Citrus Sinensis ID: 043634

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-
Protein Sequence
MATAPFDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENKHKHFEAQSISSMKEAAVTRNQ
Secondary Structure (PSIPRED)
ccccccccccccccccccccEEEEccccccccHHHHHHHHHHcccEEEEEccccccccEEEEEcccHHHHHHHHHHHcccEEcccEEEEEEcccccHHHHHccccccccccHHHccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccHHcccccEEEEEccccHHccHHHHHHHHHHccccEEEEccccccccEEEEEcccHHHHHHHHHHHccccEcccEEEEEEccccccccHcHHcccccccccccccccccc
Coil and Loop (DISEMBL)
matapfdsgpqnkqETENLVTLLIKhlpdaipqdtLSRIFshygassvrpcsagrlrncvfvdfgneplaSQAQMQLNGLRFLGKVLSveraskpneenkhkhfeAQSISSMKEAAVTRNQ
Flexible Loop (DISEMBL)
matapfdsgpqnkQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERaskpneenkhkhfeaqsissmkeaavtrnq
Low Complexity Region (SEG)
MATAPFDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENKHKHFEAQSISSMKEAAVTRNQ
Disordered region (IsUnstruct)
******************LVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVL**********************************
Disordered Region (DISOPRED)
**********************LIKHLPDAIPQDTLSRIFSHYGASSVRPC*AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV********************************
Disordered Region (DISEMBL)
************KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENKHKHFEAQSIS***********
Disordered Region (DISPRO)
****************ENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK***************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MATAPFDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENKHKHFEAQSISSMKEAAVTRNQ
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	121	2.2.26 [Sep-21-2011]
Q3MHP0	516	RNA-binding protein 40 OS	yes	no	0.595	0.139	0.397	7e-07
Q4G055	515	RNA-binding protein 40 OS	yes	no	0.595	0.139	0.397	1e-06
Q3UZ01	514	RNA-binding protein 40 OS	yes	no	0.595	0.140	0.397	1e-06
Q5R6C7	517	RNA-binding protein 40 OS	yes	no	0.595	0.139	0.397	1e-06
Q96LT9	517	RNA-binding protein 40 OS	yes	no	0.595	0.139	0.397	1e-06
Q9WX37	99	Putative RNA-binding prot	yes	no	0.644	0.787	0.289	0.0002
Q9WX39	105	Putative RNA-binding prot	no	no	0.644	0.742	0.301	0.0003
Q74ZS6	585	Polyadenylate-binding pro	yes	no	0.776	0.160	0.282	0.0003
Q05196	682	Polyadenylate-binding pro	no	no	0.768	0.136	0.316	0.0004
Q7S6N6	764	Polyadenylate-binding pro	N/A	no	0.735	0.116	0.308	0.0004

>sp|Q3MHP0|RBM40_BOVIN RNA-binding protein 40 OS=Bos taurus GN=RNPC3 PE=2 SV=1

 Score = 52.4 bits (124), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 29/73 (39%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNG 79
           TLL++HLP  +  +    +  ++GA SVR  S  GRL++  F  F NE  A +A  +L+ 
Sbjct: 28  TLLVRHLPAELTAEEKEDLLKYFGAQSVRDLSDKGRLKHTAFATFPNEKTAVKALTRLHQ 87

Query: 80  LRFLGKVLSVERA 92
           L+ LG  L VE A
Sbjct: 88  LKLLGHTLVVEFA 100

Participates in pre-mRNA U12-dependent splicing, performed by the minor spliceosome which removes U12-type introns. U12-type introns comprises less than 1% of all non-coding sequences. Binds to the 3'-stem-loop of m(7)G-capped U12 snRNA.
Bos taurus (taxid: 9913)

>sp|Q4G055|RBM40_RAT RNA-binding protein 40 OS=Rattus norvegicus GN=Rnpc3 PE=2 SV=2

 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/73 (39%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNG 79
           TLL++HLP  +  +    +  ++GA SVR  S  GRL++  F  F NE  A +A  +L+ 
Sbjct: 28  TLLVRHLPAELTAEEKEDLLKYFGAQSVRVLSDKGRLKHTAFATFPNEKAAIKALTRLHQ 87

Query: 80  LRFLGKVLSVERA 92
           L+ LG  L VE A
Sbjct: 88  LKLLGHTLVVEFA 100

Participates in pre-mRNA U12-dependent splicing, performed by the minor spliceosome which removes U12-type introns. U12-type introns comprises less than 1% of all non-coding sequences. Binds to the 3'-stem-loop of m(7)G-capped U12 snRNA.

