.+++.
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            4799999999999999999999999999999999876 4888999999999999999999855 5699999999998764

>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=99.71  E-value=3e-17  Score=129.48  Aligned_cols=84  Identities=24%  Similarity=0.379  Sum_probs=76.6

Q ss_pred             CCCCCCeEEEcCCCCC-CcHHHHHHHhhcCCceeEEEEeecCC-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           15 TGNPGNTLYVTGLSTR-VTERDLEKHFSKEGKVASCFLVVEPR-TRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~-~t~~~L~~~f~~~G~i~~~~i~~~~~-~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      ...+.++|||+|||.. +++++|+++|++||.|..|.|+.+.. |+.++|||||+|.+.++|++|| .||+..|.|+.|.
T Consensus       206 ~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~  284 (292)
T 2ghp_A          206 ATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREIS  284 (292)
T ss_dssp             -CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEE
T ss_pred             cCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEE
Confidence            4567799999999999 99999999999999999999998776 5889999999999999999999 9999999999999


Q ss_pred             EEeccCC
Q 029810           93 VERSRRK   99 (187)
Q Consensus        93 v~~a~~~   99 (187)
                      |.+++++
T Consensus       285 V~~a~~k  291 (292)
T 2ghp_A          285 VSLADKK  291 (292)
T ss_dssp             EEECCCC
T ss_pred             EEEecCC
Confidence            9999875

>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=1e-16  Score=125.80  Aligned_cols=78  Identities=19%  Similarity=0.225  Sum_probs=72.0

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-CeEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE-GRYITV   93 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~-g~~l~v   93 (187)
                      ...++++|||+|||..+++++|+++|++||.|..|.|+.+.     +|||||+|.+.++|++||+.||+..|. |+.|.|
T Consensus       203 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v  277 (282)
T 3pgw_A          203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKI  277 (282)
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEE
Confidence            34567899999999999999999999999999999998553     579999999999999999999999999 999999


Q ss_pred             Eecc
Q 029810           94 ERSR   97 (187)
Q Consensus        94 ~~a~   97 (187)
                      .|++
T Consensus       278 ~~ak  281 (282)
T 3pgw_A          278 SFAK  281 (282)
T ss_pred             EEec
Confidence            9986

>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=99.70  E-value=1.2e-16  Score=125.46  Aligned_cols=87  Identities=20%  Similarity=0.171  Sum_probs=79.8

Q ss_pred             CCCCCCCeEEEcCCCCCC-cHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           14 ETGNPGNTLYVTGLSTRV-TERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~-t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      ......++|||+|||..+ ++++|+++|+.||.|..|.|+.+. ++.++|||||+|.+.++|++|+..|++..|.|+.|.
T Consensus       179 ~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  257 (284)
T 3smz_A          179 PALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLR  257 (284)
T ss_dssp             TTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             cccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEE
Confidence            345678999999999995 999999999999999999998876 688899999999999999999999999999999999


Q ss_pred             EEeccCCCC
Q 029810           93 VERSRRKRP  101 (187)
Q Consensus        93 v~~a~~~~~  101 (187)
                      |.++.++..
T Consensus       258 v~~a~~~~~  266 (284)
T 3smz_A          258 VSFCAPGPP  266 (284)
T ss_dssp             EEECCSSSC
T ss_pred             EEEecCCCc
Confidence            999987654

>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=99.69  E-value=2.2e-16  Score=123.98  Aligned_cols=85  Identities=25%  Similarity=0.332  Sum_probs=79.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ...++|||+|||.++++++|.++|..||.|..+.|+.+..++.++|||||+|.+.++|++|++.|++..|.|+.|.|.++
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a  172 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT  172 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            35689999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 029810           97 RRKRP  101 (187)
Q Consensus        97 ~~~~~  101 (187)
                      .+...
T Consensus       173 ~~~~~  177 (284)
T 3smz_A          173 DAGQL  177 (284)
T ss_dssp             CGGGC
T ss_pred             CCCCC
Confidence            86543

>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=99.67  E-value=2e-17  Score=120.92  Aligned_cols=86  Identities=21%  Similarity=0.339  Sum_probs=73.8

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      .+..+.++|||+|||.++++++|+++|..||.|.. .++.+..++.++|||||+|.+.++|++||+ |++..|.|+.|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v   85 (175)
T 1fje_B            8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKL   85 (175)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEE
Confidence            35677899999999999999999999999997765 233344467789999999999999999995 9999999999999


Q ss_pred             EeccCCCC
Q 029810           94 ERSRRKRP  101 (187)
Q Consensus        94 ~~a~~~~~  101 (187)
                      .++.++..
T Consensus        86 ~~~~~~~~   93 (175)
T 1fje_B           86 EKPKGRDS   93 (175)
T ss_dssp             ECCCCSSC
T ss_pred             ecCCCccc
Confidence            99986543

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

Probab=99.67  E-value=1.3e-16  Score=118.88  Aligned_cols=78  Identities=26%  Similarity=0.328  Sum_probs=72.4

Q ss_pred             CCCeEEEcCCCC-CCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           18 PGNTLYVTGLST-RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        18 ~~~~l~V~~Lp~-~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      .+++|||+|||+ .+++++|+++|++||.|..|.|+.+.     +|||||+|.+.++|++||+.|++..|.|+.|.|.++
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            358999999999 99999999999999999999998764     679999999999999999999999999999999999


Q ss_pred             cCCC
Q 029810           97 RRKR  100 (187)
Q Consensus        97 ~~~~  100 (187)
                      ....
T Consensus        77 ~~~~   80 (198)
T 1qm9_A           77 KHQN   80 (198)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            8654

>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=99.66  E-value=1.3e-16  Score=120.22  Aligned_cols=78  Identities=18%  Similarity=0.180  Sum_probs=69.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCce--eEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe----E
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKV--ASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGR----Y   90 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i--~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~----~   90 (187)
                      .++.+|||+|||+.+++++|+++|++||.|  ..+.|+.+.  +..+|||||+|.+.++|++||..||+..|.+.    +
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p  198 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP  198 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcc
Confidence            467899999999999999999999999998  888887664  44569999999999999999999999999876    5


Q ss_pred             EEEEec
Q 029810           91 ITVERS   96 (187)
Q Consensus        91 l~v~~a   96 (187)
                      +.|+++
T Consensus       199 ~~vk~~  204 (205)
T 3tyt_A          199 YTLKLC  204 (205)
T ss_dssp             EECEEE
T ss_pred             eEEEec
Confidence            777765

>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=3.9e-16  Score=119.31  Aligned_cols=78  Identities=27%  Similarity=0.386  Sum_probs=71.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCC-ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-CeEEEEE
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEG-KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE-GRYITVE   94 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G-~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~-g~~l~v~   94 (187)
                      .+.++|||+|||..+++++|+++|++|| .|..|.|+.+     .++||||+|.+.++|++||+.|++..|. |+.|.|.
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~  223 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  223 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEE
Confidence            4579999999999999999999999999 9999998643     2679999999999999999999999999 9999999


Q ss_pred             eccCC
Q 029810           95 RSRRK   99 (187)
Q Consensus        95 ~a~~~   99 (187)
                      |++++
T Consensus       224 ~a~~~  228 (229)
T 2adc_A          224 FSKST  228 (229)
T ss_dssp             ECSSC
T ss_pred             EecCC
Confidence            99864

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

Probab=99.66  E-value=2.2e-16  Score=117.66  Aligned_cols=78  Identities=27%  Similarity=0.381  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCC-ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-CeEEEEE
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEG-KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE-GRYITVE   94 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G-~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~-g~~l~v~   94 (187)
                      .+.++|||+|||..+++++|+++|++|| .|..|.|+.+.     +|+|||+|.+.++|++|+..||+..|. |+.|.|.
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  192 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  192 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEE
Confidence            4589999999999999999999999999 99999986542     689999999999999999999999999 9999999


Q ss_pred             eccCC
Q 029810           95 RSRRK   99 (187)
Q Consensus        95 ~a~~~   99 (187)
                      |++++
T Consensus       193 ~a~~~  197 (198)
T 1qm9_A          193 FSKST  197 (198)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            99864

>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=99.65  E-value=4.2e-16  Score=121.41  Aligned_cols=79  Identities=25%  Similarity=0.445  Sum_probs=72.2

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      ....+.++|||+|||+++|+++|+++|++||.|..|.|..+      +|||||+|.+.++|++||..|++..|.|+.|.|
T Consensus        17 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v   90 (261)
T 3sde_A           17 KTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRI   90 (261)
T ss_dssp             CSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEe
Confidence            34456689999999999999999999999999999998643      689999999999999999999999999999999


Q ss_pred             EeccC
Q 029810           94 ERSRR   98 (187)
Q Consensus        94 ~~a~~   98 (187)
                      .++.+
T Consensus        91 ~~a~~   95 (261)
T 3sde_A           91 RFATH   95 (261)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            99875

>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=99.65  E-value=5.3e-16  Score=104.83  Aligned_cols=82  Identities=18%  Similarity=0.217  Sum_probs=70.7

Q ss_pred             CCCCeEEEcCC--CCCCc--------HHHHHHHhhcCCceeEEEEeecCCC--CCcceEEEEEecCHHHHHHHHHHhCCC
Q 029810           17 NPGNTLYVTGL--STRVT--------ERDLEKHFSKEGKVASCFLVVEPRT--RISRGFAFVTMDGVEDAERCIKYLNQS   84 (187)
Q Consensus        17 ~~~~~l~V~~L--p~~~t--------~~~L~~~f~~~G~i~~~~i~~~~~~--~~~~g~afV~f~~~~~a~~ai~~l~g~   84 (187)
                      .++..|.|.|+  |..+.        +++|+++|++||.|..|.|+.+..+  +.++|+|||+|++.++|++|++.|||.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            46789999998  33332        3789999999999999999887654  357899999999999999999999999


Q ss_pred             ccCCeEEEEEeccC
Q 029810           85 VLEGRYITVERSRR   98 (187)
Q Consensus        85 ~i~g~~l~v~~a~~   98 (187)
                      .|+|+.|.|.++..
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            99999999998753

>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=99.64  E-value=7.5e-16  Score=119.94  Aligned_cols=83  Identities=27%  Similarity=0.323  Sum_probs=74.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC-CccC---CeEEEE
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQ-SVLE---GRYITV   93 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g-~~i~---g~~l~v   93 (187)
                      +.++|||+|||..+++++|+++|+.||.|..|.|+.+ .++.++|||||+|.+.++|.+||..|++ ..+.   +++|.|
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v  173 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIV  173 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEE
Confidence            4689999999999999999999999999999999998 5899999999999999999999999955 4444   899999


Q ss_pred             EeccCCCC
Q 029810           94 ERSRRKRP  101 (187)
Q Consensus        94 ~~a~~~~~  101 (187)
                      .++.....
T Consensus       174 ~~~~~~~~  181 (261)
T 3sde_A          174 EPMEQFDD  181 (261)
T ss_dssp             EECCCEES
T ss_pred             eeccccCc
Confidence            99886543

>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=99.63  E-value=1.5e-15  Score=104.68  Aligned_cols=81  Identities=16%  Similarity=0.193  Sum_probs=70.8

Q ss_pred             CCCeEEEcCCCC--C---CcHHHHHHHhhcCCceeEEEEeecCC----CCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 029810           18 PGNTLYVTGLST--R---VTERDLEKHFSKEGKVASCFLVVEPR----TRISRGFAFVTMDGVEDAERCIKYLNQSVLEG   88 (187)
Q Consensus        18 ~~~~l~V~~Lp~--~---~t~~~L~~~f~~~G~i~~~~i~~~~~----~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g   88 (187)
                      ++.+|+|.|+-.  +   -.++||+++|++||+|..|.|+.+..    ++.++|++||+|.+.++|++|++.|||..|+|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            678999999842  2   23689999999999999999998754    45678999999999999999999999999999


Q ss_pred             eEEEEEeccC
Q 029810           89 RYITVERSRR   98 (187)
Q Consensus        89 ~~l~v~~a~~   98 (187)
                      +.|.|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999753

>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=99.62  E-value=9.2e-16  Score=120.92  Aligned_cols=83  Identities=24%  Similarity=0.309  Sum_probs=71.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCC-ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEG-KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G-~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ..++|||+|||..+++++|.++|.+|| .|..|.|+.+.. +.++|||||+|.+.++|++|++.|++..|.|+.|.|.++
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  194 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            578999999999999999999999999 999999988765 678899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 029810           97 RRKRP  101 (187)
Q Consensus        97 ~~~~~  101 (187)
                      .+...
T Consensus       195 ~~~~~  199 (292)
T 2ghp_A          195 NPLEK  199 (292)
T ss_dssp             CCC--
T ss_pred             CCCcc
Confidence            86543

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

Probab=99.62  E-value=7.7e-15  Score=98.15  Aligned_cols=77  Identities=17%  Similarity=0.096  Sum_probs=64.1

Q ss_pred             CCeEEEcCCC-------CCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           19 GNTLYVTGLS-------TRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        19 ~~~l~V~~Lp-------~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ...|.|.-..       ..+++++|+++|++||+|..|.|+     +.++|||||+|++.++|++||+.++  .+.++.|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEV--GLVDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeE
Confidence            5677775443       458999999999999999999987     3568999999999999999999754  4679999


Q ss_pred             EEEeccCCCCC
Q 029810           92 TVERSRRKRPR  102 (187)
Q Consensus        92 ~v~~a~~~~~~  102 (187)
                      .|+|++++...
T Consensus        83 ~V~~a~~~~~~   93 (100)
T 2d9o_A           83 KISWLEGQPQD   93 (100)
T ss_dssp             EEECSSCCCCC
T ss_pred             EEEEccCCCCC
Confidence            99999876543

>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=2.7e-16  Score=106.16  Aligned_cols=72  Identities=26%  Similarity=0.380  Sum_probs=63.0

Q ss_pred             EcCCCCCCcHHHHHHHh------------hcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           24 VTGLSTRVTERDLEKHF------------SKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        24 V~~Lp~~~t~~~L~~~f------------~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      +.||++.+++++|+++|            ++||.|..|.|+.+.. +.++|||||+|.+.++|++|++.|||..|+|+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56677777777776666            9999999999987764 6789999999999999999999999999999999


Q ss_pred             EEEec
Q 029810           92 TVERS   96 (187)
Q Consensus        92 ~v~~a   96 (187)
                      .|+++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>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=99.61  E-value=1.5e-15  Score=110.45  Aligned_cols=76  Identities=18%  Similarity=0.447  Sum_probs=67.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcC----C-------ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKE----G-------KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVL   86 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~----G-------~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i   86 (187)
                      +.++|||+|||.++++++|+++|++|    |       .|..+.+..      ++|||||+|.+.++|++|| .|++..|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            46899999999999999999999999    6       666666643      3789999999999999999 7999999


Q ss_pred             CCeEEEEEeccCCC
Q 029810           87 EGRYITVERSRRKR  100 (187)
Q Consensus        87 ~g~~l~v~~a~~~~  100 (187)
                      .|+.|.|.++....
T Consensus        76 ~g~~i~v~~~~~~~   89 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQ   89 (172)
T ss_dssp             TTEECEEECCSSCC
T ss_pred             cCceeeecCCcccC
Confidence            99999999977543

>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=2.1e-15  Score=111.97  Aligned_cols=76  Identities=18%  Similarity=0.433  Sum_probs=66.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcC----C-------ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKE----G-------KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVL   86 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~----G-------~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i   86 (187)
                      ..++|||+|||+++++++|+++|++|    |       .|..+.+.      .++|||||+|.+.++|++|| .|++..|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~------~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE------TTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec------CCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            56899999999999999999999999    4       55555553      34789999999999999999 7999999


Q ss_pred             CCeEEEEEeccCCC
Q 029810           87 EGRYITVERSRRKR  100 (187)
Q Consensus        87 ~g~~l~v~~a~~~~  100 (187)
                      .|+.|.|.++....
T Consensus        76 ~g~~i~v~~~~~~~   89 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQ   89 (198)
T ss_dssp             TTEEEEEECCCCCC
T ss_pred             cCceEEEeCCCCCC
Confidence            99999999987653

>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=99.57  E-value=5.2e-15  Score=119.11  Aligned_cols=79  Identities=18%  Similarity=0.260  Sum_probs=66.7

Q ss_pred             CCCCCCCCeEEEcC--CCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC---
Q 029810           13 TETGNPGNTLYVTG--LSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE---   87 (187)
Q Consensus        13 ~~~~~~~~~l~V~~--Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~---   87 (187)
                      .....++.+|||+|  |+..+++++|+++|++||+|..|.|..      .+|||||+|++.++|++||+.|||.++.   
T Consensus        12 ~~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~   85 (345)
T 3tht_A           12 ETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDL   85 (345)
T ss_dssp             CCCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTT
T ss_pred             eecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCcccccc
Confidence            34567889999999  578999999999999999999987753      3789999999999999999999999773   


Q ss_pred             Ce--EEEEEecc
Q 029810           88 GR--YITVERSR   97 (187)
Q Consensus        88 g~--~l~v~~a~   97 (187)
                      |+  .|.|.++.
T Consensus        86 g~~~~ly~~~~~   97 (345)
T 3tht_A           86 GQKITLYLNFVE   97 (345)
T ss_dssp             SCEEECEEEECS
T ss_pred             CCceEEEEEEee
Confidence            44  56777764

>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=99.51  E-value=7.4e-14  Score=95.54  Aligned_cols=80  Identities=14%  Similarity=0.200  Sum_probs=66.7

Q ss_pred             CCCCCCeEEEcCCCCCC----------cHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC
Q 029810           15 TGNPGNTLYVTGLSTRV----------TERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS   84 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~----------t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~   84 (187)
                      +..++..|.|.|+=...          .++||+++|++||.|..|.|..+.    .+|++||+|.+.++|++|++.|||.
T Consensus         3 ~p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~   78 (114)
T 3s6e_A            3 QPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGR   78 (114)
T ss_dssp             CCCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTC
T ss_pred             CCCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCC
Confidence            34567888888873321          236799999999999999886543    4799999999999999999999999