Rattus norvegicus (taxid: 10116)

>sp|Q3UZ01|RBM40_MOUSE RNA-binding protein 40 OS=Mus musculus GN=Rnpc3 PE=2 SV=2

 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/73 (39%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNG 79
           TLL++HLP  +  +    +  ++GA SVR  S  GRL++  F  F NE  A +A  +L+ 
Sbjct: 28  TLLVRHLPAELTAEEKEDLLKYFGAQSVRVLSDKGRLKHTAFATFPNEKAAIKALTRLHQ 87

Query: 80  LRFLGKVLSVERA 92
           L+ LG  L VE A
Sbjct: 88  LKLLGHTLVVEFA 100

Participates in pre-mRNA U12-dependent splicing, performed by the minor spliceosome which removes U12-type introns. U12-type introns comprises less than 1% of all non-coding sequences. Binds to the 3'-stem-loop of m(7)G-capped U12 snRNA.

Mus musculus (taxid: 10090)

>sp|Q5R6C7|RBM40_PONAB RNA-binding protein 40 OS=Pongo abelii GN=RNPC3 PE=2 SV=1

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/73 (39%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNG 79
           TLL++HLP  +  +    +  ++GA SVR  S  GRL++  F  F NE  A +A  +L+ 
Sbjct: 28  TLLVRHLPAELTAEEKEDLLKYFGAQSVRVLSDKGRLKHTAFATFPNEKAAIKALTRLHQ 87

Query: 80  LRFLGKVLSVERA 92
           L+ LG  L VE A
Sbjct: 88  LKLLGHTLVVEFA 100

Participates in pre-mRNA U12-dependent splicing, performed by the minor spliceosome which removes U12-type introns. U12-type introns comprises less than 1% of all non-coding sequences. Binds to the 3'-stem-loop of m(7)G-capped U12 snRNA.

Pongo abelii (taxid: 9601)

>sp|Q96LT9|RBM40_HUMAN RNA-binding protein 40 OS=Homo sapiens GN=RNPC3 PE=1 SV=1

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/73 (39%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNG 79
           TLL++HLP  +  +    +  ++GA SVR  S  GRL++  F  F NE  A +A  +L+ 
Sbjct: 28  TLLVRHLPAELTAEEKEDLLKYFGAQSVRVLSDKGRLKHTAFATFPNEKAAIKALTRLHQ 87

Query: 80  LRFLGKVLSVERA 92
           L+ LG  L VE A
Sbjct: 88  LKLLGHTLVVEFA 100

Participates in pre-mRNA U12-dependent splicing, performed by the minor spliceosome which removes U12-type introns. U12-type introns comprises less than 1% of all non-coding sequences. Binds to the 3'-stem-loop of m(7)G-capped U12 snRNA.

Homo sapiens (taxid: 9606)

>sp|Q9WX37|RBPE_NOSS1 Putative RNA-binding protein RbpE OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=rbpE PE=3 SV=3

 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 45/83 (54%), Gaps = 5/83 (6%)

Query: 20 VTLLIKHLPDAIPQDTLSRIFSHYGASSVRPC----SAGRLRNCVFVDFGNEPLASQAQM 75
          +++ + +L  ++ QD L+++FS YG+ +          GR+R   FV+  +      A  
Sbjct: 1  MSIYVGNLSYSVTQDDLTKVFSEYGSVTRVQLPTDRETGRVRGFGFVEMESSAAEDAAIQ 60

Query: 76 QLNGLRFLGKVLSVERASKPNEE 98
           L+G  ++G+VL V +A +P EE
Sbjct: 61 ALDGAEWMGRVLKVNKA-RPREE 82

Nostoc sp. (strain PCC 7120 / UTEX 2576) (taxid: 103690)

>sp|Q9WX39|RBPF_NOSS1 Putative RNA-binding protein RbpF OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=rbpF PE=3 SV=3

 Score = 43.9 bits (102), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 46/83 (55%), Gaps = 5/83 (6%)

Query: 20 VTLLIKHLPDAIPQDTLSRIFSHYGASS--VRPCS--AGRLRNCVFVDFGNEPLASQAQM 75
          +++ + +L   + Q+ +S +F+ YG+    V P     GRLR   FV+ G++   + A  
Sbjct: 1  MSIYVGNLSYEVTQEDISNVFAEYGSVKRVVLPTDRETGRLRGFAFVEMGSDAEETAAIE 60

Query: 76 QLNGLRFLGKVLSVERASKPNEE 98
           L+G  ++G+ L V +A KP E+
Sbjct: 61 GLDGAEWMGRDLKVNKA-KPKED 82

Nostoc sp. (strain PCC 7120 / UTEX 2576) (taxid: 103690)

>sp|Q74ZS6|PABP_ASHGO Polyadenylate-binding protein, cytoplasmic and nuclear OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=PAB1 PE=3 SV=1

 Score = 43.9 bits (102), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/99 (28%), Positives = 48/99 (48%), Gaps = 5/99 (5%)