Q ss_pred             ccCCeEEEEEeccC
Q 029810           85 VLEGRYITVERSRR   98 (187)
Q Consensus        85 ~i~g~~l~v~~a~~   98 (187)
                      .|+|+.|.|+++..
T Consensus        79 ~f~GR~i~v~~~~~   92 (114)
T 3s6e_A           79 WFAGKMITAAYVPL   92 (114)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EECCEEEEEEEEcH
Confidence            99999999999753

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

Probab=99.49  E-value=1.4e-13  Score=94.59  Aligned_cols=80  Identities=19%  Similarity=0.138  Sum_probs=71.2

Q ss_pred             CCCCCCCCeEEEcCCCCC-CcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecC-HHHHHHHHHHhC--CCccCC
Q 029810           13 TETGNPGNTLYVTGLSTR-VTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDG-VEDAERCIKYLN--QSVLEG   88 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~-~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~-~~~a~~ai~~l~--g~~i~g   88 (187)
                      +-+..+++.|||+||+.. ++.++|+++|++||+|..|.+..+..      .|||.|.+ .++|++|+..|+  +.+|++
T Consensus        12 ~~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g   85 (121)
T 1owx_A           12 SLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRN   85 (121)
T ss_dssp             CCSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTS
T ss_pred             cccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeC
Confidence            446788999999999999 99999999999999999999987753      69999999 899999999995  678999


Q ss_pred             eEEEEEeccC
Q 029810           89 RYITVERSRR   98 (187)
Q Consensus        89 ~~l~v~~a~~   98 (187)
                      ..+++++...
T Consensus        86 ~~~~~evL~G   95 (121)
T 1owx_A           86 KEVTWEVLEG   95 (121)
T ss_dssp             SSEEEEECCH
T ss_pred             cEEEEEECCC
Confidence            9999987654

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

Probab=99.41  E-value=1.2e-12  Score=84.88  Aligned_cols=76  Identities=25%  Similarity=0.278  Sum_probs=63.9

Q ss_pred             CCCCCeEEEcCCCC----CCcH----HHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 029810           16 GNPGNTLYVTGLST----RVTE----RDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLE   87 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~----~~t~----~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~   87 (187)
                      .++..||+|.-++.    +.-.    .+|.+.|.+||+|..++|+.+.        +||+|.+.++|.+||+ |||..|+
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~   74 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELL   74 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEET
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeC
Confidence            46778888876652    2222    6799999999999999998653        8999999999999999 9999999


Q ss_pred             CeEEEEEeccCCC
Q 029810           88 GRYITVERSRRKR  100 (187)
Q Consensus        88 g~~l~v~~a~~~~  100 (187)
                      |+.|+|+++++.-
T Consensus        75 Gr~LkV~lkt~dW   87 (91)
T 2dnr_A           75 NRTITIALKSPSG   87 (91)
T ss_dssp             TEEEEEEECCCSS
T ss_pred             CeEEEEEeCCCCc
Confidence            9999999998653

>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=99.26  E-value=7.8e-12  Score=81.43  Aligned_cols=74  Identities=16%  Similarity=0.204  Sum_probs=62.6

Q ss_pred             CCCCCCeEEEcCCCCC------CcH---HHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCc
Q 029810           15 TGNPGNTLYVTGLSTR------VTE---RDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSV   85 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~------~t~---~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~   85 (187)
                      ..++..||+|.-++..      ..+   .+|.+.|.+||+|..++|+.+        -+||+|.+.++|.+||+ |+|..
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d--------~~fVtF~d~~sAl~AI~-ldG~~   81 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC--------cEEEEEcChHHHHHHHh-cCCee
Confidence            4567889999877632      221   569999999999999999866        39999999999999999 99999


Q ss_pred             cCCeEEEEEecc
Q 029810           86 LEGRYITVERSR   97 (187)
Q Consensus        86 i~g~~l~v~~a~   97 (187)
                      |+|+.|+|++..
T Consensus        82 v~Gr~L~V~~k~   93 (95)
T 1ufw_A           82 VKGRAVKISGPS   93 (95)
T ss_dssp             ETTEEEEEECCC
T ss_pred             eCCeEEEEeccC
Confidence            999999999854

>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=99.15  E-value=1.3e-10  Score=88.10  Aligned_cols=67  Identities=19%  Similarity=0.192  Sum_probs=60.1

Q ss_pred             CcHHHHHHHhhcCCceeEEEEeecC----CCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           31 VTERDLEKHFSKEGKVASCFLVVEP----RTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        31 ~t~~~L~~~f~~~G~i~~~~i~~~~----~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      -.+++|.+.|++||.|..+.|+.+.    .++..+|++||+|.+.++|++|+..|||..|+|+.|.|.++.
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            3567899999999999999998554    355889999999999999999999999999999999999975

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

Probab=98.87  E-value=1.4e-08  Score=67.49  Aligned_cols=74  Identities=18%  Similarity=0.209  Sum_probs=66.2

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcC-----CceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKE-----GKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY   90 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~-----G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~   90 (187)
                      .+...+|-|-|||..++++.|..+++++     |.|..|.+..+-      +-|+|+|.+...|-+|.-+|+|.+|.|++
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~   91 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKV   91 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEE
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeE
Confidence            3456788899999999999999999999     999999888663      36999999999999999999999999999


Q ss_pred             EEEEe
Q 029810           91 ITVER   95 (187)
Q Consensus        91 l~v~~   95 (187)
                      |.|.-
T Consensus        92 Lr~gT   96 (117)
T 2l9w_A           92 IRSGT   96 (117)
T ss_dssp             EEEEC
T ss_pred             EEecC
Confidence            99864

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

Probab=98.29  E-value=1.1e-05  Score=53.08  Aligned_cols=74  Identities=23%  Similarity=0.264  Sum_probs=61.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcC-----CceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKE-----GKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~-----G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ....+|.|.|||+.+.++.|.-+|+.-     |+|..+....        +-|+|+|.+.+.|+.+|+ -..+.|++..|
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~-k~~H~L~~~~L   76 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLA-QADHELHGAQL   76 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHT-CSCCBSSSSBC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhc-CCcceecCeEE
Confidence            356899999999999999999999862     4888887753        369999999999999988 44678999999


Q ss_pred             EEEeccCC
Q 029810           92 TVERSRRK   99 (187)
Q Consensus        92 ~v~~a~~~   99 (187)
                      .|....+.
T Consensus        77 sV~P~~~~   84 (104)
T 2dhx_A           77 SLRPAPPR   84 (104)
T ss_dssp             EEEECCCC
T ss_pred             EEEcCCCC
Confidence            99765543

>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=98.22  E-value=4.4e-06  Score=55.19  Aligned_cols=76  Identities=11%  Similarity=0.031  Sum_probs=63.9

Q ss_pred             CCCeEEEcCCCCCC-c----HHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           18 PGNTLYVTGLSTRV-T----ERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~-t----~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      ..++|+|+||+.++ .    .+.++++|..|+++....+++..      .=..|.|.++++|.+|-..||+..|.|+.|+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            45789999998865 2    25789999999999888777543      2579999999999999999999999999999


Q ss_pred             EEeccCC
Q 029810           93 VERSRRK   99 (187)
Q Consensus        93 v~~a~~~   99 (187)
                      |-++.+.
T Consensus        78 ~YFgq~~   84 (104)
T 1wey_A           78 LYFAQTL   84 (104)
T ss_dssp             EECCCCS
T ss_pred             EEecCCC
Confidence            9998743

>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=98.19  E-value=8e-06  Score=53.14  Aligned_cols=56  Identities=20%  Similarity=0.248  Sum_probs=45.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLN   82 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~   82 (187)
                      ....++| ++|.++...||.++|+.||.| .|.++.|-       .|||.|.+++.|..|+..+.
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            3455556 999999999999999999943 45665542       79999999999999999764

>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=98.18  E-value=1.9e-05  Score=51.13  Aligned_cols=80  Identities=13%  Similarity=0.102  Sum_probs=61.4

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCC--cceEEEEEecCHHHHHHHHHHhCCCccCCe-----EEE
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRI--SRGFAFVTMDGVEDAERCIKYLNQSVLEGR-----YIT   92 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~--~~g~afV~f~~~~~a~~ai~~l~g~~i~g~-----~l~   92 (187)
                      ++|.|.+||+.+|++++.+.+..+..+....++..+.+..  ...-|+|.|.+.+++....+.++|+.|-+.     ...
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            5789999999999999999999988777666654443222  235699999999999999999999976432     345


Q ss_pred             EEeccCC
Q 029810           93 VERSRRK   99 (187)
Q Consensus        93 v~~a~~~   99 (187)
                      |++|--+
T Consensus        82 VE~AP~q   88 (91)
T 1uw4_A           82 VEFAPFQ   88 (91)
T ss_dssp             EEECSSC
T ss_pred             EEEcCCC
Confidence            6776533

>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=98.03  E-value=2.6e-05  Score=52.85  Aligned_cols=73  Identities=10%  Similarity=0.140  Sum_probs=58.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC-eEEEEE
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG-RYITVE   94 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g-~~l~v~   94 (187)
                      ....+-|.|-++|+.. ...|...|++||+|.+....      ....|..|.|++..+|++||. .||..|++ ..|-|.
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~   92 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVK   92 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEE
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEE
Confidence            4456788888999885 56678889999999988762      124699999999999999999 79999985 566666


Q ss_pred             ec
Q 029810           95 RS   96 (187)
Q Consensus        95 ~a   96 (187)
                      ..
T Consensus        93 p~   94 (119)
T 1wwh_A           93 PC   94 (119)
T ss_dssp             EC
T ss_pred             EC
Confidence            64

>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=97.95  E-value=1.5e-05  Score=51.98  Aligned_cols=54  Identities=20%  Similarity=0.216  Sum_probs=45.0

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLN   82 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~   82 (187)
                      ..++| ++|.++...||.++|+.|| -..|.++.|-       .|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            45666 9999999999999999999 4446666542       79999999999999999775

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

Probab=97.77  E-value=6.2e-05  Score=49.11  Aligned_cols=79  Identities=10%  Similarity=0.063  Sum_probs=55.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCC--cceEEEEEecCHHHHHHHHHHhCCCccCCe-----EE
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRI--SRGFAFVTMDGVEDAERCIKYLNQSVLEGR-----YI   91 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~--~~g~afV~f~~~~~a~~ai~~l~g~~i~g~-----~l   91 (187)
                      .-+|.|..||+.+||+++.+.+..+-++....++..+.+.+  ...-|+|.|.+.+++....+.++|..|-+.     ..
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            46899999999999999888887665543322222222211  123589999999999999999999876432     45


Q ss_pred             EEEecc
Q 029810           92 TVERSR   97 (187)
Q Consensus        92 ~v~~a~   97 (187)
                      .|++|.
T Consensus        89 ~VE~AP   94 (97)
T 2l08_A           89 VVEFAP   94 (97)
T ss_dssp             EEEECC
T ss_pred             EEEecC
Confidence            567764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=97.49  E-value=0.00012  Score=50.32  Aligned_cols=78  Identities=14%  Similarity=0.140  Sum_probs=55.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeE-EEEee------------cCCCC-CcceEEEEEecCHHHHHHHHHHhCC
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVAS-CFLVV------------EPRTR-ISRGFAFVTMDGVEDAERCIKYLNQ   83 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~-~~i~~------------~~~~~-~~~g~afV~f~~~~~a~~ai~~l~g   83 (187)
                      ..+-|.|-+.|+..+. .|.+.|++||.|.+ +.+..            ..... ....|..|.|++..+|++||. .||
T Consensus         6 ~e~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG   83 (132)
T 3p3d_A            6 GELAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENG   83 (132)
T ss_dssp             --CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTT
T ss_pred             CceEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCC
Confidence            3467778899877664 46678999999876 22111            00001 124699999999999999999 899


Q ss_pred             CccCCeEEEEEecc
Q 029810           84 SVLEGRYITVERSR   97 (187)
Q Consensus        84 ~~i~g~~l~v~~a~   97 (187)
                      ..|+|.-|-|.+..
T Consensus        84 ~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           84 AVFNGVLLGVIPYT   97 (132)
T ss_dssp             CEETTEECEEEECC
T ss_pred             eEeCcEEEEEEECC
Confidence            99999988887764

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=97.17  E-value=0.00023  Score=59.20  Aligned_cols=54  Identities=17%  Similarity=0.197  Sum_probs=41.4

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK   79 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~   79 (187)
                      .+|||. +|..+++.+|.++|++||.|..+.+-.+.     ..||.|||.+.+++.+++.
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHh
Confidence            789997 79999999999999999999999886543     3599999999999887765

>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=96.78  E-value=0.0017  Score=45.76  Aligned_cols=35  Identities=14%  Similarity=0.164  Sum_probs=28.4

Q ss_pred             EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC
Q 029810           48 SCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS   84 (187)
Q Consensus        48 ~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~   84 (187)
                      .+.|+++..  .++|||||+|.+.++|++|++.+++.
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHHHHhhccc
Confidence            355666653  57899999999999999999988764

>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=96.59  E-value=0.0011  Score=46.52  Aligned_cols=40  Identities=18%  Similarity=0.233  Sum_probs=36.3

Q ss_pred             CCcceEEEEEecCHHHHHHHHHHh-CCCccCCeEEEEEeccC
Q 029810           58 RISRGFAFVTMDGVEDAERCIKYL-NQSVLEGRYITVERSRR   98 (187)
Q Consensus        58 ~~~~g~afV~f~~~~~a~~ai~~l-~g~~i~g~~l~v~~a~~   98 (187)
                      ...+|+++|+|.+.++|++|++.| |+..|+| .|.|.++..
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            455899999999999999999999 9999999 999998765

>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=95.29  E-value=0.062  Score=45.28  Aligned_cols=56  Identities=21%  Similarity=0.257  Sum_probs=44.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQ   83 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g   83 (187)
                      ...++|+ +|..+...+|.++|+.||.| .|.++.+       ..|||.|.+.+.|..++..+..
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd-------t~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS-------SEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC-------CeEEEEECCHHHHHHHHHHHHh
Confidence            4566666 88888999999999999953 4555433       2799999999999999998854

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=93.89  E-value=0.17  Score=30.86  Aligned_cols=68  Identities=13%  Similarity=0.329  Sum_probs=43.3

Q ss_pred             eEEEc-CCCCCCcHHHHHHHhhcCC-----ceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           21 TLYVT-GLSTRVTERDLEKHFSKEG-----KVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        21 ~l~V~-~Lp~~~t~~~L~~~f~~~G-----~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      +|||. +-...+...+|..++..-+     .|-.+.|..        .|.||+... +.|+.+++.|++..+.|+.+.|+
T Consensus         2 ~~~i~~Grk~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d--------~~s~v~v~~-~~~~~~~~~l~~~~i~g~~~~v~   72 (76)
T 2g0c_A            2 KLYFNGGKKKKIRAVDFVGTIAKIDGVSADDIGIITIMD--------NASYVEILN-GKGPHVLKVMKNTTVKGKQLKVN   72 (76)
T ss_dssp             EEEESCCCC----CHHHHHHHHTSTTCCGGGEEEEEECS--------SCEEEEECT-TCHHHHHHHHTTCCC---CCCEE
T ss_pred             EEEEeCCCccCCCHHHHHHHHHHccCCChhhccEEEEeC--------CcEEEEECH-HHHHHHHHHhccccCcCceEEEE
Confidence            56663 2233667778888876544     455666642        389998864 46888999999999999999988


Q ss_pred             ecc
Q 029810           95 RSR   97 (187)
Q Consensus        95 ~a~   97 (187)
                      .++
T Consensus        73 ~~~   75 (76)
T 2g0c_A           73 KAN   75 (76)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            764

>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=93.08  E-value=0.54  Score=38.75  Aligned_cols=9  Identities=11%  Similarity=0.073  Sum_probs=3.5

Q ss_pred             HHHHHHHHH
Q 029810           71 VEDAERCIK   79 (187)
Q Consensus        71 ~~~a~~ai~   79 (187)
                      .+++..++.
T Consensus       116 e~~L~~~F~  124 (437)
T 3pgw_S          116 ESKLRREFE  124 (437)
T ss_pred             HHHHHHHHH
Confidence            333333333

>4eyt_A Telomerase associated protein P65; RNA, LA protein, LARP7, RRM, XRRM, RNA binding protein; 2.50A {Tetrahymena thermophila} PDB: 4erd_A

Probab=92.09  E-value=1.5  Score=27.88  Aligned_cols=72  Identities=11%  Similarity=0.166  Sum_probs=52.3

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC-------ccC
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS-------VLE   87 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~-------~i~   87 (187)
                      ....++-|-|-|||..+-..++.-.....|---.|..+        -|-|.|.|.+.++...||.+|-.+       +|.
T Consensus         8 sikqnclikiinipqgtlkaevvlavrhlgyefycdyi--------dgqamirfqnsdeqrlaiqkllnhnnnklqieir   79 (129)
T 4eyt_A            8 SIKQNCLIKIINIPQGTLKAEVVLAVRHLGYEFYCDYI--------DGQAMIRFQNSDEQRLAIQKLLNHNNNKLQIEIR   79 (129)
T ss_dssp             --CCSCEEEEECCCTTCCHHHHHHHHHTTCCCEEEEEC--------SSCEEEEESSHHHHHHHHHHHEETTTTEEEEEET
T ss_pred             hhhhCcEEEEEecCCCceeeeeEEeehhcCeeEeeeee--------cCeeEEEecCChHHHHHHHHHHhcCCCEEEEEEc
Confidence            34567888899999999888887777777765556655        346999999999999999877433       345


Q ss_pred             CeEEEEE
Q 029810           88 GRYITVE   94 (187)
Q Consensus        88 g~~l~v~   94 (187)
                      |+.+.|-
T Consensus        80 gqicdvi   86 (129)
T 4eyt_A           80 GQICDVI   86 (129)
T ss_dssp             TEEEEEE
T ss_pred             ceeeeee
Confidence            6655553