Query: 19  LVTLLIKHLPDAIPQDTLSRIFSHYG---ASSVRPCSAGRLRNCVFVDFGNEPLASQAQM 75
              + +K++     Q+    +F  YG   ++ +   S G+LR   FV+F +   A++A  
Sbjct: 218 FTNVYVKNIDQETSQEEFEELFGKYGKITSAVLEKDSEGKLRGFGFVNFEDHAAAAKAVD 277

Query: 76  QLNGLRFLGKVLSVERASKPNE--ENKHKHFEAQSISSM 112
           +LN L F G+ L V RA K  E  +   K +EA  +  +
Sbjct: 278 ELNELEFKGQKLYVGRAQKKYERLQELKKQYEAARLEKL 316

Binds the poly(A) tail of mRNA. Appears to be an important mediator of the multiple roles of the poly(A) tail in mRNA biogenesis, stability and translation. In the nucleus, involved in both mRNA cleavage and polyadenylation. Is also required for efficient mRNA export to the cytoplasm. Acts in concert with a poly(A)-specific nuclease (PAN) to affect poly(A) tail shortening, which may occur concomitantly with either nucleocytoplasmic mRNA transport or translational initiation. In the cytoplasm, stimulates translation initiation and regulates mRNA decay through translation termination-coupled poly(A) shortening, probably mediated by PAN.

Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (taxid: 284811)

>sp|Q05196|PABP5_ARATH Polyadenylate-binding protein 5 OS=Arabidopsis thaliana GN=PAB5 PE=1 SV=3

 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 49/98 (50%), Gaps = 5/98 (5%)

Query: 18  NLVTLLIKHLPDAIPQDTLSRIFSHYG---ASSVRPCSAGRLRNCVFVDFGNEPLASQAQ 74
           +   + +K+LP  I  D L + F  YG   ++ V    +G  R+  FV+F +   A+ A 
Sbjct: 237 SFTNVYVKNLPKEITDDELKKTFGKYGDISSAVVMKDQSGNSRSFGFVNFVSPEAAAVAV 296

Query: 75  MQLNGLRFLGKVLSVERASKPN--EENKHKHFEAQSIS 110
            ++NG+     VL V RA K +  EE   + FE + IS
Sbjct: 297 EKMNGISLGEDVLYVGRAQKKSDREEELRRKFEQERIS 334

Binds the poly(A) tail of mRNA.

Arabidopsis thaliana (taxid: 3702)

>sp|Q7S6N6|PABP_NEUCR Polyadenylate-binding protein, cytoplasmic and nuclear OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=pab-1 PE=3 SV=1

 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/94 (30%), Positives = 48/94 (51%), Gaps = 5/94 (5%)

Query: 18  NLVTLLIKHLPDAIPQDTLSRIFSHYG---ASSVRPCSAGRLRNCVFVDFGNEPLASQAQ 74
           N   + +K++ + +  +    +F+ +G   +SS+     G+ R   FV+F     A+QA 
Sbjct: 239 NFTNVYVKNINNEVTDEEFRELFAKFGEVTSSSLARDQEGKSRGFGFVNFTTHEAAAQAV 298

Query: 75  MQLNGLRFLGKVLSVERASKPN--EENKHKHFEA 106
            +LNG  F G+ L V RA K +  EE   K +EA
Sbjct: 299 DELNGKDFRGQDLYVGRAQKKHEREEELRKSYEA 332

Binds the poly(A) tail of mRNA. Appears to be an important mediator of the multiple roles of the poly(A) tail in mRNA biogenesis, stability and translation. In the nucleus, involved in both mRNA cleavage and polyadenylation. Is also required for efficient mRNA export to the cytoplasm. Acts in concert with a poly(A)-specific nuclease (PAN) to affect poly(A) tail shortening, which may occur concomitantly with either nucleocytoplasmic mRNA transport or translational initiation. In the cytoplasm, stimulates translation initiation and regulates mRNA decay through translation termination-coupled poly(A) shortening, probably mediated by PAN.

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

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	121
357508623	492	RNA-binding protein [Medicago truncatula	0.867	0.213	0.707	2e-32
359477912	463	PREDICTED: RNA-binding protein 40-like [	0.834	0.218	0.673	3e-31
359478163	463	PREDICTED: LOW QUALITY PROTEIN: RNA-bind	0.834	0.218	0.663	5e-30
297743790	190	unnamed protein product [Vitis vinifera]	0.834	0.531	0.663	5e-30
297849226	438	RNA recognition motif-containing protein	0.710	0.196	0.686	6e-29
15217461	442	U11/U12 small nuclear ribonucleoprotein	0.603	0.165	0.674	1e-28
227204327	375	AT1G09230 [Arabidopsis thaliana]	0.710	0.229	0.674	2e-28
356560981	456	PREDICTED: uncharacterized protein LOC10	0.644	0.171	0.782	2e-28
224144758	420	predicted protein [Populus trichocarpa]	0.867	0.25	0.622	3e-28
356570297	452	PREDICTED: RNA-binding protein 40-like [	0.685	0.183	0.741	1e-27

>gi|357508623|ref|XP_003624600.1| RNA-binding protein [Medicago truncatula] gi|355499615|gb|AES80818.1| RNA-binding protein [Medicago truncatula]

 Score =  142 bits (359), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 75/106 (70%), Positives = 80/106 (75%), Gaps = 1/106 (0%)

Query: 12  NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLAS 71
           N    E+  TLLIKHLPDAIP DTLSR+ SHYGASSVRPCSAGRLRNC FVDF N+ LAS
Sbjct: 18  NPCTVESPATLLIKHLPDAIPHDTLSRLLSHYGASSVRPCSAGRLRNCAFVDFKNDMLAS 77

Query: 72  QAQMQLNGLRFLGKVLSVERASKPNEENKHKHFEAQSISSMKEAAV 117
           QAQ QLNGL+FLGKVLS ERA KPN EN  K   AQ     K +AV
Sbjct: 78  QAQRQLNGLKFLGKVLSAERAGKPN-ENVGKSSGAQLGKDSKTSAV 122

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359477912|ref|XP_002270244.2| PREDICTED: RNA-binding protein 40-like [Vitis vinifera] gi|298205172|emb|CBI17231.3| unnamed protein product [Vitis vinifera]

 Score =  138 bits (348), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 70/104 (67%), Positives = 84/104 (80%), Gaps = 3/104 (2%)

Query: 1   MATAPFDSGP--QNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRN 58
           MA+ P   GP  Q+ +  ++  TLLI+HLP+AIPQDTLSR+FS YGASSVRPC++GRLRN
Sbjct: 1   MASQPM-LGPRTQSFEAEKSAATLLIRHLPEAIPQDTLSRLFSSYGASSVRPCTSGRLRN 59

Query: 59  CVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENKHK 102
           C FVDF +E LASQA  QLNGLRFLGKVL VERA+KP E++K K
Sbjct: 60  CAFVDFKSEMLASQALRQLNGLRFLGKVLLVERANKPTEDDKQK 103

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359478163|ref|XP_003632078.1| PREDICTED: LOW QUALITY PROTEIN: RNA-binding protein 40-like [Vitis vinifera]

 Score =  134 bits (338), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 69/104 (66%), Positives = 83/104 (79%), Gaps = 3/104 (2%)

Query: 1   MATAPFDSGP--QNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRN 58
           MA+ P   GP  Q+ +  ++  TLLI+HLP+AIPQDTLSR+FS YGASSVRP ++GRLRN
Sbjct: 1   MASQPM-LGPRTQSFEAEKSAATLLIRHLPEAIPQDTLSRLFSSYGASSVRPSTSGRLRN 59

Query: 59  CVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENKHK 102
           C FVDF +E LASQA  QLNGLRFLGKVL VERA+KP E++K K
Sbjct: 60  CAFVDFKSEMLASQALRQLNGLRFLGKVLLVERANKPTEDDKQK 103

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297743790|emb|CBI36673.3| unnamed protein product [Vitis vinifera]

 Score =  134 bits (338), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 69/104 (66%), Positives = 83/104 (79%), Gaps = 3/104 (2%)

Query: 1   MATAPFDSGP--QNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRN 58
           MA+ P   GP  Q+ +  ++  TLLI+HLP+AIPQDTLSR+FS YGASSVRP ++GRLRN
Sbjct: 1   MASQPM-LGPRTQSFEAEKSAATLLIRHLPEAIPQDTLSRLFSSYGASSVRPSTSGRLRN 59

Query: 59  CVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENKHK 102
           C FVDF +E LASQA  QLNGLRFLGKVL VERA+KP E++K K
Sbjct: 60  CAFVDFKSEMLASQALRQLNGLRFLGKVLLVERANKPTEDDKQK 103

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297849226|ref|XP_002892494.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297338336|gb|EFH68753.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  131 bits (329), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 59/86 (68%), Positives = 68/86 (79%)

Query: 20  VTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNG 79
           VTLL++HLPD IP D +SR+FS YGAS+VRPCS G+LRN  FVDF NE  ASQA  QLNG
Sbjct: 28  VTLLVRHLPDGIPHDIVSRLFSQYGASAVRPCSGGKLRNAAFVDFKNEAFASQAHRQLNG 87

Query: 80  LRFLGKVLSVERASKPNEENKHKHFE 105
           LRFLGKVL V+RA+KPNE  K +  E
Sbjct: 88  LRFLGKVLQVQRANKPNENKKSRQIE 113