---

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	187
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-21
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-19
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	6e-18
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-17
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	5e-17
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	7e-17
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-16
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-16
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-16
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-16
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-16
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	6e-16
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	6e-16
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-15
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-15
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-15
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-15
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-15
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-15
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	4e-15
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-15
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-15
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	5e-15
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	6e-15
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	7e-15
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-14
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-14
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-14
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-14
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-14
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	6e-14
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	7e-14
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	9e-14
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-13
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-13
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-13
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-13
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-13
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-13
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-13
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-13
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-13
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	7e-13
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-12
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-12
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	5e-12
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	7e-09
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-12
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-11
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-11
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-11
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-11
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	5e-11
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-10
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-10
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-10
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-10
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-10
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:) 7e-10
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	7e-10
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	8e-10
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-09
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	5e-09
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	7e-09
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	8e-09
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	1e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-08
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-08
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-08
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	4e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	7e-08
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	8e-08
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-07
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-07
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-07
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-07
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	3e-07
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	7e-07
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-06
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	5e-06
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	8e-05
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	8e-05
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	8e-05

>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 = 80.3 bits (198), Expect = 5e-21
 Identities = 27/78 (34%), Positives = 42/78 (53%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          +LYV  L   VTE  L + FS  G + S  +  +  TR S G+A+V      DAER +  
Sbjct: 2  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 81 LNQSVLEGRYITVERSRR 98
          +N  V++G+ + +  S+R
Sbjct: 62 MNFDVIKGKPVRIMWSQR 79

>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 = 74.9 bits (184), Expect = 8e-19
 Identities = 23/102 (22%), Positives = 46/102 (45%), Gaps = 9/102 (8%)

Query: 7   SRSRGRTETGNPGNTLYVTGLST-RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAF 65
           S S G+T+  +  + +++  L+T  V + D+E  FSK GK+  C         + +GFAF
Sbjct: 3   SGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGC--------SVHKGFAF 54

Query: 66  VTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
           V      +A   +   +  ++ G+ + +  +   +     P 
Sbjct: 55  VQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVNRSGPS 96

>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 = 72.7 bits (178), Expect = 6e-18
 Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 2/79 (2%)

Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
             LYVT L   +T+  L+  F K G +    ++ +  T   RG AFV  +  E+A+  I
Sbjct: 6  DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 65

Query: 79 KYLNQSVLEG--RYITVER 95
            LN  + EG  + ++V  
Sbjct: 66 SALNNVIPEGGSQPLSVRL 84

>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 = 70.8 bits (173), Expect = 3e-17
 Identities = 25/84 (29%), Positives = 41/84 (48%)

Query: 17  NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
           N   T+YV GL  +V+E  L + F + G V +  +  +  T   +G+ FV     EDA+ 
Sbjct: 7   NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 66

Query: 77  CIKYLNQSVLEGRYITVERSRRKR 100
            IK ++   L G+ I V ++    
Sbjct: 67  AIKIMDMIKLYGKPIRVNKASAHN 90

>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 = 70.1 bits (171), Expect = 5e-17
 Identities = 28/85 (32%), Positives = 41/85 (48%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
               LYV GL+  V ++ L   F   G +    + ++  T   RGFAFV  +  EDA   
Sbjct: 4   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63

Query: 78  IKYLNQSVLEGRYITVERSRRKRPR 102
           I  +N+S L GR I V  ++  R +
Sbjct: 64  IDNMNESELFGRTIRVNLAKPMRIK 88

>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 = 69.7 bits (170), Expect = 7e-17
 Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 4/84 (4%)

Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPR---TRISRGFAFVTMDGVEDAERCI 78
           L++  L+   TE  L+  FSK G + SC +  +       +S GF FV     E A++ +
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 79  KYLNQSVLEGRYITVERSRRK-RP 101
           K L    ++G  + V  S R  +P
Sbjct: 61  KQLQGHTVDGHKLEVRISERATKP 84

>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 = 69.2 bits (169), Expect = 1e-16
 Identities = 19/85 (22%), Positives = 40/85 (47%), Gaps = 2/85 (2%)

Query: 17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPR-TRISRGFAFVTMDGVEDAE 75
             + + V  +  +  +R++ + FS  G++ +  L  +   T   RGF FV     +DA+
Sbjct: 6  QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 65

Query: 76 RCIKYL-NQSVLEGRYITVERSRRK 99
          +    L + + L GR + +E +  +
Sbjct: 66 KAFNALCHSTHLYGRRLVLEWADSE 90

>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 = 68.9 bits (168), Expect = 1e-16
 Identities = 20/74 (27%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          +++ GLS + T+  L ++F + G+V  C ++ +P T+ SRGF FVT       ++ +   
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 82 NQSVLEGRYITVER 95
          ++  L+ + I  + 
Sbjct: 62 SRHELDSKTIDPKV 75

>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 = 68.5 bits (167), Expect = 2e-16
 Identities = 22/85 (25%), Positives = 42/85 (49%), Gaps = 2/85 (2%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
             + L V GL  + TE+DL+++FS  G+V    +  + +T  S+GF FV     E   + 
Sbjct: 7   KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 66

Query: 78  IKYLNQSVLEGRYITVERSRRKRPR 102
           +   +   ++GR+   +    K+ +
Sbjct: 67  MSQRHM--IDGRWCDCKLPNSKQSQ 89

>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 = 67.8 bits (165), Expect = 3e-16
 Identities = 35/83 (42%), Positives = 47/83 (56%)

Query: 11 GRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDG 70
          G     +P   L V GLS   TERDL + FSK G +A   +V + ++R SRGFAFV  + 
Sbjct: 1  GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

Query: 71 VEDAERCIKYLNQSVLEGRYITV 93
          V+DA+   +  N   L+GR I V
Sbjct: 61 VDDAKEAKERANGMELDGRRIRV 83

>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 = 67.3 bits (164), Expect = 5e-16
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          +++ GLS   T++DL+ +FSK G+V  C L ++P T  SRGF FV     E  ++ +   
Sbjct: 2  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 82 NQSVLEGRYITVER 95
           +  L G+ I  +R
Sbjct: 61 KEHKLNGKVIDPKR 74

>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 = 67.3 bits (164), Expect = 6e-16
 Identities = 23/77 (29%), Positives = 39/77 (50%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           L V  L   +T+R+L   F   G + +C ++ + +T  S G+AFV      D++R IK 
Sbjct: 4  NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 81 LNQSVLEGRYITVERSR 97
          LN   +  + + V  +R
Sbjct: 64 LNGITVRNKRLKVSYAR 80

>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 = 68.1 bits (166), Expect = 6e-16
 Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 3/86 (3%)

Query: 17  NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
                LY+  L  ++T  ++   F K G +          T  +RG A+V  + + DA+ 
Sbjct: 5   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIR---VGNTPETRGTAYVVYEDIFDAKN 61

Query: 77  CIKYLNQSVLEGRYITVERSRRKRPR 102
              +L+   +  RY+ V      R  
Sbjct: 62  ACDHLSGFNVCNRYLVVLYYNANRAF 87

>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 = 66.9 bits (163), Expect = 1e-15
 Identities = 24/85 (28%), Positives = 39/85 (45%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
              TLYV  LS   TE  + + FSK G +    + ++   + + GF FV      DAE  
Sbjct: 6   KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 65

Query: 78  IKYLNQSVLEGRYITVERSRRKRPR 102
           ++Y+N + L+ R I  +     +  
Sbjct: 66  MRYINGTRLDDRIIRTDWDAGFKEG 90

>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 = 66.1 bits (161), Expect = 1e-15
 Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V GLS    E  + ++F   G+V S  L ++ +T   RGF F+T    E  ++ ++  
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60

Query: 82 NQSVLEGRYITVER 95
              +      ++ 
Sbjct: 61 KYHNVGLSKCEIKV 74

>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 = 66.6 bits (162), Expect = 1e-15
 Identities = 30/95 (31%), Positives = 49/95 (51%), Gaps = 3/95 (3%)

Query: 9   SRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTM 68
           S G +E+ +    L+V+ +  R  + DL + F + GK+      +    R S+GF FVT 
Sbjct: 1   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVE--IIFNERGSKGFGFVTF 58

Query: 69  DGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRT 103
           +   DA+R  + L+ +V+EGR I V  +   R  T
Sbjct: 59  ENSADADRAREKLHGTVVEGRKIEVNNA-TARVMT 92

>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 = 66.7 bits (162), Expect = 2e-15
 Identities = 28/93 (30%), Positives = 46/93 (49%), Gaps = 2/93 (2%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
            ++V GL    T+  L K+F   G +    ++ + +T  SRG+ FVTM     AER  K 
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 81  LNQSVLEGRYITVERSRRK-RPRTPTPGHYLGL 112
            N  +++GR   V  +    +PR+   G  +G+
Sbjct: 72  PNP-IIDGRKANVNLAYLGAKPRSLQTGFAIGV 103

>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 = 66.6 bits (162), Expect = 2e-15
 Identities = 23/94 (24%), Positives = 44/94 (46%)

Query: 9   SRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTM 68
           + G  + G  G  L++  L     ++DL + F   G V S  + ++ +T +S+ F FV+ 
Sbjct: 8   AAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 67

Query: 69  DGVEDAERCIKYLNQSVLEGRYITVERSRRKRPR 102
           D    A+  I+ +N   +  + + V+  R K   
Sbjct: 68  DNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS 101

>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 = 66.1 bits (161), Expect = 3e-15
 Identities = 17/90 (18%), Positives = 38/90 (42%), Gaps = 6/90 (6%)

Query: 14  ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
           ++     T+Y  G+++ +T++ + + FS  G++    +  E        ++FV     E 
Sbjct: 13  QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHES 66

Query: 74  AERCIKYLNQSVLEGRYITVERSRRKRPRT 103
           A   I  +N + +EG  +     +     T
Sbjct: 67  AAHAIVSVNGTTIEGHVVKCYWGKESPDMT 96

>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 = 65.0 bits (158), Expect = 4e-15
 Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          L V+ L   V++ D+++ F++ G +     V   R+  S G A V  +   DA + +K  
Sbjct: 3  LLVSNLDFGVSDADIQELFAEFGTLKKAA-VHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 82 NQSVLEGRYITVE 94
          N   L+GR + ++
Sbjct: 62 NGVPLDGRPMNIQ 74

>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 = 65.0 bits (158), Expect = 4e-15
 Identities = 17/80 (21%), Positives = 39/80 (48%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
          + L++ GL   + +  +++  +  G + +  LV +  T +S+G+AF     +   ++ I 
Sbjct: 2  HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 80 YLNQSVLEGRYITVERSRRK 99
           LN   L  + + V+R+   
Sbjct: 62 GLNGMQLGDKKLLVQRASVG 81

>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 = 65.1 bits (158), Expect = 4e-15
 Identities = 24/83 (28%), Positives = 41/83 (49%)

Query: 17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
          +   T+ VT LS    E DL++ F   G ++  +L  +  T  S+GFAF++    EDA R
Sbjct: 6  DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 65

Query: 77 CIKYLNQSVLEGRYITVERSRRK 99
           I  ++    +   + VE ++  
Sbjct: 66 AIAGVSGFGYDHLILNVEWAKPS 88

>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 = 64.8 bits (157), Expect = 5e-15
 Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 1/82 (1%)

Query: 22  LYVTGLSTRVTERDLEKHFSKEGKVASCFLVV-EPRTRISRGFAFVTMDGVEDAERCIKY 80
           +++  L   + E+ L   FS  G +     ++ +P T  S+G+AF+     + ++  I+ 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 81  LNQSVLEGRYITVERSRRKRPR 102
           +N   L  R ITV  + +K  +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>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 = 64.7 bits (157), Expect = 6e-15
 Identities = 25/90 (27%), Positives = 37/90 (41%), Gaps = 6/90 (6%)

Query: 14  ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
           +T +    LYV  L    +E  +EK F+              R +  R +AFV     ED
Sbjct: 3   DTMSSVKILYVRNLMLSTSEEMIEKEFNN------IKPGAVERVKKIRDYAFVHFSNRED 56

Query: 74  AERCIKYLNQSVLEGRYITVERSRRKRPRT 103
           A   +K LN  VL+G  I V  ++     +
Sbjct: 57  AVEAMKALNGKVLDGSPIEVTLAKPVDKDS 86

>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 = 64.7 bits (157), Expect = 7e-15
 Identities = 25/71 (35%), Positives = 41/71 (57%)

Query: 19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
             LYV+GL   +T+++LE+ FS+ G++ +  ++V+  T +SRG  F+  D   +AE  I
Sbjct: 6  DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 65

Query: 79 KYLNQSVLEGR 89
          K LN     G 
Sbjct: 66 KGLNGQKPSGA 76

>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 = 64.4 bits (156), Expect = 1e-14
 Identities = 28/90 (31%), Positives = 43/90 (47%)

Query: 14  ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
             G P   LY+  LS RVTERDL   F++  +     +     T   RG AF+T    E 
Sbjct: 13  NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEI 72

Query: 74  AERCIKYLNQSVLEGRYITVERSRRKRPRT 103
           A + +  +N   L G+ + +E  + K+ R+
Sbjct: 73  AWQALHLVNGYKLYGKILVIEFGKNKKQRS 102

>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 = 64.0 bits (155), Expect = 1e-14
 Identities = 21/77 (27%), Positives = 35/77 (45%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          TL++T      T+R++         VA    +   R   SR FA++ +   EDA  C++ 
Sbjct: 3  TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 81 LNQSVLEGRYITVERSR 97
          LN   +EG  +  + S 
Sbjct: 63 LNGLKIEGYTLVTKVSN 79

>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 = 63.6 bits (154), Expect = 2e-14
 Identities = 21/82 (25%), Positives = 41/82 (50%)

Query: 18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
           G  L+VT +     E ++++ F   G++ +  L ++ RT  S+G+A V  +  + A   
Sbjct: 6  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 65

Query: 78 IKYLNQSVLEGRYITVERSRRK 99
           + LN + + G+ I V+    K
Sbjct: 66 KEALNGAEIMGQTIQVDWCFVK 87

>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 = 63.1 bits (153), Expect = 3e-14
 Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           L++ GLS   T+  L  HF + G +  C ++ +P T+ SRGF FVT   VE+ +  +  
Sbjct: 8  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 66

Query: 81 LNQSVLEGRYITVER 95
               ++GR +  +R
Sbjct: 67 ARPHKVDGRVVEPKR 81

>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 = 63.5 bits (154), Expect = 3e-14
 Identities = 26/97 (26%), Positives = 43/97 (44%), Gaps = 1/97 (1%)

Query: 6   RSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAF 65
           R      +       T++   L+ R+  RDLE  FS  GKV    ++ +  +R S+G A+
Sbjct: 5   REPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAY 64

Query: 66  VTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPR 102
           V    ++     I  L    L G  I V+ S+ ++ R
Sbjct: 65  VEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKNR 100

>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 = 62.8 bits (152), Expect = 6e-14
 Identities = 21/82 (25%), Positives = 42/82 (51%), Gaps = 1/82 (1%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
            L++ GLS   TE  L  ++ + GK+  C ++ +P ++ SRGF FVT   + + +  +  
Sbjct: 22  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA- 80

Query: 81  LNQSVLEGRYITVERSRRKRPR 102
                ++GR +  +R+  +   
Sbjct: 81  ARPHSIDGRVVEPKRAVAREES 102

>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 = 62.0 bits (150), Expect = 7e-14
 Identities = 14/83 (16%), Positives = 36/83 (43%), Gaps = 1/83 (1%)

Query: 18 PGNTLYVTGLSTRVTERDLEKHFSKE-GKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
          P +T+Y+  L+ ++ + +L+K       +      ++  R+   RG AFV    V  A  
Sbjct: 2  PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 77 CIKYLNQSVLEGRYITVERSRRK 99
           ++ +       + + ++ ++  
Sbjct: 62 ALRSMQGFPFYDKPMRIQYAKTD 84

>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 = 61.7 bits (149), Expect = 9e-14
 Identities = 25/77 (32%), Positives = 37/77 (48%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           L V  L   +T+ +    F   G++ SC LV +  T  S G+ FV     +DAE+ I  
Sbjct: 4  NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 81 LNQSVLEGRYITVERSR 97
          LN   L+ + I V  +R
Sbjct: 64 LNGLRLQTKTIKVSYAR 80

>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 = 61.6 bits (149), Expect = 1e-13
 Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 5/85 (5%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
              TL    LS  +TE +L++ F    ++         +   S+G A++      DAE+ 
Sbjct: 15  AARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKN 69

Query: 78  IKYLNQSVLEGRYITVERSRRKRPR 102
           ++    + ++GR +++  +  K   
Sbjct: 70  LEEKQGAEIDGRSVSLYYTGEKGGT 94

>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 = 61.2 bits (148), Expect = 1e-13
 Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 8/82 (9%)

Query: 18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
           GNTLYV G    +T   L   FS  G +    +         R  AFVT + +E A++ 
Sbjct: 4  KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQA 55

Query: 78 IKYLNQSVLEGRYITVERSRRK 99
          +  LN + +E   + V  +R++
Sbjct: 56 VAELNGTQVESVQLKVNIARKQ 77

>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 = 61.2 bits (148), Expect = 1e-13
 Identities = 22/86 (25%), Positives = 36/86 (41%), Gaps = 2/86 (2%)

Query: 17  NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
               TLYV  LS  VTE  + + FS+ G   SC ++ E  +     + FV      DA  
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAA 63

Query: 77  CIKYLNQSVLEGRYITVERSRRKRPR 102
            +  +N   + G+ + V  +     +
Sbjct: 64  ALAAMNGRKILGKEVKVNWATTPSSQ 89

>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 = 61.6 bits (149), Expect = 1e-13
 Identities = 16/88 (18%), Positives = 31/88 (35%), Gaps = 4/88 (4%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVV--EPRTRISRGFAFVTMDGVEDAERCI 78
            L++ G+       ++ +  +K  +     +V         +RGFAFV  +    A    
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 79  KYLNQS--VLEGRYITVERSRRKRPRTP 104
           + L      L G  I V+ +  +     
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEIDVDE 90

>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 = 60.9 bits (147), Expect = 1e-13
 Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          ++V GLS   T  D++ +F + GKV    L+ +  T   RGF FVT +  +  E+  + +
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 82 NQSVLEGRYITVER 95
          +   +  + +  ++
Sbjct: 61 HFHEINNKMVECKK 74