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15217461|ref|NP_172394.1| U11/U12 small nuclear ribonucleoprotein 65 kDa protein [Arabidopsis thaliana] gi|20258828|gb|AAM13896.1| unknown protein [Arabidopsis thaliana] gi|21689717|gb|AAM67480.1| unknown protein [Arabidopsis thaliana] gi|332190295|gb|AEE28416.1| U11/U12 small nuclear ribonucleoprotein 65 kDa protein [Arabidopsis thaliana]

 Score =  129 bits (325), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 58/86 (67%), Positives = 68/86 (79%)

Query: 20  VTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNG 79
           VTLL++HLPD IP D +SR+FS YGAS+VRPCS G+LRN  FVDF NE  ASQA  QLNG
Sbjct: 28  VTLLVRHLPDGIPHDIVSRLFSQYGASAVRPCSGGKLRNAAFVDFKNEAFASQAHRQLNG 87

Query: 80  LRFLGKVLSVERASKPNEENKHKHFE 105
           LRFLGKVL V+RA+KPN+  K +  E
Sbjct: 88  LRFLGKVLQVQRANKPNDNKKSRQIE 113

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|227204327|dbj|BAH57015.1| AT1G09230 [Arabidopsis thaliana]

 Score =  129 bits (325), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 58/86 (67%), Positives = 68/86 (79%)

Query: 20  VTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNG 79
           VTLL++HLPD IP D +SR+FS YGAS+VRPCS G+LRN  FVDF NE  ASQA  QLNG
Sbjct: 28  VTLLVRHLPDGIPHDIVSRLFSQYGASAVRPCSGGKLRNAAFVDFKNEAFASQAHRQLNG 87

Query: 80  LRFLGKVLSVERASKPNEENKHKHFE 105
           LRFLGKVL V+RA+KPN+  K +  E
Sbjct: 88  LRFLGKVLQVQRANKPNDNKKSRQIE 113

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356560981|ref|XP_003548764.1| PREDICTED: uncharacterized protein LOC100818499 [Glycine max]

 Score =  129 bits (324), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 61/78 (78%), Positives = 67/78 (85%)

Query: 20  VTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNG 79
           VTLLIKHLP+AIP DTLSRIF+++GAS VRPCS+ RLRNC F DF NE +ASQAQ QLNG
Sbjct: 24  VTLLIKHLPEAIPHDTLSRIFANFGASFVRPCSSARLRNCAFADFKNEIVASQAQRQLNG 83

Query: 80  LRFLGKVLSVERASKPNE 97
           LRFLGKVLS ERAS P E
Sbjct: 84  LRFLGKVLSAERASNPTE 101

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224144758|ref|XP_002325403.1| predicted protein [Populus trichocarpa] gi|222862278|gb|EEE99784.1| predicted protein [Populus trichocarpa]

 Score =  129 bits (323), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 66/106 (62%), Positives = 80/106 (75%), Gaps = 1/106 (0%)

Query: 15  ETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQ 74
           E +  VTLLIKHLP+AIP  TLSR+FSHYGA SVRPC++GRL+NC FVDF +E LA QA 
Sbjct: 31  EPQVTVTLLIKHLPEAIPFKTLSRLFSHYGAVSVRPCNSGRLKNCAFVDFKSESLAYQAH 90

Query: 75  MQLNGLRFLGKVLSVERASKPNEENKHKHFEAQSISSMKEAAVTRN 120
            QLNGL FLGKVLSVERASK +E  + K       S +++A+V R+
Sbjct: 91  TQLNGLSFLGKVLSVERASKLSEAQQGKE-SVPPTSLIEDASVPRD 135

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356570297|ref|XP_003553326.1| PREDICTED: RNA-binding protein 40-like [Glycine max]

 Score =  127 bits (318), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 63/85 (74%), Positives = 70/85 (82%), Gaps = 2/85 (2%)

Query: 15  ETENLV--TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQ 72
           + E+LV  TLLIKHLP+AIP  TLSRI +++GASSVRPCS GRLRNC F DF NE +ASQ
Sbjct: 27  DAESLVPATLLIKHLPEAIPDVTLSRILANFGASSVRPCSTGRLRNCAFADFKNEIVASQ 86