>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 = 61.3 bits (148), Expect = 2e-13
 Identities = 21/94 (22%), Positives = 40/94 (42%), Gaps = 8/94 (8%)

Query: 17  NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLV--------VEPRTRISRGFAFVTM 68
           +  + +YV GL+  VT  DL   F + G V              ++  T   +G A V+ 
Sbjct: 6   SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSY 65

Query: 69  DGVEDAERCIKYLNQSVLEGRYITVERSRRKRPR 102
           +    A+  +++ +    +G  + V  +R+K P 
Sbjct: 66  EDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 99

>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 = 60.8 bits (147), Expect = 2e-13
 Identities = 14/81 (17%), Positives = 30/81 (37%), Gaps = 1/81 (1%)

Query: 15 TGNPGNT-LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVED 73
          +G PG T + V  +   V+  ++   F     +     +      +  G A V  +  ++
Sbjct: 4  SGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDE 63

Query: 74 AERCIKYLNQSVLEGRYITVE 94
          A   +  LN   +  R + + 
Sbjct: 64 ATAAVIDLNDRPIGSRKVKLV 84

>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 = 60.9 bits (147), Expect = 3e-13
 Identities = 19/100 (19%), Positives = 38/100 (38%), Gaps = 1/100 (1%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G     +P  T ++  L   VTE  +++ F      A             +GF + 
Sbjct: 3   SGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYA 62

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTP 106
             + ++     +  LN+  L  + I V+ + + + +   P
Sbjct: 63  EFEDLDSLLSALS-LNEESLGNKRIRVDVADQAQDKDSGP 101

>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 = 60.5 bits (146), Expect = 3e-13
 Identities = 27/86 (31%), Positives = 43/86 (50%)

Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
             L+V  LS   +E DLEK FS  G ++     ++  T+  +GFAFVT    E A +   
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 80  YLNQSVLEGRYITVERSRRKRPRTPT 105
            ++  V +GR + V  S  K+  + +
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEASQS 94

>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 = 60.1 bits (145), Expect = 4e-13
 Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 2/83 (2%)

Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
             +++  L   +  + L   FS  G + SC +V +     S+G+ FV  +  E AER I+
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIE 66

Query: 80  YLNQSVLEGRYITVERSRRKRPR 102
            +N  +L  R + V R + ++ R
Sbjct: 67  KMNGMLLNDRKVFVGRFKSRKER 89

>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 = 59.7 bits (144), Expect = 7e-13
 Identities = 24/91 (26%), Positives = 34/91 (37%), Gaps = 3/91 (3%)

Query: 12  RTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGV 71
           R   GN    +YV  L   +  +D+E  F K G +           R    FAFV  +  
Sbjct: 7   RGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDID---LKNRRGGPPFAFVEFEDP 63

Query: 72  EDAERCIKYLNQSVLEGRYITVERSRRKRPR 102
            DAE  +   +    +G  + VE  R  R  
Sbjct: 64  RDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT 94

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

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

 Score = 58.4 bits (141), Expect = 2e-12
 Identities = 20/80 (25%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
          + L+V  L   +TE ++ K F K GK    F          +GF F+ ++    AE    
Sbjct: 9  SRLFVGNLPPDITEEEMRKLFEKYGKAGEVF------IHKDKGFGFIRLETRTLAEIAKV 62

Query: 80 YLNQSVLEGRYITVERSRRK 99
           L+   L G+ + V  +   
Sbjct: 63 ELDNMPLRGKQLRVRFACHS 82

>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 = 57.8 bits (139), Expect = 3e-12
 Identities = 28/83 (33%), Positives = 49/83 (59%)

Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
             L+V GLS    E+ LE+ FSK G+++   +V +  T+ SRGF FVT + ++DA+  + 
Sbjct: 6   GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 65

Query: 80  YLNQSVLEGRYITVERSRRKRPR 102
            +N   ++GR I V+++ +    
Sbjct: 66  AMNGKSVDGRQIRVDQAGKSSDN 88

>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 = 59.6 bits (143), Expect = 5e-12
 Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 1/88 (1%)

Query: 18  PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
               ++V G+     E  L  +F + GK+    ++ +  +   RGFAFVT D  +  ++ 
Sbjct: 96  TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 155

Query: 78  IKYLNQSVLEGRYITVERSRRKRPRTPT 105
           +       + G    V ++  K+     
Sbjct: 156 VI-QKYHTVNGHNCEVRKALSKQEMASA 182

>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 = 50.8 bits (120), Expect = 7e-09
 Identities = 21/63 (33%), Positives = 33/63 (52%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           L++ GLS   T+  L  HF + G +  C ++ +P T+ SRGF FVT   VE+ +  +  
Sbjct: 8  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 81 LNQ 83
             
Sbjct: 68 RPH 70

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 5e-12
 Identities = 21/94 (22%), Positives = 40/94 (42%), Gaps = 8/94 (8%)

Query: 16  GNPGNT-LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDA 74
           G+ G++ ++V   +  +TE +L + FS+ G V   F       +  R FAFVT    + A
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVF-----IPKPFRAFAFVTFADDQIA 55

Query: 75  ERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGH 108
           +         +++G  + +  +  K      P  
Sbjct: 56  QSLCG--EDLIIKGISVHISNAEPKHNSNSGPSS 87

>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 = 56.7 bits (136), Expect = 1e-11
 Identities = 22/91 (24%), Positives = 39/91 (42%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           +++V  +    TE  L+  FS+ G V S  LV +  T   +G+ F      E A   ++ 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 81  LNQSVLEGRYITVERSRRKRPRTPTPGHYLG 111
           LN     GR + V+ +  ++ +        G
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEELKSLGTG 100

>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 = 56.4 bits (135), Expect = 1e-11
 Identities = 21/89 (23%), Positives = 39/89 (43%), Gaps = 6/89 (6%)

Query: 17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
            G T+++  LS    E  L +   + G +    +V+ P T  S+G AF      E A++
Sbjct: 6  TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 65

Query: 77 CIKYLNQS------VLEGRYITVERSRRK 99
          C+   +         L+GR + V+ +  +
Sbjct: 66 CLAAASLEAEGGGLKLDGRQLKVDLAVTR 94

>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 = 56.8 bits (136), Expect = 2e-11
 Identities = 24/93 (25%), Positives = 38/93 (40%)

Query: 17  NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
           +    L V  + T V E  L + F + G + S  +V +  TR SRG+ FV       A++
Sbjct: 40  DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99

Query: 77  CIKYLNQSVLEGRYITVERSRRKRPRTPTPGHY 109
            I  LN   +  + + V  +     R    G  
Sbjct: 100 AIAGLNGFNILNKRLKVALAASGHQRPGIAGAV 132

>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 = 54.8 bits (131), Expect = 3e-11
 Identities = 19/70 (27%), Positives = 34/70 (48%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          LY+ GL    T++DL K     GK+ S   +++  T   +G+ FV  D    A++ +  L
Sbjct: 1  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 82 NQSVLEGRYI 91
            S ++ +  
Sbjct: 61 KASGVQAQMA 70

>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 = 54.3 bits (130), Expect = 5e-11
 Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 7/85 (8%)

Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
           N LY+  LS  VT  DL + F            +  +  +  G+AFV       A R I+
Sbjct: 2   NKLYIGNLSPAVTADDLRQLFGDRKL------PLAGQVLLKSGYAFVDYPDQNWAIRAIE 55

Query: 80  YLNQSV-LEGRYITVERSRRKRPRT 103
            L+  V L G+ + V+ S  K+ R+
Sbjct: 56  TLSGKVELHGKIMEVDYSVSKKLRS 80

>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 = 54.0 bits (129), Expect = 1e-10
 Identities = 11/95 (11%), Positives = 25/95 (26%), Gaps = 12/95 (12%)

Query: 16  GNPGN-TLYVTGLSTRVTE-----RDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMD 69
           G+ G+  L     +  V          E  F    K  +           S     +   
Sbjct: 1   GSSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQY------FKSFKRVRINFS 54

Query: 70  GVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTP 104
               A      L+++   G+ + +  ++     + 
Sbjct: 55  NPLSAADARLRLHKTEFLGKEMKLYFAQTLHIGSS 89

>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 = 53.6 bits (128), Expect = 2e-10
 Identities = 22/101 (21%), Positives = 37/101 (36%), Gaps = 8/101 (7%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G     +    ++V GL   V E DL +   K G +    ++   R       A V
Sbjct: 3   SGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALV 56

Query: 67  TMDGVEDAERCIKYL--NQSVLEGRYITVERSRRKRPRTPT 105
             + ++ A+ C+ +       + G+      S  KR   P 
Sbjct: 57  EFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPG 97

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 2e-10
 Identities = 17/89 (19%), Positives = 31/89 (34%), Gaps = 9/89 (10%)

Query: 8  RSRGRTETGNPGNTLYVT--GLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAF 65
          R  G         +L V   GL   V+   L     K G V +           ++ ++F
Sbjct: 7  RHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALL------MPPNKPYSF 60

Query: 66 VTMDGVEDAERCIKYLN-QSVLEGRYITV 93
                E+++R    LN + V++     +
Sbjct: 61 ARYRTTEESKRAYVTLNGKEVVDDLGQKI 89

>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 = 52.8 bits (126), Expect = 2e-10
 Identities = 17/92 (18%), Positives = 38/92 (41%), Gaps = 9/92 (9%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFL-----VVEPRTRISRGFAFVTMDGVEDAE 75
            LYV  +   +TE  +   F+ + ++          V+  +    + FAF+    V++  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 76  RCIKYLNQSVLEGRYITVERSRRKRPRTPTPG 107
           + +   +  + +G+ + +   RR     P PG
Sbjct: 63  QAM-AFDGIIFQGQSLKI---RRPHDYQPLPG 90

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {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: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.5 bits (125), Expect = 4e-10
 Identities = 24/100 (24%), Positives = 41/100 (41%), Gaps = 1/100 (1%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G +        + + GL    ++ ++ + FS    V +   +       S G AFV
Sbjct: 3   SGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFV 62

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTP 106
                E AE+ +   ++  +  RYI + +S R   RT  P
Sbjct: 63  QFASQEIAEKAL-KKHKERIGHRYIEIFKSSRAEVRTSGP 101

>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 = 52.3 bits (125), Expect = 5e-10
 Identities = 15/90 (16%), Positives = 29/90 (32%), Gaps = 6/90 (6%)

Query: 17  NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
           +P   + V  L   VT   L + FSK G V       +     ++  A +       A+ 
Sbjct: 5   SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQH 60

Query: 77  CIKYLNQSVL--EGRYITVERSRRKRPRTP 104
               L+   +      + ++ S+       
Sbjct: 61  AKLSLDGQNIYNACCTLRIDFSKLTSLNVK 90

>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 = 52.0 bits (124), Expect = 7e-10
 Identities = 18/90 (20%), Positives = 31/90 (34%), Gaps = 1/90 (1%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           + S+      +  + + +        E    +   K G+V     V +       G  +V
Sbjct: 15  NSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYV 73

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVERS 96
                EDAE+ +  LN     G+ I  E S
Sbjct: 74  KFRREEDAEKAVIDLNNRWFNGQPIHAELS 103

>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 = 51.3 bits (122), Expect = 7e-10
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
           ++V G+     E  L  +F + GK+    ++ +  +   RGFAFVT D  +  ++ +  
Sbjct: 4  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI- 62

Query: 81 LNQSVLEGRYITVERS 96
               + G    V ++
Sbjct: 63 QKYHTVNGHNCEVRKA 78

>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 = 52.1 bits (124), Expect = 8e-10
 Identities = 24/110 (21%), Positives = 43/110 (39%), Gaps = 7/110 (6%)

Query: 20  NTLYVTGLSTR-VTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCI 78
           + L V+ L+   VT + L   F   G V    ++   +       A V M     A+  +
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLAM 57

Query: 79  KYLNQSVLEGRYITVERSRRKRPRTPTPGHYLGLKSSRDIGRGDRGRYRS 128
            +LN   L G+ I +  S+ +  + P  G       ++D G     R++ 
Sbjct: 58  SHLNGHKLHGKPIRITLSKHQNVQLPREGQE-DQGLTKDYGNSPLHRFKK 106

>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 = 50.1 bits (119), Expect = 2e-09
 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 3/83 (3%)

Query: 19 GNTLYVTGLSTRVT-ERDLEKHFSKEGKVASCFLVVEPR-TRISRGFAFVTMDGVEDAER 76
          G  + +  LST +  E  L + F   G +    +    +    +   AF+  +  + AER
Sbjct: 4  GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 77 CIKYLNQSVLEGRYITVERSRRK 99
           ++ +N+S+L  R I+V  + +K
Sbjct: 64 ALQ-MNRSLLGNREISVSLADKK 85

>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 = 49.4 bits (117), Expect = 5e-09
 Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 6/80 (7%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTR------ISRGFAFVTMDGVED 73
          N ++V GLS R+ + ++ K     GK      VV   +            A+VT    ED
Sbjct: 9  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 74 AERCIKYLNQSVLEGRYITV 93
          A R I+ +N  V++GR +  
Sbjct: 69 ALRAIQCVNNVVVDGRTLKA 88

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.9 bits (116), Expect = 7e-09
 Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 8/86 (9%)

Query: 17  NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
           NP   L+V GL    +   L + F + G + +              FA++  + ++ A+ 
Sbjct: 15  NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTID------HVKGDSFAYIQYESLDAAQA 68

Query: 77  CIKYLNQSVLEG--RYITVERSRRKR 100
               +    L G  R + V+ ++   
Sbjct: 69  ACAKMRGFPLGGPDRRLRVDFAKSGP 94

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.7 bits (115), Expect = 8e-09
 Identities = 18/90 (20%), Positives = 30/90 (33%), Gaps = 8/90 (8%)

Query: 16  GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAE 75
           G P   L++  L   VTE ++               V        +  AF+ +   E A 
Sbjct: 5   GAPSRVLHIRKLPGEVTETEVIALGLP------FGKVTNILMLKGKNQAFLELATEEAAI 58

Query: 76  RCIKY--LNQSVLEGRYITVERSRRKRPRT 103
             + Y       L  + I ++ S  K  +T
Sbjct: 59  TMVNYYSAVTPHLRNQPIYIQYSNHKELKT 88

>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 = 48.6 bits (115), Expect = 1e-08
 Identities = 13/83 (15%), Positives = 27/83 (32%), Gaps = 1/83 (1%)

Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
             LY++ L   + E++LE      G+V S  ++ +                 E  E  I 
Sbjct: 19  TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMES-TEKCEAVIG 77

Query: 80  YLNQSVLEGRYITVERSRRKRPR 102
           + N   ++        +     +
Sbjct: 78  HFNGKFIKTPPGVSAPTEPLLCK 100

>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 = 48.4 bits (115), Expect = 1e-08
 Identities = 18/67 (26%), Positives = 27/67 (40%), Gaps = 4/67 (5%)

Query: 33 ERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT 92
            DL    SK G++      +    R   G A V+    E+A+ CI+ L+     GR IT
Sbjct: 33 REDLRVECSKFGQIRK----LLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 88

Query: 93 VERSRRK 99
           +     
Sbjct: 89 AQAWDGT 95

>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 = 48.3 bits (114), Expect = 2e-08
 Identities = 15/86 (17%), Positives = 31/86 (36%), Gaps = 1/86 (1%)

Query: 17  NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
           +     ++T +   +T+ D+ +         +   V+        G A V     +DA +
Sbjct: 6   SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARK 65

Query: 77  CIKYLNQSVLEGRYITVERSRRKRPR 102
             + L++  L GR   V     +  R
Sbjct: 66  SER-LHRKKLNGREAFVHVVTLEDMR 90

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.5 bits (112), Expect = 3e-08
 Identities = 21/102 (20%), Positives = 32/102 (31%), Gaps = 7/102 (6%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G   T      + V+GL    + +DL+ H  + G V               G   V
Sbjct: 3   SGSSGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYAD-------VQKDGMGMV 55

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTPGH 108
                ED E  ++ L+ +            R    R+  P  
Sbjct: 56  EYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPERSSGPSS 97

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 46.8 bits (110), Expect = 4e-08
 Identities = 11/82 (13%), Positives = 23/82 (28%), Gaps = 6/82 (7%)

Query: 18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
          P   L++T L     E  L   F++                     AFV       +   
Sbjct: 7  PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVR-----LVPNRHDIAFVEFTTELQSNAA 61

Query: 78 IKYLN-QSVLEGRYITVERSRR 98
           + L    +     + +  +++
Sbjct: 62 KEALQGFKITPTHAMKITFAKK 83

>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 = 45.9 bits (108), Expect = 7e-08
 Identities = 15/92 (16%), Positives = 31/92 (33%), Gaps = 8/92 (8%)

Query: 16  GNPGNT-LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDA 74
           G+ G++ + V  L      +++                       ++  AFVT+   E A
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYV-------DRNKRTAFVTLLNGEQA 53

Query: 75  ERCIKYLNQSVLEGRYITVERSRRKRPRTPTP 106
           +  I+  +Q    G+ + V+           P
Sbjct: 54  QNAIQMFHQYSFRGKDLIVQLQPTDALLCSGP 85

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

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

 Score = 45.9 bits (108), Expect = 8e-08
 Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 5/81 (6%)

Query: 18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERC 77
          P  TL+++ +   V+E DL+  FS  G V   F       +  R  A + M  VE+A + 
Sbjct: 9  PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF----KFFQKDRKMALIQMGSVEEAVQA 64

Query: 78 IKYLN-QSVLEGRYITVERSR 97
          +  L+   + E  ++ V  S+
Sbjct: 65 LIDLHNHDLGENHHLRVSFSK 85

>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 = 45.7 bits (108), Expect = 1e-07
 Identities = 13/76 (17%), Positives = 21/76 (27%), Gaps = 2/76 (2%)

Query: 27  LSTRVTERDLEKHFSKEGKVASCFLVVEPRTR--ISRGFAFVTMDGVEDAERCIKYLNQS 84
                   D+    SK G V S  +            G  FV    V D ++ ++ L   
Sbjct: 22  EEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR 81

Query: 85  VLEGRYITVERSRRKR 100
               R +  +      
Sbjct: 82  KFANRVVVTKYCDPDS 97

>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 = 44.9 bits (106), Expect = 2e-07
 Identities = 8/81 (9%), Positives = 22/81 (27%), Gaps = 9/81 (11%)

Query: 20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
            + V G         L   F++         +++     +  +  +       A + + 
Sbjct: 5  TWVTVFGFPQASASYIL-LQFAQ------YGNILKHVMSNTGNWMHIRYQSKLQARKALS 57

Query: 80 YLNQSVLEGRY-ITVERSRRK 99
            +  +      I V+    K
Sbjct: 58 -KDGRIFGESIMIGVKPCIDK 77

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

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

 Score = 44.7 bits (105), Expect = 2e-07
 Identities = 13/76 (17%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          ++Y+ G  T  T  D+++    +G+V +   +     +  +G  FV  D +E A++ ++ 
Sbjct: 8  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIESAKKFVE- 65

Query: 81 LNQSVLEGRYITVERS 96
                +   + +   
Sbjct: 66 TPGQKYKETDLLILFK 81

>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 = 44.6 bits (104), Expect = 3e-07
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAER 76
               L++  L+   +  +L+   S+     +   VV+ RT  +R F +V  +  ED E+
Sbjct: 11 TTPFNLFIGNLNPNKSVAELKVAISELFAK-NDLAVVDVRTGTNRKFGYVDFESAEDLEK 69

Query: 77 CIKYLNQSVLEGRYITVERSRRK 99
           +  L    + G  I +E+ + +
Sbjct: 70 AL-ELTGLKVFGNEIKLEKPKGR 91

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 44.1 bits (103), Expect = 3e-07
 Identities = 13/75 (17%), Positives = 26/75 (34%), Gaps = 3/75 (4%)

Query: 21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
          T+ V  L     +  + K+F   G +    +      + +  FA +     + A   I  
Sbjct: 2  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALAAITK 59

Query: 81 LNQSVLEGRYITVER 95
           ++ V+    I V  
Sbjct: 60 THK-VVGQNEIIVSH 73

>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 = 44.1 bits (103), Expect = 7e-07
 Identities = 19/96 (19%), Positives = 34/96 (35%), Gaps = 2/96 (2%)

Query: 4  RSRSRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGF 63
            + RSR R+     G  +Y+ GL      + +   F K   V     +       + G 
Sbjct: 4  SGQKRSRSRSPH-EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGE 62

Query: 64 AFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK 99
           FV      D +  +   ++  +  R+I V    +K
Sbjct: 63 GFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKK 97

>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 = 42.4 bits (99), Expect = 2e-06
 Identities = 21/100 (21%), Positives = 38/100 (38%), Gaps = 3/100 (3%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S G +     G+ +++ GL  R TE D+   FS    +     +         G A V
Sbjct: 3   SGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM--RVHIEIGPDGRVTGEADV 60

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTP 106
                EDA   +   +++ ++ RY+ +  +         P
Sbjct: 61  EFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGTSGSGP 99

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.0 bits (95), Expect = 5e-06
 Identities = 16/89 (17%), Positives = 27/89 (30%), Gaps = 7/89 (7%)

Query: 20  NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK 79
           N + V+GL    + +DL+ H             V        G   V     ED    ++
Sbjct: 1   NRVVVSGLPPSGSWQDLKDHM-------REAGDVCYADVYRDGTGVVEFVRKEDMTYAVR 53

Query: 80  YLNQSVLEGRYITVERSRRKRPRTPTPGH 108
            L+ +            R K     +P +
Sbjct: 54  KLDNTKFRSHEGETAYIRVKVDGPRSPSY 82

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.9 bits (92), Expect = 2e-05
 Identities = 15/100 (15%), Positives = 31/100 (31%), Gaps = 11/100 (11%)

Query: 7   SRSRGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFV 66
           S S GR++T      +    L       ++++ FS+ G +                 A V
Sbjct: 3   SGSSGRSKT-----VILAKNLPAGTLAAEIQETFSRFGSLGRV------LLPEGGITAIV 51

Query: 67  TMDGVEDAERCIKYLNQSVLEGRYITVERSRRKRPRTPTP 106
                 +A +  ++L  S      + +E +          
Sbjct: 52  EFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQ 91

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

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

 Score = 38.2 bits (88), Expect = 8e-05
 Identities = 14/82 (17%), Positives = 24/82 (29%), Gaps = 5/82 (6%)

Query: 21  TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKY 80
             +   L  +    DL   FS  G++     V   +  I         +  ++A    K 
Sbjct: 13  LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIIL-----FKEKAKEALGKAKD 67

Query: 81  LNQSVLEGRYITVERSRRKRPR 102
            N   L+ R   V     +   
Sbjct: 68  ANNGNLQLRNKEVTWEVLEGEV 89

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {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: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.8 bits (87), Expect = 8e-05
 Identities = 15/94 (15%), Positives = 35/94 (37%), Gaps = 12/94 (12%)

Query: 10  RGRTETGNPGNTLYVTGL-STRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTM 68
           +GR E       +++      +     L +     G +++               AF+ M
Sbjct: 2   KGRVE---TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNH------LILNKINEAFIEM 52

Query: 69  DGVEDAERCIKY--LNQSVLEGRYITVERSRRKR 100
              EDA+  + Y     +++ G+ + V  S++ +
Sbjct: 53  ATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYK 86

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.2 bits (85), Expect = 8e-05
 Identities = 19/78 (24%), Positives = 30/78 (38%), Gaps = 7/78 (8%)

Query: 22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL 81
          + + GL   VT +++    S                   +G AFVT+   E AE  I   
Sbjct: 1  ILIRGLPGDVTNQEVHDLLSDYELKYCF-------VDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 82 NQSVLEGRYITVERSRRK 99
          +QS L  R ++V+     
Sbjct: 54 HQSRLRERELSVQLQPTD 71

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	187
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.92
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.91
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.91
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.91
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.91
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.91
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.91
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.91
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.91
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.91
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.91
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.9
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.9
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.9
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.9
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.9
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.9
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.9
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.89
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.89
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.89
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.89
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.89
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.89
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.89
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.89
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.88
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.88
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.88
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.88
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.88
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.88
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.88
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.88
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.88
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.88
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.87
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.87
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.87
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.87
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.87
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.87
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.86
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.86
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.86
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.86
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.85
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.85
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.85
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.85
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.85
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.85
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.85
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.85
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.84
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.84
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.84
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.84
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.84
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.84
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.84
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.84
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.83
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.83
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.83
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.83
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.83
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.83
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.83
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.83
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.81
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.81
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.8
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.79
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.78
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.78
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.74
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.72
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	99.68
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.67
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.65
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.63
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.61
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.57
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.55
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	98.4
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.29
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.0
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	97.35

>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=99.92  E-value=7.5e-25  Score=140.64  Aligned_cols=80  Identities=29%  Similarity=0.458  Sum_probs=77.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccC
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR   98 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   98 (187)
                      +++|||+|||.++++++|+++|++||.|..+.|+.+..++.++|||||+|.+.++|++||+.||+..|.|+.|.|++|+|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999974

>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=99.91  E-value=2.3e-24  Score=143.95  Aligned_cols=89  Identities=25%  Similarity=0.403  Sum_probs=82.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      ..+.+++++|||+|||+++++++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|+.||+.||+..|.|+.|.
T Consensus        12 ~~~~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~   91 (102)
T d2cpza1          12 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK   91 (102)
T ss_dssp             CCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEE
Confidence            33446678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeccCCCC
Q 029810           93 VERSRRKRP  101 (187)
Q Consensus        93 v~~a~~~~~  101 (187)
                      |++++++..
T Consensus        92 V~~a~~k~~  100 (102)
T d2cpza1          92 VQLKRSKND  100 (102)
T ss_dssp             EECCCCSCC
T ss_pred             EEEeCCCCC
Confidence            999987754

>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=99.91  E-value=1.4e-24  Score=142.59  Aligned_cols=86  Identities=29%  Similarity=0.414  Sum_probs=81.0

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      +.++.++|||+|||.++++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+.||+..|.|+.|.|+
T Consensus         5 ~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   84 (93)
T d1x5ua1           5 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   84 (93)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34556899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCC
Q 029810           95 RSRRKR  100 (187)
Q Consensus        95 ~a~~~~  100 (187)
                      +|+++.
T Consensus        85 ~A~~~~   90 (93)
T d1x5ua1          85 KASAHN   90 (93)
T ss_dssp             ETTTTS
T ss_pred             EcCCCC
Confidence            998764

>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=99.91  E-value=2e-24  Score=140.49  Aligned_cols=84  Identities=25%  Similarity=0.399  Sum_probs=79.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ..++.+|||+|||.++++++|.++|++||+|..|.|+.+..++.++|||||+|.+.++|++||..||+..|.|+.|.|+|
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~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 029810           96 SRRK   99 (187)
Q Consensus        96 a~~~   99 (187)
                      |.++
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            9865

>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=99.91  E-value=3.4e-24  Score=142.37  Aligned_cols=85  Identities=32%  Similarity=0.432  Sum_probs=80.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ...++|||+|||+++++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|++||+.||+..|.|+.|+|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 029810           97 RRKRP  101 (187)
Q Consensus        97 ~~~~~  101 (187)
                      +.+..
T Consensus        86 ~~~~~   90 (99)
T d1whwa_          86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCCc
Confidence            87654

>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=99.91  E-value=2e-24  Score=141.04  Aligned_cols=84  Identities=29%  Similarity=0.415  Sum_probs=79.9

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      .++.++|||+|||.++++++|.++|++||+|..|.|+.+..++.++|||||+|.+.++|++||+.|++..|.|+.|.|+|
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~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            44568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 029810           96 SRRK   99 (187)
Q Consensus        96 a~~~   99 (187)
                      |+++
T Consensus        85 akp~   88 (90)
T d2cq0a1          85 AKPS   88 (90)
T ss_dssp             SSCC
T ss_pred             eeCC
Confidence            9865

>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=99.91  E-value=6.2e-24  Score=149.44  Aligned_cols=87  Identities=26%  Similarity=0.347  Sum_probs=81.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ....++|||+|||+++++++|+++|++||+|..|.|+.+..|+.++|||||+|.+.++|+.||+.||+..|+|+.|.|++
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34457899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 029810           96 SRRKRPR  102 (187)
Q Consensus        96 a~~~~~~  102 (187)
                      ++++..+
T Consensus       119 a~~~~~~  125 (139)
T d1u6fa1         119 AASGHQR  125 (139)
T ss_dssp             SSCCCCC
T ss_pred             cCCCCCC
Confidence            9876554

>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=99.91  E-value=3.2e-24  Score=137.66  Aligned_cols=80  Identities=31%  Similarity=0.428  Sum_probs=76.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccC
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR   98 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   98 (187)
                      .++|||+|||.++++++|+++|++||+|..|.|+.+..++.++|||||+|.+.++|++|++.||+..|.|+.|.|++|+|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            36899999999999999999999999999999999998999999999999999999999999999999999999999975

>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=99.91  E-value=6e-24  Score=139.53  Aligned_cols=84  Identities=29%  Similarity=0.423  Sum_probs=79.8

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ...+++|||+|||+++++++|+++|++||+|..|.|+.+..++.++|||||+|.+.++|+.||+.||+..|+|+.|.|+|
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~   83 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW   83 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 029810           96 SRRK   99 (187)
Q Consensus        96 a~~~   99 (187)
                      +...
T Consensus        84 a~~~   87 (93)
T d1h2vz_          84 DAGF   87 (93)
T ss_dssp             ESCC
T ss_pred             cCCC
Confidence            8644

>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=1.6e-24  Score=141.24  Aligned_cols=84  Identities=33%  Similarity=0.471  Sum_probs=79.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ...+|||+|||+++++++|+++|++||+|..|.|+.+..++.++|||||+|.+.++|++||+.||+..|+|+.|.|++|+
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 029810           98 RKRP  101 (187)
Q Consensus        98 ~~~~  101 (187)
                      ++..
T Consensus        84 p~~~   87 (89)
T d2cqba1          84 PMRI   87 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>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=99.91  E-value=4.2e-24  Score=137.41  Aligned_cols=80  Identities=43%  Similarity=0.580  Sum_probs=75.8

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      +++++.++|||+|||.++|+++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+.||+..|+|+.|+|
T Consensus         4 ~~p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           4 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            44566789999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.90  E-value=4.9e-24  Score=137.71  Aligned_cols=81  Identities=21%  Similarity=0.380  Sum_probs=77.8

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccCC
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK   99 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   99 (187)
                      .+|||+|||+++++++|+++|++||+|..|.|+.++.|+.++|||||+|.++++|+.|++.||+..|.|+.|.|++|.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             C
Q 029810          100 R  100 (187)
Q Consensus       100 ~  100 (187)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.90  E-value=1.8e-23  Score=139.80  Aligned_cols=85  Identities=28%  Similarity=0.422  Sum_probs=77.8

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ....++|||+|||+.+++++|+++|++||+|..|.|+.+..|+.++|||||+|.+.++|++||+.+++ .|+|+.|.|++
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~   85 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   85 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEE
Confidence            33457899999999999999999999999999999999999999999999999999999999998775 79999999999


Q ss_pred             ccCCCC
Q 029810           96 SRRKRP  101 (187)
Q Consensus        96 a~~~~~  101 (187)
                      +..+..
T Consensus        86 a~~~~~   91 (103)
T d2cqda1          86 AYLGAK   91 (103)
T ss_dssp             STTTCC
T ss_pred             cCCCCC
Confidence            986543

>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=7.5e-24  Score=135.30  Aligned_cols=77  Identities=34%  Similarity=0.475  Sum_probs=75.2

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        21 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      +|||+|||+++|+++|.++|++||+|..|.|+.+..++.++|||||+|.++++|+.||+.|++..|.|+.|+|++++
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~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.90  E-value=1.7e-23  Score=136.45  Aligned_cols=85  Identities=26%  Similarity=0.404  Sum_probs=78.0

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      .....++|||+|||+++|+++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+.  .+.|+|+.|.|+
T Consensus         4 ~~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~   81 (90)
T d2cqga1           4 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCK   81 (90)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEE
T ss_pred             CCcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEE
Confidence            345678999999999999999999999999999999999999999999999999999999999984  448999999999


Q ss_pred             eccCCCC
Q 029810           95 RSRRKRP  101 (187)
Q Consensus        95 ~a~~~~~  101 (187)
                      ++.++..
T Consensus        82 ~a~~k~~   88 (90)
T d2cqga1          82 LPNSKQS   88 (90)
T ss_dssp             CCCTTCC
T ss_pred             eCCCCCC
Confidence            9987654

>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=99.90  E-value=1.6e-23  Score=135.22  Aligned_cols=81  Identities=30%  Similarity=0.445  Sum_probs=76.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--eEEEE
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG--RYITV   93 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g--~~l~v   93 (187)
                      ...+++|||+|||.++++++|+++|++||+|..+.|+.++.++.++|||||+|.+.++|++||+.||+..+.|  ++|.|
T Consensus         3 ~~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V   82 (85)
T d1b7fa2           3 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV   82 (85)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEE
Confidence            3456789999999999999999999999999999999999999999999999999999999999999999876  78999


Q ss_pred             Eec
Q 029810           94 ERS   96 (187)
Q Consensus        94 ~~a   96 (187)
                      +||
T Consensus        83 ~~A   85 (85)
T d1b7fa2          83 RLA   85 (85)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            986

>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=99.90  E-value=2e-23  Score=134.74  Aligned_cols=79  Identities=35%  Similarity=0.549  Sum_probs=74.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--eEEEEEe
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG--RYITVER   95 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g--~~l~v~~   95 (187)
                      .+++|||+|||+++++++|+++|++||+|..+.|+.+..++.++|||||+|.+.++|++|++.||+..|.|  .+|.|+|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            45789999999999999999999999999999999999999999999999999999999999999999987  4699988


Q ss_pred             c
Q 029810           96 S   96 (187)
Q Consensus        96 a   96 (187)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.90  E-value=5.2e-23  Score=135.03  Aligned_cols=88  Identities=31%  Similarity=0.531  Sum_probs=79.8

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE
Q 029810           11 GRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY   90 (187)
Q Consensus        11 ~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~   90 (187)
                      +..+.....++|||+|||+++++++|+++|++||+|..|.|+.+..+  +++||||+|.+.++|++||+.||+..|.|+.
T Consensus         3 g~~~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~--~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~   80 (93)
T d2cq3a1           3 GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGRK   80 (93)
T ss_dssp             CCSCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT--TCCEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC--CcceeEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            44556667789999999999999999999999999999999887643  5899999999999999999999999999999


Q ss_pred             EEEEeccCCC
Q 029810           91 ITVERSRRKR  100 (187)
Q Consensus        91 l~v~~a~~~~  100 (187)
                      |.|++|+++.
T Consensus        81 l~V~~A~~r~   90 (93)
T d2cq3a1          81 IEVNNATARV   90 (93)
T ss_dssp             CEEEECCSSC
T ss_pred             EEEEecCcCC
Confidence            9999998764

>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=3.1e-23  Score=136.34  Aligned_cols=86  Identities=22%  Similarity=0.356  Sum_probs=78.9

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHHHh-CCCccCCeEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEP-RTRISRGFAFVTMDGVEDAERCIKYL-NQSVLEGRYIT   92 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~-~~~~~~g~afV~f~~~~~a~~ai~~l-~g~~i~g~~l~   92 (187)
                      .....++|||+|||.++++++|+++|++||.|..|.|+.+. .++.++|||||+|.+.++|++||..| |+..|.|+.|.
T Consensus         4 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~   83 (94)
T d2cpha1           4 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   83 (94)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEE
Confidence            34567899999999999999999999999999999998875 47899999999999999999999998 89999999999


Q ss_pred             EEeccCCC
Q 029810           93 VERSRRKR  100 (187)
Q Consensus        93 v~~a~~~~  100 (187)
                      |+||+.+.
T Consensus        84 V~~A~~~~   91 (94)
T d2cpha1          84 LEWADSEV   91 (94)
T ss_dssp             EEECCCCC
T ss_pred             EEEcCCCC
Confidence            99998764