Query: 73  AQMQLNGLRFLGKVLSVERASKPNE 97
           AQ QLNGLRFLGKVLS ERAS P E
Sbjct: 87  AQRQLNGLRFLGKVLSAERASNPTE 111

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	121
TAIR|locus:2195311	442	AT1G09230 [Arabidopsis thalian	0.793	0.217	0.632	3.9e-28
ZFIN|ZDB-GENE-060312-35	505	rnpc3 "RNA-binding region (RNP	0.859	0.205	0.333	2.1e-08
RGD|1582776	515	Rnpc3 "RNA-binding region (RNP	0.752	0.176	0.340	3.4e-07
UNIPROTKB|Q3MHP0	516	RNPC3 "RNA-binding protein 40"	0.743	0.174	0.347	3.4e-07
UNIPROTKB|F1MJQ8	516	RNPC3 "RNA-binding protein 40"	0.743	0.174	0.347	4.3e-07
MGI|MGI:1914475	514	Rnpc3 "RNA-binding region (RNP	0.611	0.143	0.386	7.1e-07
UNIPROTKB|A8K1C9	516	RNPC3 "cDNA FLJ77710" [Homo sa	0.611	0.143	0.386	7.1e-07
UNIPROTKB|Q96LT9	517	RNPC3 "RNA-binding protein 40"	0.611	0.143	0.386	7.2e-07
UNIPROTKB|F1PE39	518	RNPC3 "Uncharacterized protein	0.611	0.142	0.386	7.2e-07
UNIPROTKB|F1S572	517	LOC100522864 "Uncharacterized	0.768	0.179	0.326	5.2e-06

TAIR|locus:2195311 AT1G09230 [Arabidopsis thaliana (taxid:3702)]

 Score = 314 (115.6 bits), Expect = 3.9e-28, P = 3.9e-28
 Identities = 62/98 (63%), Positives = 75/98 (76%)

Query:    14 QETENL-VTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQ 72
             Q TE   VTLL++HLPD IP D +SR+FS YGAS+VRPCS G+LRN  FVDF NE  ASQ
Sbjct:    21 QVTEPFGVTLLVRHLPDGIPHDIVSRLFSQYGASAVRPCSGGKLRNAAFVDFKNEAFASQ 80

Query:    73 AQMQLNGLRFLGKVLSVERASKPNEENKHKHFEAQSIS 110
             A  QLNGLRFLGKVL V+RA+KPN+  K +  E +S++
Sbjct:    81 AHRQLNGLRFLGKVLQVQRANKPNDNKKSRQIE-ESVT 117

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

ZFIN|ZDB-GENE-060312-35 rnpc3 "RNA-binding region (RNP1, RRM) containing 3" [Danio rerio (taxid:7955)]

 Score = 137 (53.3 bits), Expect = 2.1e-08, P = 2.1e-08
 Identities = 36/108 (33%), Positives = 58/108 (53%)

Query:    15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSA-GRLRNCVFVDFGNEPLASQA 73
             +T+   TL+I+HLP  + +D    +  ++GASSVR  S  G L++  F  F +E  AS+A
Sbjct:    10 QTKKSKTLIIRHLPRELSRDEKEDLLKYFGASSVRVLSEKGPLKHMAFATFSSETSASKA 69

Query:    74 QMQLNGLRFLGKVLSVERASKPNEENKHKHFEAQSISSMKEAAVTRNQ 121
               +L+ LR LG+ L VE A    +++     +   +S    AAV   +
Sbjct:    70 LNRLHQLRILGRTLVVEFAK---DQDSASVLKDPPVSDRTAAAVAEKE 114

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

RGD|1582776 Rnpc3 "RNA-binding region (RNP1, RRM) containing 3" [Rattus norvegicus (taxid:10116)]

 Score = 126 (49.4 bits), Expect = 3.4e-07, P = 3.4e-07
 Identities = 32/94 (34%), Positives = 49/94 (52%)

Query:    21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNG 79
             TLL++HLP  +  +    +  ++GA SVR  S  GRL++  F  F NE  A +A  +L+ 
Sbjct:    28 TLLVRHLPAELTAEEKEDLLKYFGAQSVRVLSDKGRLKHTAFATFPNEKAAIKALTRLHQ 87

Query:    80 LRFLGKVLSVERASKPNEENKHKHFEAQSISSMK 113
             L+ LG  L VE A +  ++  H    A +    K
Sbjct:    88 LKLLGHTLVVEFAKE--QDRVHSSCPASNAEKKK 119

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

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

UNIPROTKB|Q3MHP0 RNPC3 "RNA-binding protein 40" [Bos taurus (taxid:9913)]

 Score = 126 (49.4 bits), Expect = 3.4e-07, P = 3.4e-07
 Identities = 33/95 (34%), Positives = 50/95 (52%)

Query:    21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNG 79
             TLL++HLP  +  +    +  ++GA SVR  S  GRL++  F  F NE  A +A  +L+ 
Sbjct:    28 TLLVRHLPAELTAEEKEDLLKYFGAQSVRDLSDKGRLKHTAFATFPNEKTAVKALTRLHQ 87