>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=99.89  E-value=1.9e-23  Score=136.31  Aligned_cols=84  Identities=33%  Similarity=0.586  Sum_probs=79.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ...+|||+|||+++++++|+++|++||.|..+.++.+..++.++|||||+|.++++|+.||+.|++..|.|+.|.|+++.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45789999999999999999999999999999999998999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 029810           98 RKRP  101 (187)
Q Consensus        98 ~~~~  101 (187)
                      ++..
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6643

>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=99.89  E-value=5.5e-23  Score=134.10  Aligned_cols=84  Identities=26%  Similarity=0.368  Sum_probs=76.7

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      +..+.++|||+|||.++++++|+++|++||+|..|.|+.+..++  ++||||+|.+.++|+.|+..|++..|.|+.|.|.
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~   81 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   81 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44566899999999999999999999999999999999887554  7899999999999999999999999999999999


Q ss_pred             eccCCC
Q 029810           95 RSRRKR  100 (187)
Q Consensus        95 ~a~~~~  100 (187)
                      ||+++.
T Consensus        82 ~a~~~~   87 (90)
T d2cqia1          82 WATTPS   87 (90)
T ss_dssp             ECCCTT
T ss_pred             EcCCCC
Confidence            998654

>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=99.89  E-value=3.5e-23  Score=133.30  Aligned_cols=80  Identities=30%  Similarity=0.591  Sum_probs=75.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      +...+|||+|||+++++++|+++|++||.|..+.|+.+..++.++|||||+|.+.++|++||+ ++++.|+|+.|.|+.|
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEee
Confidence            345799999999999999999999999999999999999999999999999999999999998 7999999999999887


Q ss_pred             c
Q 029810           97 R   97 (187)
Q Consensus        97 ~   97 (187)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            5

>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=99.89  E-value=1.4e-23  Score=134.30  Aligned_cols=80  Identities=26%  Similarity=0.379  Sum_probs=70.0

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccC
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR   98 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   98 (187)
                      .++|||+|||+++|+++|+++|++||.|..+.++.+..++.++|||||+|.+.++|++||+.||+..|.|+.|.|++++|
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            36999999999999999999999999999888888888899999999999999999999999999999999999999976

>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=99.89  E-value=3.7e-23  Score=138.09  Aligned_cols=83  Identities=25%  Similarity=0.538  Sum_probs=78.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ..++|||+|||+++++++|+++|.+||+|..+.|+.+..++.++|||||+|.+.++|++||+ ++++.|+|+.|.|.+|.
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECc
Confidence            44799999999999999999999999999999999999999999999999999999999997 89999999999999998


Q ss_pred             CCCC
Q 029810           98 RKRP  101 (187)
Q Consensus        98 ~~~~  101 (187)
                      ++.+
T Consensus        98 ~ke~  101 (103)
T d1x4ba1          98 AREE  101 (103)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            7754

>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=99.89  E-value=2.4e-23  Score=133.80  Aligned_cols=80  Identities=25%  Similarity=0.425  Sum_probs=74.7

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCceeEE-EEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccCCC
Q 029810           22 LYVTGLSTRVTERDLEKHFSKEGKVASC-FLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRKR  100 (187)
Q Consensus        22 l~V~~Lp~~~t~~~L~~~f~~~G~i~~~-~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~~  100 (187)
                      |||+|||.++++++|+++|++||.|..+ .|+.+..+++++|||||+|.+.++|++||+.|++..|.|+.|.|++|.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            8999999999999999999999998764 788888899999999999999999999999999999999999999998765


Q ss_pred             C
Q 029810          101 P  101 (187)
Q Consensus       101 ~  101 (187)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.89  E-value=3.5e-23  Score=138.59  Aligned_cols=82  Identities=26%  Similarity=0.415  Sum_probs=78.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccC
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR   98 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   98 (187)
                      ..+|||+|||+++++++|+++|++||+|..|.|+.+..++.++|||||+|.+.++|++||+.||+..|.|+.|.|+++.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             CC
Q 029810           99 KR  100 (187)
Q Consensus        99 ~~  100 (187)
                      +.
T Consensus        88 ~~   89 (104)
T d1p1ta_          88 EK   89 (104)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.88  E-value=7.4e-23  Score=132.06  Aligned_cols=78  Identities=31%  Similarity=0.516  Sum_probs=72.5

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCC---CcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccC
Q 029810           22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTR---ISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR   98 (187)
Q Consensus        22 l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~---~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   98 (187)
                      |||+|||+++++++|+++|++||.|..|.|+.+..++   .++|||||+|.+.++|++||+.||+..|+|+.|.|++++.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            8999999999999999999999999999999887655   4589999999999999999999999999999999999864


Q ss_pred             C
Q 029810           99 K   99 (187)
Q Consensus        99 ~   99 (187)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.88  E-value=9.6e-23  Score=135.64  Aligned_cols=88  Identities=24%  Similarity=0.425  Sum_probs=79.2

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCcee--------EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCc
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVA--------SCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSV   85 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~--------~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~   85 (187)
                      ++....++|||+|||..+++++|+++|.+||.|.        .+.+..+..++.+++||||+|.+.++|++||+.||+..
T Consensus         3 ~~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~   82 (101)
T d2cpea1           3 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   82 (101)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             CCCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCE
Confidence            4456778999999999999999999999999874        46667778889999999999999999999999999999


Q ss_pred             cCCeEEEEEeccCCCC
Q 029810           86 LEGRYITVERSRRKRP  101 (187)
Q Consensus        86 i~g~~l~v~~a~~~~~  101 (187)
                      |+|+.|.|++++++..
T Consensus        83 ~~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          83 FQGSKLKVSLARKKPP   98 (101)
T ss_dssp             ETTEECEEECSSCCCC
T ss_pred             ECCEEEEEEEcCCCCC
Confidence            9999999999987644

>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=99.88  E-value=7.2e-23  Score=130.03  Aligned_cols=76  Identities=24%  Similarity=0.328  Sum_probs=72.8

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        21 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      +|||+|||+++++++|+++|++||.|..+.|+.+. ++.++|||||+|.+.++|++|++.||+..|+|+.|.|+++.
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-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999999876 78889999999999999999999999999999999999986

>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=99.88  E-value=4.5e-23  Score=134.23  Aligned_cols=81  Identities=27%  Similarity=0.503  Sum_probs=74.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccC
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRR   98 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   98 (187)
                      ..+|||+|||+++++++|+++|++||.|..+.|+.+..  .++|||||+|++.++|++||+.||+..|+|+.|.|+++++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            45899999999999999999999999999999998864  3679999999999999999999999999999999999987


Q ss_pred             CCC
Q 029810           99 KRP  101 (187)
Q Consensus        99 ~~~  101 (187)
                      +.+
T Consensus        86 ~~~   88 (89)
T d1cvja2          86 RKE   88 (89)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            654

>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=2e-23  Score=132.25  Aligned_cols=76  Identities=26%  Similarity=0.514  Sum_probs=73.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ++|||+|||+++++++|+++|++||.|..+.|+.++.|+.++|||||+|.++++|++||+ ++++.|+|+.|.|+.|
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-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            579999999999999999999999999999999999999999999999999999999998 7999999999999886

>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=99.88  E-value=2e-22  Score=133.36  Aligned_cols=86  Identities=24%  Similarity=0.394  Sum_probs=79.0

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC------CCccCC
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLN------QSVLEG   88 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~------g~~i~g   88 (187)
                      +..++++|||+|||+++++++|+++|.+||.|..+.++.+..++.++|||||+|.+.++|++||+.|+      +..|.|
T Consensus         4 ~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC
Confidence            44567899999999999999999999999999999999999999999999999999999999999987      557899


Q ss_pred             eEEEEEeccCCC
Q 029810           89 RYITVERSRRKR  100 (187)
Q Consensus        89 ~~l~v~~a~~~~  100 (187)
                      +.|.|++++++.
T Consensus        84 r~l~v~~a~~k~   95 (98)
T d1x4ha1          84 RQLKVDLAVTRD   95 (98)
T ss_dssp             CEEEEECCCCCC
T ss_pred             EEEEEEECCCCC
Confidence            999999998764

>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=99.88  E-value=3.4e-23  Score=138.13  Aligned_cols=89  Identities=31%  Similarity=0.425  Sum_probs=82.1

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      .+.+++++|||+|||.++++++|+++|.+||.|..+.++.+..++.+++||||+|.+.++|+.||+.||+..|.|+.|.|
T Consensus        13 ~~~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   92 (102)
T d2cpxa1          13 NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVI   92 (102)
T ss_dssp             CCCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEE
Confidence            34567899999999999999999999999999999988888778899999999999999999999999999999999999


Q ss_pred             EeccCCCCC
Q 029810           94 ERSRRKRPR  102 (187)
Q Consensus        94 ~~a~~~~~~  102 (187)
                      +||+++..+
T Consensus        93 ~~ak~k~~r  101 (102)
T d2cpxa1          93 EFGKNKKQR  101 (102)
T ss_dssp             EECCCCSCC
T ss_pred             EeCCCcccC
Confidence            999987654

>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=99.88  E-value=2.5e-22  Score=132.23  Aligned_cols=83  Identities=28%  Similarity=0.358  Sum_probs=74.6

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      +...++++|||+|||+++++++|+++|++||.|..+.+..+   ...++||||+|++.++|++||+.||+..|.|+.|.|
T Consensus         9 p~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V   85 (95)
T d1x4aa1           9 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV   85 (95)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            45567789999999999999999999999999999887644   345789999999999999999999999999999999


Q ss_pred             EeccCC
Q 029810           94 ERSRRK   99 (187)
Q Consensus        94 ~~a~~~   99 (187)
                      +++++.
T Consensus        86 ~~a~~~   91 (95)
T d1x4aa1          86 EFPRSG   91 (95)
T ss_dssp             ECCCCC
T ss_pred             EeccCC
Confidence            998753

>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=99.88  E-value=8.4e-23  Score=128.75  Aligned_cols=75  Identities=35%  Similarity=0.616  Sum_probs=71.4

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        21 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      +|||+|||+++++++|.++|++||+|..+.|+.+..+++++|||||+|.+.++|++||+ +++..|+|+.|.|+.|
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-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            59999999999999999999999999999999999999999999999999999999998 8999999999998654

>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=99.88  E-value=2.9e-22  Score=132.54  Aligned_cols=84  Identities=23%  Similarity=0.443  Sum_probs=74.2

Q ss_pred             CCCCCCCCCCCeEEEcCCC-CCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 029810           10 RGRTETGNPGNTLYVTGLS-TRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG   88 (187)
Q Consensus        10 ~~~~~~~~~~~~l~V~~Lp-~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g   88 (187)
                      ....++....++|||+||+ ..+++++|+++|++||.|..|.|.        ++||||+|++.++|++||+.||+..|.|
T Consensus         6 s~~~~~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g   77 (98)
T d1wf2a_           6 SGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAG   77 (98)
T ss_dssp             CCCCCCSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETT
T ss_pred             CCCCCCCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECC
Confidence            3445566777899999997 578899999999999999999884        6899999999999999999999999999


Q ss_pred             eEEEEEeccCCCC
Q 029810           89 RYITVERSRRKRP  101 (187)
Q Consensus        89 ~~l~v~~a~~~~~  101 (187)
                      +.|.|++++++..
T Consensus        78 ~~l~V~~a~~~~~   90 (98)
T d1wf2a_          78 QVLDINLAAEPKV   90 (98)
T ss_dssp             EECEEEETTSCCC
T ss_pred             EEEEEEECCCCCC
Confidence            9999999986543

>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=3.9e-23  Score=137.55  Aligned_cols=81  Identities=30%  Similarity=0.451  Sum_probs=76.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ..++|||+|||.++++++|+++|+.||+|..|.|+.+..+++++|||||+|.+.++|++||+ ||+..|.|+.|.|++++
T Consensus        17 ~~~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          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            35789999999999999999999999999999999999999999999999999999999996 99999999999999987


Q ss_pred             CC
Q 029810           98 RK   99 (187)
Q Consensus        98 ~~   99 (187)
                      ++
T Consensus        96 ~~   97 (101)
T d2cq4a1          96 AE   97 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>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=99.87  E-value=4.4e-22  Score=126.60  Aligned_cols=77  Identities=22%  Similarity=0.432  Sum_probs=73.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ..+|||+|||+++|+++|+++|++||.|..+.++.+..++.++|||||+|.+.++|++|++ |+++.|+|+.|.|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            3689999999999999999999999999999999999999999999999999999999996 8999999999999876

>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=99.87  E-value=5e-23  Score=129.68  Aligned_cols=75  Identities=23%  Similarity=0.360  Sum_probs=71.3

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        21 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      +|||+|||+++|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+ ++++.|+|+.|.|+.|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999998 6778999999999875

>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=99.87  E-value=1.7e-22  Score=130.62  Aligned_cols=81  Identities=25%  Similarity=0.404  Sum_probs=71.2

Q ss_pred             CCCeEEEcCCCCCCc-HHHHHHHhhcCCceeEEEEeec-CCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           18 PGNTLYVTGLSTRVT-ERDLEKHFSKEGKVASCFLVVE-PRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t-~~~L~~~f~~~G~i~~~~i~~~-~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ...+|||+|||++++ +++|+++|++||.|..|.|+.+ ..++.++|||||+|.+.++|++||+ ||+..|.|+.|.|++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            568999999999876 5669999999999999998764 5688899999999999999999996 999999999999999


Q ss_pred             ccCC
Q 029810           96 SRRK   99 (187)
Q Consensus        96 a~~~   99 (187)
                      ++++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9865

>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=99.87  E-value=6.7e-22  Score=132.22  Aligned_cols=87  Identities=20%  Similarity=0.373  Sum_probs=75.3

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEP-RTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~-~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .+..+.++|||+|||+++++++|+++|++|| |..+.++.+. .++.++|||||+|.+.++|++|++ ||+..|.|+.|.
T Consensus        10 ~p~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~   87 (104)
T d1wi8a_          10 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIR   87 (104)
T ss_dssp             CCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECE
T ss_pred             CCCCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEE
Confidence            3456679999999999999999999999999 6677666554 578889999999999999988775 999999999999


Q ss_pred             EEeccCCCCC
Q 029810           93 VERSRRKRPR  102 (187)
Q Consensus        93 v~~a~~~~~~  102 (187)
                      |+++.++...
T Consensus        88 V~~a~~~~~~   97 (104)
T d1wi8a_          88 VDVADQAQDK   97 (104)
T ss_dssp             EEECCCCCCC
T ss_pred             EEECCCCCCC
Confidence            9999876544

>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=99.87  E-value=6.7e-22  Score=134.32  Aligned_cols=82  Identities=21%  Similarity=0.288  Sum_probs=74.5

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      +++.+++|||+|||.++++++|.++|++||.|..|.|..+   +.++|||||+|.+.++|+.||+.|||..|.|+.|.|.
T Consensus         3 pp~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~   79 (114)
T d2f9da1           3 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVL   79 (114)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3456789999999999999999999999999999998754   4558999999999999999999999999999999999


Q ss_pred             eccCC
Q 029810           95 RSRRK   99 (187)
Q Consensus        95 ~a~~~   99 (187)
                      ++...
T Consensus        80 ~a~~~   84 (114)
T d2f9da1          80 YYNAN   84 (114)
T ss_dssp             ECCHH
T ss_pred             EcCCC
Confidence            98653

>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=99.86  E-value=1.5e-21  Score=130.55  Aligned_cols=93  Identities=24%  Similarity=0.288  Sum_probs=82.5

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe
Q 029810           10 RGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGR   89 (187)
Q Consensus        10 ~~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~   89 (187)
                      .+..++.....+|||+|||+++|+++|+++|..+|.|..+.++.+..++.++|||||+|.++++|++|++ +|+..|.++
T Consensus         6 ~~~~~~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR   84 (104)
T d1wg5a_           6 SGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHR   84 (104)
T ss_dssp             CCCCSSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSS
T ss_pred             CCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcce
Confidence            4455566677789999999999999999999999999887777777889999999999999999999997 999999999


Q ss_pred             EEEEEeccCCCCCC
Q 029810           90 YITVERSRRKRPRT  103 (187)
Q Consensus        90 ~l~v~~a~~~~~~~  103 (187)
                      .|.|.++.+.+...
T Consensus        85 ~i~V~~~~~~~~~~   98 (104)
T d1wg5a_          85 YIEIFKSSRAEVRT   98 (104)
T ss_dssp             CCEEEEECTTTSCC
T ss_pred             EEEEEECCHHHhcc
Confidence            99999998776544

>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=99.86  E-value=8.3e-22  Score=126.50  Aligned_cols=79  Identities=16%  Similarity=0.191  Sum_probs=71.3

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc-CCeEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVL-EGRYIT   92 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i-~g~~l~   92 (187)
                      .+.+|+++|||+|||.++++++|.++|++||.|..|.++.+.     ++||||+|.+.++|++|++.|||..| +++.|.
T Consensus         3 ~~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~   77 (83)
T d2b0ga1           3 TEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMK   77 (83)
T ss_dssp             CCCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEE
Confidence            345678999999999999999999999999999999997542     67999999999999999999999988 468999


Q ss_pred             EEecc
Q 029810           93 VERSR   97 (187)
Q Consensus        93 v~~a~   97 (187)
                      |.||+
T Consensus        78 v~~ak   82 (83)
T d2b0ga1          78 ITFAK   82 (83)
T ss_dssp             EEECC
T ss_pred             EEEec
Confidence            99986

>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=3e-22  Score=126.08  Aligned_cols=75  Identities=25%  Similarity=0.500  Sum_probs=72.0

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           21 TLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        21 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      +|||+|||.++|+++|+++|++||.|..+.++.+..++.+++||||+|.+.++|++||+ ||++.|+|+.|+|++|
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-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999997 9999999999999876

>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=99.86  E-value=1.1e-21  Score=129.30  Aligned_cols=78  Identities=22%  Similarity=0.410  Sum_probs=72.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      +..++|||+|||..+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|++||..|++..|.|+.|+|.|+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~a   89 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   89 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45689999999999999999999999999999999865      679999999999999999999999999999999999


Q ss_pred             cCCC
Q 029810           97 RRKR  100 (187)
Q Consensus        97 ~~~~  100 (187)
                      ++++
T Consensus        90 k~~p   93 (96)
T d1x4ga1          90 KESP   93 (96)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.85  E-value=4.9e-21  Score=123.62  Aligned_cols=80  Identities=30%  Similarity=0.327  Sum_probs=71.8

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ....++|||+|||+++++++|+++|++||.|..+.+..      +++||||+|.+.++|+.||..||+..|.|+.|.|+|
T Consensus         5 ~~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~   78 (86)
T d2cpda1           5 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTL   78 (86)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             ccCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            44568999999999999999999999999988877743      367999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 029810           96 SRRKRP  101 (187)
Q Consensus        96 a~~~~~  101 (187)
                      ++|+..
T Consensus        79 akP~~~   84 (86)
T d2cpda1          79 AKPVDK   84 (86)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            987643

>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=99.85  E-value=2.1e-21  Score=129.09  Aligned_cols=83  Identities=22%  Similarity=0.332  Sum_probs=75.2

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      .....++|||+|||.++++++|+++|++||.|..+.+..+. ++.++|||||+|.+.++|++||+.|||..|.|++|.|.
T Consensus        14 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~   92 (101)
T d1x5oa1          14 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   92 (101)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccC
Confidence            34456899999999999999999999999999999888774 78889999999999999999999999999999998887


Q ss_pred             eccC
Q 029810           95 RSRR   98 (187)
Q Consensus        95 ~a~~   98 (187)
                      +++|
T Consensus        93 ~~~P   96 (101)
T d1x5oa1          93 PTEP   96 (101)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            7664

>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=99.85  E-value=9.8e-22  Score=125.30  Aligned_cols=77  Identities=31%  Similarity=0.431  Sum_probs=69.4

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC-ccCCeEEEEEeccC
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS-VLEGRYITVERSRR   98 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~-~i~g~~l~v~~a~~   98 (187)
                      ++|||+|||.++++++|+++|++||.|..+.+...      +|||||+|.+.++|++||+.|||. .|.|+.|.|+++.+
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 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            47999999999999999999999999887766643      679999999999999999999986 69999999999998


Q ss_pred             CCCC
Q 029810           99 KRPR  102 (187)
Q Consensus        99 ~~~~  102 (187)
                      +..+
T Consensus        76 k~~r   79 (80)
T d2cqha1          76 KKLR   79 (80)
T ss_dssp             CCCC
T ss_pred             cCcC
Confidence            7654

>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=99.85  E-value=2.5e-21  Score=123.11  Aligned_cols=77  Identities=31%  Similarity=0.414  Sum_probs=70.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      +..+++|||+||+  +|+++|+++|++||.|..|.+..+      ++||||+|.+.++|+.|++.||+..|.|+.|.|+|
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   73 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   73 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3467899999995  899999999999999999998744      57999999999999999999999999999999999


Q ss_pred             ccCCC
Q 029810           96 SRRKR  100 (187)
Q Consensus        96 a~~~~  100 (187)
                      +++++
T Consensus        74 a~~~P   78 (79)
T d2bz2a1          74 ARKQP   78 (79)
T ss_dssp             CCSSC
T ss_pred             ecCCC
Confidence            98664

>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=99.85  E-value=2.8e-21  Score=124.77  Aligned_cols=77  Identities=26%  Similarity=0.434  Sum_probs=71.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ..++|||+|||.++++++|+++|++||+|..|.+..+      ++||||+|++.++|++|++.||+..|.|+.|.|+||.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            4578999999999999999999999999999999754      5799999999999999999999999999999999998


Q ss_pred             CCC
Q 029810           98 RKR  100 (187)
Q Consensus        98 ~~~  100 (187)
                      ...
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            653

>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=99.85  E-value=1.7e-21  Score=125.80  Aligned_cols=80  Identities=13%  Similarity=0.161  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      +..++|||+|||++++++||+++|..||.|....++....++.++|+|||+|.+.++|++||+.||+..|.|+.|+|+++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            44578999999999999999999999999877544455568999999999999999999999999999999999999875

>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=99.85  E-value=4.2e-21  Score=129.28  Aligned_cols=78  Identities=26%  Similarity=0.327  Sum_probs=71.3

Q ss_pred             CCeEEEcCCCC-CCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           19 GNTLYVTGLST-RVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        19 ~~~l~V~~Lp~-~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      +++|||+||++ .+++++|.++|++||+|..|.|+.+.     +|||||+|++.++|++||+.|++..|.|+.|.|++++
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~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            57999999965 69999999999999999999998764     6899999999999999999999999999999999987


Q ss_pred             CCCC
Q 029810           98 RKRP  101 (187)
Q Consensus        98 ~~~~  101 (187)
                      ....
T Consensus        77 ~~~~   80 (109)
T d2adca1          77 HQNV   80 (109)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            5543

>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=99.85  E-value=1.7e-22  Score=132.01  Aligned_cols=83  Identities=20%  Similarity=0.302  Sum_probs=74.4

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           15 TGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        15 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      ++....+|||+|||+.+++++|+++|++||.|..+.|+.+ .++.++|||||+|.+.++|++||+ ||+..|.|+.|.|+
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~   86 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEE
Confidence            3445679999999999999999999999999988877644 578889999999999999999996 99999999999999


Q ss_pred             eccCC
Q 029810           95 RSRRK   99 (187)
Q Consensus        95 ~a~~~   99 (187)
                      +|+.+
T Consensus        87 ~ak~k   91 (91)
T d1fjeb1          87 KPKGR   91 (91)
T ss_dssp             CCCCS
T ss_pred             ecCCC
Confidence            99753

>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=99.84  E-value=3e-21  Score=127.21  Aligned_cols=84  Identities=20%  Similarity=0.308  Sum_probs=74.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEE
Q 029810           13 TETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYIT   92 (187)
Q Consensus        13 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~   92 (187)
                      .....+.++|||+|||.++++++|+++|.+||.|..+..     ++.+++||||+|.+.++|++||+.||+..|.|+.|.
T Consensus        10 ~~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~   84 (96)
T d1fjca_          10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVS   84 (96)
T ss_dssp             TSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEE
T ss_pred             cCcCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEE
Confidence            344556789999999999999999999999998876543     467799999999999999999999999999999999


Q ss_pred             EEeccCCCC
Q 029810           93 VERSRRKRP  101 (187)
Q Consensus        93 v~~a~~~~~  101 (187)
                      |.|+.++..
T Consensus        85 V~~a~~k~~   93 (96)
T d1fjca_          85 LYYTGEKGG   93 (96)
T ss_dssp             EEECSSSCC
T ss_pred             EEEeCCCCC
Confidence            999987643

>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=99.84  E-value=6.6e-21  Score=126.89  Aligned_cols=88  Identities=22%  Similarity=0.292  Sum_probs=76.2

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE
Q 029810           11 GRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY   90 (187)
Q Consensus        11 ~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~   90 (187)
                      +.......+.+|||.|||+++|+++|+++|..|+. ..|.++.+. ++..+|||||+|.++++|++||+ ||+..|.|+.
T Consensus         7 ~~~~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~   83 (102)
T d1weza_           7 GSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRY   83 (102)
T ss_dssp             CSSCCCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSC
T ss_pred             CCCCcCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEE
Confidence            34455667789999999999999999999999974 567777665 57889999999999999999997 8999999999


Q ss_pred             EEEEeccCCCC
Q 029810           91 ITVERSRRKRP  101 (187)
Q Consensus        91 l~v~~a~~~~~  101 (187)
                      |.|.++.....
T Consensus        84 I~V~~s~~~~~   94 (102)
T d1weza_          84 VELFLNSTAGT   94 (102)
T ss_dssp             CEEEEECCCCC
T ss_pred             EEEEEcCCCCC
Confidence            99999886644

>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=99.84  E-value=4.7e-21  Score=126.64  Aligned_cols=82  Identities=21%  Similarity=0.235  Sum_probs=73.7

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      +......+|||+|||+.+++++|+++|++||+|..+.|..       +|||||+|.+.++|++||+.||+..|.|+.|.|
T Consensus        10 ~~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v   82 (98)
T d1wg4a_          10 PTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGET   82 (98)
T ss_dssp             CCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEE
Confidence            4445677999999999999999999999999999998863       479999999999999999999999999999999


Q ss_pred             EeccCCCCC
Q 029810           94 ERSRRKRPR  102 (187)
Q Consensus        94 ~~a~~~~~~  102 (187)
                      .+++.+..+
T Consensus        83 ~~~~~~~~~   91 (98)
T d1wg4a_          83 SYIRVYPER   91 (98)
T ss_dssp             EEEEEECCC
T ss_pred             EEEecCCCC
Confidence            999876544

>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=99.84  E-value=7.3e-21  Score=122.53  Aligned_cols=78  Identities=17%  Similarity=0.308  Sum_probs=72.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ...+|||+|||.++|+++|.++|+.||.|..|.|..+. ++.++|||||+|.++++|++||+ +++..|.|+.|.|.++.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            35799999999999999999999999999999998765 78899999999999999999997 89999999999999864

>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=99.84  E-value=6.8e-22  Score=128.02  Aligned_cols=75  Identities=21%  Similarity=0.244  Sum_probs=68.5

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccCC
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK   99 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   99 (187)
                      ++|||+|||+++++++|+++|++||+|..+.|..       .|||||+|++.++|++||+.||+..|.|+.|.|.+++.+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc-------cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            4799999999999999999999999999998864       369999999999999999999999999999999888755


Q ss_pred             CC
Q 029810          100 RP  101 (187)
Q Consensus       100 ~~  101 (187)
                      ..
T Consensus        74 ~~   75 (87)
T d3begb1          74 VD   75 (87)
T ss_dssp             EC
T ss_pred             cC
Confidence            43

>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=99.84  E-value=6.9e-21  Score=123.45  Aligned_cols=79  Identities=29%  Similarity=0.424  Sum_probs=70.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc-CCeEEEEEe
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVL-EGRYITVER   95 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i-~g~~l~v~~   95 (187)
                      +++++|||+|||.++++++|+++|++||.|..+.+...    ..++||||+|++.++|++|+..||+..| +|+.|.|+|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            56789999999999999999999999999988877643    3467999999999999999999999988 589999999


Q ss_pred             ccCC
Q 029810           96 SRRK   99 (187)
Q Consensus        96 a~~~   99 (187)
                      +++.
T Consensus        84 sk~~   87 (88)
T d2adca2          84 SKST   87 (88)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            9753

>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=99.84  E-value=2e-21  Score=126.01  Aligned_cols=79  Identities=23%  Similarity=0.356  Sum_probs=69.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           17 NPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ...++|||+|||+++++++|+++|++||.|..|.+..     .+++||||+|++.++|++||.  +++.|+|+.|.|+++
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            3568999999999999999999999999999997753     347899999999999999985  778999999999999


Q ss_pred             cCCCCC
Q 029810           97 RRKRPR  102 (187)
Q Consensus        97 ~~~~~~  102 (187)
                      +++...
T Consensus        76 ~~k~~~   81 (88)
T d1wf0a_          76 EPKHNS   81 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.84  E-value=9.8e-21  Score=122.71  Aligned_cols=77  Identities=17%  Similarity=0.288  Sum_probs=66.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ..++|||+|||++++++||+++|.+|| +..+.+      +..++||||+|.+.++|++||+.||+..|.|+.|.|++++
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            457899999999999999999999999 233333      2347899999999999999999999999999999999997


Q ss_pred             CCCC
Q 029810           98 RKRP  101 (187)
Q Consensus        98 ~~~~  101 (187)
                      .+..
T Consensus        77 ~~~~   80 (88)
T d1wg1a_          77 TDAL   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6544

>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=99.83  E-value=5.3e-21  Score=125.98  Aligned_cols=85  Identities=19%  Similarity=0.274  Sum_probs=74.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCc-eeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHHHhCCC--ccCCeEEEEE
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGK-VASCFLVVEP-RTRISRGFAFVTMDGVEDAERCIKYLNQS--VLEGRYITVE   94 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~-i~~~~i~~~~-~~~~~~g~afV~f~~~~~a~~ai~~l~g~--~i~g~~l~v~   94 (187)
                      +++|||+|||.++++++|+++|++||+ |..+.|+.+. .++.++|||||+|.+.++|+.||+.|++.  .+.|+.|.|+
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            468999999999999999999999996 8889988775 46888999999999999999999999754  5679999999


Q ss_pred             eccCCCCCC
Q 029810           95 RSRRKRPRT  103 (187)
Q Consensus        95 ~a~~~~~~~  103 (187)
                      ||+++....
T Consensus        81 ~A~p~~~~~   89 (96)
T d2disa1          81 WAEPEIDVD   89 (96)
T ss_dssp             ESCSSCSTT
T ss_pred             EcCCCCCCC
Confidence            998776543

>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=99.83  E-value=5.9e-21  Score=128.92  Aligned_cols=77  Identities=14%  Similarity=0.141  Sum_probs=70.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ..++|||+|||+++++++|+++|++||+|..|.|..      .++||||+|.+.++|++||+.||+..|.|+.|.|+|+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            347999999999999999999999999999998843      36899999999999999999999999999999999987


Q ss_pred             CCC
Q 029810           98 RKR  100 (187)
Q Consensus        98 ~~~  100 (187)
                      ...
T Consensus        83 ~~~   85 (111)
T d1whxa_          83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            554

>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=99.83  E-value=1e-20  Score=119.03  Aligned_cols=74  Identities=18%  Similarity=0.183  Sum_probs=68.4

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ++|||+|||+++++++|+++|..||.|..|.|+.+....  .+||||+|+++++|++||. ++++.|+|+.|.|+.+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN--FRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS--SEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc--ceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            589999999999999999999999999999999887543  5799999999999999996 8999999999999875

>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=3.9e-21  Score=124.87  Aligned_cols=77  Identities=30%  Similarity=0.424  Sum_probs=69.7

Q ss_pred             CCCeEEEcCCCCCCcHHHH---HHHhhcCCceeEEEEeecCCCCCc---ceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           18 PGNTLYVTGLSTRVTERDL---EKHFSKEGKVASCFLVVEPRTRIS---RGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L---~~~f~~~G~i~~~~i~~~~~~~~~---~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ..++|||+|||+++++++|   .++|++||+|..|.|+.++.++..   .+||||+|++.++|++||+.|||..|.|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            4568999999999999999   778999999999999988766544   4899999999999999999999999999999


Q ss_pred             EEE
Q 029810           92 TVE   94 (187)
Q Consensus        92 ~v~   94 (187)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            874

>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=99.83  E-value=1.5e-20  Score=124.02  Aligned_cols=79  Identities=22%  Similarity=0.384  Sum_probs=71.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--eEEEE
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEG--RYITV   93 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g--~~l~v   93 (187)
                      ..+.++|||+|||.++++++|+++|++||+|..|.+..+      ++||||+|.+.++|++|++.||+..|.|  ..|.|
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v   87 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEE
Confidence            456799999999999999999999999999999998754      5799999999999999999999999976  48999


Q ss_pred             EeccCCC
Q 029810           94 ERSRRKR  100 (187)
Q Consensus        94 ~~a~~~~  100 (187)
                      +|+++.+
T Consensus        88 ~~ak~~~   94 (97)
T d1whya_          88 DFAKSGP   94 (97)
T ss_dssp             EECCCCC
T ss_pred             EeCCCCC
Confidence            9998643

>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=99.83  E-value=2.3e-21  Score=121.11  Aligned_cols=70  Identities=27%  Similarity=0.476  Sum_probs=67.7

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        22 l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      |||+|||.++++++|.++|++||.|..+.++.+..++.++|||||+|.+.++|++||+.|||..|.|+.|
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~   70 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   70 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEC
Confidence            7999999999999999999999999999999999999999999999999999999999999999999875

>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=99.83  E-value=6.3e-21  Score=124.42  Aligned_cols=80  Identities=20%  Similarity=0.417  Sum_probs=71.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHH----HhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           18 PGNTLYVTGLSTRVTERDLEK----HFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~----~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      |+++|||+|||+.+++++|++    +|++||+|..|.+..   ++.++|||||+|++.++|++|++.||+..|.|+.|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            578999999999999998864    589999999988754   3556899999999999999999999999999999999


Q ss_pred             EeccCCC
Q 029810           94 ERSRRKR  100 (187)
Q Consensus        94 ~~a~~~~  100 (187)
                      .||+++.
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9998653

>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=99.83  E-value=9.5e-20  Score=121.58  Aligned_cols=88  Identities=20%  Similarity=0.337  Sum_probs=75.9

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC--CCccC
Q 029810           10 RGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLN--QSVLE   87 (187)
Q Consensus        10 ~~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~--g~~i~   87 (187)
                      .+......++.+|||+|||..+++++|.++|++||.|..+.|..+      +++|||+|++.++|+.||..|+  +..|.
T Consensus         6 ~g~~~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~   79 (104)
T d1wexa_           6 SGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIA   79 (104)
T ss_dssp             CCSCCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSS
T ss_pred             CCCCCcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEe
Confidence            344556678899999999999999999999999999999988643      6799999999999999999874  56789


Q ss_pred             CeEEEEEeccCCCCCC
Q 029810           88 GRYITVERSRRKRPRT  103 (187)
Q Consensus        88 g~~l~v~~a~~~~~~~  103 (187)
                      |++|.|.|++.+....
T Consensus        80 g~~l~v~~s~~~~~~~   95 (104)
T d1wexa_          80 GQQAFFNYSTSKRITR   95 (104)
T ss_dssp             SSBCEEEECSSSSCCC
T ss_pred             eEEEEEEEcCCCccCC
Confidence            9999999998765443

>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=99.83  E-value=4.6e-20  Score=119.50  Aligned_cols=81  Identities=23%  Similarity=0.292  Sum_probs=72.6

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh--CCCccCCeEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL--NQSVLEGRYI   91 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l--~g~~i~g~~l   91 (187)
                      .+.+|+.+|||+|||.++++++|+++|++||.|..+.+..+      ++||||+|++.++|++|++.+  ++..|.|+.|
T Consensus         3 ~~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l   76 (88)
T d2cq1a1           3 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI   76 (88)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEE
Confidence            35678999999999999999999999999999999988754      569999999999999999866  4678999999