Query:    80 LRFLGKVLSVERASKPNEENKHKHFEAQSISSMKE 114
             L+ LG  L VE A    +E    H    S+ + K+
Sbjct:    88 LKLLGHTLVVEFA----KEQDRVHSPCPSLGTEKK 118

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1MJQ8 RNPC3 "RNA-binding protein 40" [Bos taurus (taxid:9913)]

 Score = 125 (49.1 bits), Expect = 4.3e-07, P = 4.3e-07
 Identities = 33/95 (34%), Positives = 50/95 (52%)

Query:    21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNG 79
             TLL++HLP  +  +    +  ++GA SVR  S  GRL++  F  F NE  A +A  +L+ 
Sbjct:    28 TLLVRHLPAELTAEEKEDLLKYFGAQSVRVLSDKGRLKHTAFATFPNEKTAVKALTRLHQ 87

Query:    80 LRFLGKVLSVERASKPNEENKHKHFEAQSISSMKE 114
             L+ LG  L VE A    +E    H    S+ + K+
Sbjct:    88 LKLLGHTLVVEFA----KEQDRVHSPCPSLGTEKK 118

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:1914475 Rnpc3 "RNA-binding region (RNP1, RRM) containing 3" [Mus musculus (taxid:10090)]

 Score = 123 (48.4 bits), Expect = 7.1e-07, P = 7.1e-07
 Identities = 29/75 (38%), Positives = 43/75 (57%)

Query:    21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNG 79
             TLL++HLP  +  +    +  ++GA SVR  S  GRL++  F  F NE  A +A  +L+ 
Sbjct:    28 TLLVRHLPAELTAEEKEDLLKYFGAQSVRVLSDKGRLKHTAFATFPNEKAAIKALTRLHQ 87

Query:    80 LRFLGKVLSVERASK 94
             L+ LG  L VE A +
Sbjct:    88 LKLLGHTLVVEFAKE 102

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISS

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

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|A8K1C9 RNPC3 "cDNA FLJ77710" [Homo sapiens (taxid:9606)]

 Score = 123 (48.4 bits), Expect = 7.1e-07, P = 7.1e-07
 Identities = 29/75 (38%), Positives = 43/75 (57%)

Query:    21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNG 79
             TLL++HLP  +  +    +  ++GA SVR  S  GRL++  F  F NE  A +A  +L+ 
Sbjct:    28 TLLVRHLPAELTAEEKEDLLKYFGAQSVRVLSDKGRLKHTAFATFPNEKAAIKALTRLHQ 87

Query:    80 LRFLGKVLSVERASK 94
             L+ LG  L VE A +
Sbjct:    88 LKLLGHTLVVEFAKE 102

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q96LT9 RNPC3 "RNA-binding protein 40" [Homo sapiens (taxid:9606)]

 Score = 123 (48.4 bits), Expect = 7.2e-07, P = 7.2e-07
 Identities = 29/75 (38%), Positives = 43/75 (57%)

Query:    21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNG 79
             TLL++HLP  +  +    +  ++GA SVR  S  GRL++  F  F NE  A +A  +L+ 
Sbjct:    28 TLLVRHLPAELTAEEKEDLLKYFGAQSVRVLSDKGRLKHTAFATFPNEKAAIKALTRLHQ 87

Query:    80 LRFLGKVLSVERASK 94
             L+ LG  L VE A +
Sbjct:    88 LKLLGHTLVVEFAKE 102

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IC

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

GO:0005634 "nucleus" evidence=IDA

UNIPROTKB|F1PE39 RNPC3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 123 (48.4 bits), Expect = 7.2e-07, P = 7.2e-07
 Identities = 29/75 (38%), Positives = 43/75 (57%)

Query:    21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNG 79
             TLL++HLP  +  +    +  ++GA SVR  S  GRL++  F  F NE  A +A  +L+ 
Sbjct:    29 TLLVRHLPAELTAEEKEDLLKYFGAQSVRVLSDKGRLKHTAFATFPNEKAAIKALTRLHQ 88

Query:    80 LRFLGKVLSVERASK 94
             L+ LG  L VE A +
Sbjct:    89 LKLLGHTLVVEFAKE 103

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1S572 LOC100522864 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 115 (45.5 bits), Expect = 5.2e-06, P = 5.2e-06
 Identities = 32/98 (32%), Positives = 50/98 (51%)

Query:    21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQ--AQMQL 77
             TLL++HLP  +  +    +  ++GA SVR  S  GRL++  F  F NE  A +  A  +L
Sbjct:    28 TLLVRHLPAELTAEEKEDLLKYFGAQSVRVLSDKGRLKHTAFATFPNEKAAIKLKALTRL 87

Query:    78 NGLRFLGKVLSVERASKPNEENKHKHFEAQSISSMKEA 115
             + L+ LG  L VE A +  ++  H    + S    K +
Sbjct:    88 HQLKLLGHTLVVEFAKE--QDQVHSPCPSSSTEKKKRS 123