Q ss_pred             EEEeccCCC
Q 029810           92 TVERSRRKR  100 (187)
Q Consensus        92 ~v~~a~~~~  100 (187)
                      .|.|++.+.
T Consensus        77 ~v~~sk~~~   85 (88)
T d2cq1a1          77 YIQYSNHKE   85 (88)
T ss_dssp             EEEECSCSS
T ss_pred             EEEECCCCC
Confidence            999998654

>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=99.81  E-value=7.2e-20  Score=123.00  Aligned_cols=81  Identities=19%  Similarity=0.123  Sum_probs=72.2

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc--CCeEEEE
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVL--EGRYITV   93 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i--~g~~l~v   93 (187)
                      ..+..+|||+|||+.+|+++|+++|++||.|..|.|+.++    .+|||||+|++.++|+.||..||+..|  .+..|.|
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v   79 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI   79 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEE
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEE
Confidence            3456789999999999999999999999999999998764    378999999999999999999999988  5778999


Q ss_pred             EeccCCC
Q 029810           94 ERSRRKR  100 (187)
Q Consensus        94 ~~a~~~~  100 (187)
                      .+++++.
T Consensus        80 ~~s~~~~   86 (108)
T d2adba1          80 DFSKLTS   86 (108)
T ss_dssp             EECSSCS
T ss_pred             EecCCcc
Confidence            9987654

>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=99.81  E-value=2.6e-20  Score=124.16  Aligned_cols=82  Identities=17%  Similarity=0.170  Sum_probs=73.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEe
Q 029810           16 GNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVER   95 (187)
Q Consensus        16 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   95 (187)
                      ....++|||+|||+++++++|.++|..||.|..+.++....++.++|||||+|.+.++|++||+ ||+..|+|+.|.|.+
T Consensus         5 ~~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~   83 (103)
T d2cpya1           5 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHV   83 (103)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEE
Confidence            3455789999999999999999999999998876566666689999999999999999999997 999999999999998


Q ss_pred             ccC
Q 029810           96 SRR   98 (187)
Q Consensus        96 a~~   98 (187)
                      +..
T Consensus        84 ~~~   86 (103)
T d2cpya1          84 VTL   86 (103)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            764

>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=99.80  E-value=2e-19  Score=113.00  Aligned_cols=71  Identities=30%  Similarity=0.442  Sum_probs=63.5

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEeccCC
Q 029810           22 LYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSRRK   99 (187)
Q Consensus        22 l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   99 (187)
                      |||+|||.++++++|+++|.+|| +..+.+      +.+++||||+|.+.++|++|+..||+..|.|+.|.|++++..
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------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 444444      234789999999999999999999999999999999999754

>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=99.79  E-value=7.5e-20  Score=123.69  Aligned_cols=84  Identities=17%  Similarity=0.281  Sum_probs=75.6

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      .+.....+|||+|||+++|+++|.++|+.||.|..+.++.+..++.++|||||+|.+.++|++|++ ||+..|+|+.|.|
T Consensus        13 ~~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V   91 (112)
T d1wela1          13 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQV   91 (112)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEE
T ss_pred             CCCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEE
Confidence            345567899999999999999999999999999877677777789999999999999999999997 9999999999999


Q ss_pred             EeccC
Q 029810           94 ERSRR   98 (187)
Q Consensus        94 ~~a~~   98 (187)
                      ..+..
T Consensus        92 ~~~~~   96 (112)
T d1wela1          92 HPITK   96 (112)
T ss_dssp             EEECH
T ss_pred             EEcCh
Confidence            88754

>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=99.78  E-value=3.2e-19  Score=117.89  Aligned_cols=80  Identities=20%  Similarity=0.309  Sum_probs=70.6

Q ss_pred             CCCCCCCeEEEcCCCCC-CcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH--HhCCCccCCeE
Q 029810           14 ETGNPGNTLYVTGLSTR-VTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIK--YLNQSVLEGRY   90 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~-~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~--~l~g~~i~g~~   90 (187)
                      +...++++|||+|||.+ +|+++|.++|++||.|..|.|+.+      +++|||+|.+.++|+.||+  .+++..|.|+.
T Consensus        13 ~~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~   86 (99)
T d1x4fa1          13 QKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRC   86 (99)
T ss_dssp             CSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSC
T ss_pred             cCCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEE
Confidence            34566789999999985 899999999999999999998754      5799999999999999998  46788999999


Q ss_pred             EEEEeccCC
Q 029810           91 ITVERSRRK   99 (187)
Q Consensus        91 l~v~~a~~~   99 (187)
                      |.|.+++.+
T Consensus        87 l~V~~s~~~   95 (99)
T d1x4fa1          87 VKVDLSEKY   95 (99)
T ss_dssp             CEEEEECSC
T ss_pred             EEEEEcCCc
Confidence            999999754

>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=99.78  E-value=4.5e-19  Score=114.93  Aligned_cols=80  Identities=15%  Similarity=0.232  Sum_probs=70.6

Q ss_pred             CCCCCCCeEEEcCCCCC-CcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh--CCCccCCeE
Q 029810           14 ETGNPGNTLYVTGLSTR-VTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYL--NQSVLEGRY   90 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~-~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l--~g~~i~g~~   90 (187)
                      ...++..+|||+|||.. +|++||.++|++||+|..|.|+.+      +++|||+|++.++|+.|++.|  ++..|.|++
T Consensus         3 ~~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~   76 (89)
T d1x4da1           3 GRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKP   76 (89)
T ss_dssp             CCCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEE
T ss_pred             CCCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCce
Confidence            34567899999999985 899999999999999999999755      458999999999999999966  567899999


Q ss_pred             EEEEeccCC
Q 029810           91 ITVERSRRK   99 (187)
Q Consensus        91 l~v~~a~~~   99 (187)
                      |.|.||+..
T Consensus        77 l~V~~s~~~   85 (89)
T d1x4da1          77 VRVHLSQKY   85 (89)
T ss_dssp             CEEEEECCC
T ss_pred             EEEEECCCc
Confidence            999999754

>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=99.76  E-value=3.1e-18  Score=124.74  Aligned_cols=86  Identities=21%  Similarity=0.378  Sum_probs=79.5

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEE
Q 029810           14 ETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITV   93 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v   93 (187)
                      ......++|||+|||..+++++|.++|..||.|..+.|+.+..++.++|||||+|.+.++|++||+ ++++.|+|+.|.|
T Consensus        92 ~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V  170 (183)
T d1u1qa_          92 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEV  170 (183)
T ss_dssp             TTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEE
T ss_pred             ccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEE
Confidence            345567899999999999999999999999999999999999999999999999999999999998 7889999999999


Q ss_pred             EeccCCC
Q 029810           94 ERSRRKR  100 (187)
Q Consensus        94 ~~a~~~~  100 (187)
                      .+|.++.
T Consensus       171 ~~A~~k~  177 (183)
T d1u1qa_         171 RKALSKQ  177 (183)
T ss_dssp             EECCCHH
T ss_pred             EecCCcc
Confidence            9987654

>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=9.7e-19  Score=116.50  Aligned_cols=79  Identities=10%  Similarity=0.028  Sum_probs=69.6

Q ss_pred             CCCCeEEEcCCCCCC-c----HHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEE
Q 029810           17 NPGNTLYVTGLSTRV-T----ERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYI   91 (187)
Q Consensus        17 ~~~~~l~V~~Lp~~~-t----~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l   91 (187)
                      ...++|||+||+..+ +    +++|+++|++||.|+.+.++..      ++||||+|.+.++|++||..|||..|.|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            356899999999875 3    3569999999999999998743      5699999999999999999999999999999


Q ss_pred             EEEeccCCCC
Q 029810           92 TVERSRRKRP  101 (187)
Q Consensus        92 ~v~~a~~~~~  101 (187)
                      .|.|++++..
T Consensus        77 ~v~~a~~~~~   86 (104)
T d1weya_          77 KLYFAQTLHI   86 (104)
T ss_dssp             EEECCCCSSC
T ss_pred             EEeecccCCC
Confidence            9999986654

>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=99.72  E-value=9.3e-20  Score=118.50  Aligned_cols=77  Identities=16%  Similarity=0.406  Sum_probs=66.9

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEe-----ecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEE
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLV-----VEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVE   94 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~-----~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~   94 (187)
                      .+|||+|||.++++++|+++|++||.|..+.+.     .+..++.+++||||+|.+.++|++|++ ||+..|.|+.|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            589999999999999999999999987665442     345567789999999999999999996 99999999999997


Q ss_pred             ecc
Q 029810           95 RSR   97 (187)
Q Consensus        95 ~a~   97 (187)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            544

>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=99.68  E-value=4.1e-18  Score=113.41  Aligned_cols=76  Identities=21%  Similarity=0.176  Sum_probs=69.8

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEec
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      +.++|.+++.++++++|+++|++||+|..|.|+.+ .+++++|||||+|.+.++|++|+..|||..|+|+.|.|+++
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 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            35777888888999999999999999999999765 57899999999999999999999999999999999999985

>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=99.67  E-value=6e-17  Score=107.11  Aligned_cols=67  Identities=19%  Similarity=0.286  Sum_probs=59.8

Q ss_pred             CCCCCCCeEEEcC--CCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc
Q 029810           14 ETGNPGNTLYVTG--LSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVL   86 (187)
Q Consensus        14 ~~~~~~~~l~V~~--Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i   86 (187)
                      ....++.+|||.|  ||..+|+++|+++|++||.|..|.++.+      ++||||+|.+.++|++|+..|||..|
T Consensus        13 ~~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CCSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             cCCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            4456778999955  9999999999999999999999988754      56999999999999999999999877

>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=99.65  E-value=1.5e-16  Score=107.35  Aligned_cols=72  Identities=18%  Similarity=0.109  Sum_probs=61.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCH-HHHHHHHHHhCCCccCCeEEEEEec
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGV-EDAERCIKYLNQSVLEGRYITVERS   96 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~-~~a~~ai~~l~g~~i~g~~l~v~~a   96 (187)
                      ...+||+|||..+|+++|+++|++||+|..|.|+.+      ++||||.|.+. ++|.+|+..|++..|.+..+.|.++
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            445699999999999999999999999999999754      67999999985 7899999999998777665555554

>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=99.63  E-value=4.5e-16  Score=113.04  Aligned_cols=81  Identities=30%  Similarity=0.590  Sum_probs=72.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           18 PGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        18 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      ..++|||+|||+++|+++|.++|++||.|..+.|+.+..++.++|||||+|.+.++|++|+. +++..+....+.+....
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhh
Confidence            34799999999999999999999999999999999999999999999999999999999999 56677888888887765


Q ss_pred             CC
Q 029810           98 RK   99 (187)
Q Consensus        98 ~~   99 (187)
                      +.
T Consensus        84 ~~   85 (183)
T d1u1qa_          84 SR   85 (183)
T ss_dssp             CT
T ss_pred             hc
Confidence            44

>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=99.61  E-value=2.2e-15  Score=99.07  Aligned_cols=82  Identities=22%  Similarity=0.306  Sum_probs=69.3

Q ss_pred             CCCCCCeEEEcCC--CCCCc---------HHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q 029810           15 TGNPGNTLYVTGL--STRVT---------ERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQ   83 (187)
Q Consensus        15 ~~~~~~~l~V~~L--p~~~t---------~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g   83 (187)
                      ......+|+|.||  |.++.         +++|.+.|++||.|..|.+..+.    .+|+|||+|+++++|++|+..|||
T Consensus         4 ~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~----~~G~~fV~f~~~e~A~~A~~~lng   79 (99)
T d2dita1           4 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLDG   79 (99)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC----TTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC----CccEEEEEECCHHHHHHHHHHhCC
Confidence            3456789999999  54432         36799999999999999887543    468999999999999999999999


Q ss_pred             CccCCeEEEEEeccCCC
Q 029810           84 SVLEGRYITVERSRRKR  100 (187)
Q Consensus        84 ~~i~g~~l~v~~a~~~~  100 (187)
                      ..|+|+.|.|+++.++.
T Consensus        80 ~~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          80 RWFGGRQITAQAWDGTT   96 (99)
T ss_dssp             CEETTEECEEEECCSCC
T ss_pred             cEECCEEEEEEEeCCcC
Confidence            99999999999987553

>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=99.57  E-value=2.2e-15  Score=95.37  Aligned_cols=72  Identities=11%  Similarity=0.174  Sum_probs=60.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeE-EEEEecc
Q 029810           19 GNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRY-ITVERSR   97 (187)
Q Consensus        19 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~-l~v~~a~   97 (187)
                      .+.|+|.|||++++++.| ++|++||+|.++.+..      .++||||+|.++++|++||+ +||..|+|.. |.|..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            467999999999987655 5799999999998743      36899999999999999997 9999999974 5687765


Q ss_pred             C
Q 029810           98 R   98 (187)
Q Consensus        98 ~   98 (187)
                      .
T Consensus        76 ~   76 (81)
T d1wwha1          76 D   76 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.55  E-value=5.8e-15  Score=97.91  Aligned_cols=82  Identities=18%  Similarity=0.220  Sum_probs=69.1

Q ss_pred             CCCCeEEEcCC--CCCC--------cHHHHHHHhhcCCceeEEEEeecCCC--CCcceEEEEEecCHHHHHHHHHHhCCC
Q 029810           17 NPGNTLYVTGL--STRV--------TERDLEKHFSKEGKVASCFLVVEPRT--RISRGFAFVTMDGVEDAERCIKYLNQS   84 (187)
Q Consensus        17 ~~~~~l~V~~L--p~~~--------t~~~L~~~f~~~G~i~~~~i~~~~~~--~~~~g~afV~f~~~~~a~~ai~~l~g~   84 (187)
                      .|+.+|.|.||  +.++        ..+||++.|++||.|..|.|+.+..+  ....|++||+|.+.++|.+|+..|||.
T Consensus         2 ~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_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            46889999999  4443        23679999999999999999876543  234589999999999999999999999


Q ss_pred             ccCCeEEEEEeccC
Q 029810           85 VLEGRYITVERSRR   98 (187)
Q Consensus        85 ~i~g~~l~v~~a~~   98 (187)
                      .|+|+.|.|.++..
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            99999999999763

>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=98.40  E-value=5.2e-07  Score=56.12  Aligned_cols=74  Identities=16%  Similarity=0.194  Sum_probs=58.8

Q ss_pred             CCCCCCCeEEEcCCCCCCcH---------HHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC
Q 029810           14 ETGNPGNTLYVTGLSTRVTE---------RDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQS   84 (187)
Q Consensus        14 ~~~~~~~~l~V~~Lp~~~t~---------~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~   84 (187)
                      -..++.-||.|.=+.+...+         .+|.+.|..||+|.-|.++.+        -.+|+|.+-+.|.+|+. +++.
T Consensus        10 ~qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~   80 (95)
T d1ufwa_          10 FQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGM   80 (95)
T ss_dssp             CCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGS
T ss_pred             ccCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCe
Confidence            34556677777544333222         468888999999999998854        69999999999999999 9999


Q ss_pred             ccCCeEEEEEec
Q 029810           85 VLEGRYITVERS   96 (187)
Q Consensus        85 ~i~g~~l~v~~a   96 (187)
                      +|.|+.|+|...
T Consensus        81 ~v~G~~l~It~~   92 (95)
T d1ufwa_          81 KVKGRAVKISGP   92 (95)
T ss_dssp             EETTEEEEEECC
T ss_pred             EEcceEEEEecC
Confidence            999999999764

>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=98.29  E-value=2.8e-06  Score=53.37  Aligned_cols=79  Identities=13%  Similarity=0.105  Sum_probs=62.8

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCc--ceEEEEEecCHHHHHHHHHHhCCCccCCe-----EEE
Q 029810           20 NTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRIS--RGFAFVTMDGVEDAERCIKYLNQSVLEGR-----YIT   92 (187)
Q Consensus        20 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~--~g~afV~f~~~~~a~~ai~~l~g~~i~g~-----~l~   92 (187)
                      ++|.|..||+.+|++++.+.+...+++........+.+.+.  ..-|+|.|.+.+++....+.++|+.+.+.     .-.
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            68999999999999999999999998888777665543332  24699999999999999999999976332     346


Q ss_pred             EEeccC
Q 029810           93 VERSRR   98 (187)
Q Consensus        93 v~~a~~   98 (187)
                      |++|--
T Consensus        82 VE~AP~   87 (91)
T d1uw4a_          82 VEFAPF   87 (91)
T ss_dssp             EEECSS
T ss_pred             EEEcCc
Confidence            676643

>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=98.00  E-value=1.8e-05  Score=46.68  Aligned_cols=61  Identities=25%  Similarity=0.292  Sum_probs=52.5

Q ss_pred             HHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeEEEEEecc
Q 029810           34 RDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLNQSVLEGRYITVERSR   97 (187)
Q Consensus        34 ~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   97 (187)
                      +.|.+.|.+++.|..+.|....+ +  .-.|-|...+.++|.-|+..||-..|+.+.|.|.++.
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-Y--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCS-T--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccC-C--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            45677889999999999875543 2  3369999999999999999999999999999999986

>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=97.35  E-value=0.00059  Score=42.73  Aligned_cols=65  Identities=17%  Similarity=0.253  Sum_probs=51.7

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCcHHHHHHHhhcCCceeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 029810           10 RGRTETGNPGNTLYVTGLSTRVTERDLEKHFSKEGKVASCFLVVEPRTRISRGFAFVTMDGVEDAERCIKYLN   82 (187)
Q Consensus        10 ~~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~ai~~l~   82 (187)
                      .+.+++.+.-..||.-.+|..+...||.++|+.||.|.-..| .+  |     -|||...+.++|+.++..+.
T Consensus         6 ~~G~d~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-dd--T-----Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_           6 SGGPDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DD--T-----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSCCCCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ET--T-----EEEEECSCHHHHHHHHHHHH
T ss_pred             cCCCCCCCCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cC--c-----eEEEEecCHHHHHHHHHHhc
Confidence            345566667778888889999999999999999998764333 22  1     69999999999999988654