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00001951001 SubName- Full=Chromosome chr5 scaffold_124, whole genome shotgun sequence; (157 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	121
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	7e-25
smart00360	73	smart00360, RRM, RNA recognition motif	3e-09
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	8e-09
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-07
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	3e-07
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	9e-07
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	2e-06
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	4e-05
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-04
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-04
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	1e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	6e-04
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	6e-04
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	0.001
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	0.002
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	0.002
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	0.003
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	0.003
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	0.004

>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 89.2 bits (222), Expect = 7e-25
 Identities = 35/73 (47%), Positives = 46/73 (63%), Gaps = 1/73 (1%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSA-GRLRNCVFVDFGNEPLASQAQMQLNG 79
          TLL++HLP  + +D    +  H+GASSVR  S  G+L+N  F  F NE  ASQA  +L+ 
Sbjct: 1  TLLVRHLPPELSEDDKEDLLKHFGASSVRVMSRRGKLKNTAFATFDNEQAASQALSRLHQ 60

Query: 80 LRFLGKVLSVERA 92
          L+ LGK L VE A
Sbjct: 61 LKILGKRLVVEYA 73

This subfamily corresponds to the RRM1 of 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 repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), 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. . Length = 73

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

 Score = 49.5 bits (119), Expect = 3e-09
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQ 76
          TL + +LP    ++ L  +FS +G       VR    G+ +   FV+F +E  A +A   
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 77 LNGLRFLGKVLSV 89
          LNG    G+ L V
Sbjct: 61 LNGKELDGRPLKV 73

Length = 73

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

 Score = 48.1 bits (115), Expect = 8e-09
 Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 22 LLIKHLPDAIPQDTLSRIFSHYGA-SSVR--PCSAGRLRNCVFVDFGNEPLASQAQMQLN 78
          L + +LP    ++ L  +FS +G   SVR      G+ +   FV+F +   A +A   LN
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 79 GLRFLGKVLSVE 90
          G    G+ L V 
Sbjct: 61 GKELDGRKLKVS 72

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

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

 Score = 45.5 bits (108), Expect = 1e-07
 Identities = 22/78 (28%), Positives = 44/78 (56%), Gaps = 3/78 (3%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQL 77
           L +  LP ++ ++ L ++F  +G   SVR  +  +G+ +   +V++ NE  ASQA +++
Sbjct: 4  KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 78 NGLRFLGKVLSVERASKP 95
          +G     K +SV  ++ P
Sbjct: 64 DGTEIKEKTISVAISNPP 81

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

 Score = 44.4 bits (106), Expect = 3e-07
 Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 5/77 (6%)

Query: 21 TLLIKHLPDAIPQDTLSR----IFSHYGAS-SVRPCSAGRLRNCVFVDFGNEPLASQAQM 75
          TL I +L + I +D L R    +FS +G    +      ++R   FV F +   A+ A  
Sbjct: 1  TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALR 60

Query: 76 QLNGLRFLGKVLSVERA 92
           L G  F  K + ++ A
Sbjct: 61 ALQGFPFYDKPMRIQYA 77

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 43.0 bits (102), Expect = 9e-07
 Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 3/69 (4%)

Query: 22 LLIKHLPDAIPQDTLSRIFSHYG---ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLN 78
          L + +LP    ++ L  +FS +G   +  +     GR +   FV+F +E  A +A   LN
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 79 GLRFLGKVL 87
          G    G+ L
Sbjct: 61 GKELGGREL 69

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

 Score = 42.2 bits (100), Expect = 2e-06
 Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 3/71 (4%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYG-ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNG 79
          TLL+ +L   I    L  +FS +G    +R        +  FV+F +   A  A   LNG
Sbjct: 3  TLLVFNLDSPISDQELRSLFSQFGEVKDIRE--TPLRPSQKFVEFYDIRAAEAALDALNG 60

Query: 80 LRFLGKVLSVE 90
            FLG  L V+
Sbjct: 61 RPFLGGRLKVK 71

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

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

 Score = 39.1 bits (92), Expect = 4e-05
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 8/78 (10%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASS--------VRPCSAGRLRNCVFVDFGNEPLASQ 72
           L +K+L   + ++ L  IF  +  SS        +R  + GR++   FV F +E +A++
Sbjct: 3  RLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATK 62

Query: 73 AQMQLNGLRFLGKVLSVE 90
          A   +NG    GK + ++
Sbjct: 63 ALNLVNGYVLKGKPMVIQ 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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 37.7 bits (88), Expect = 1e-04
 Identities = 23/77 (29%), Positives = 33/77 (42%), Gaps = 8/77 (10%)

Query: 22 LLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNC------VFVDFGNEPLASQAQM 75
          L++ +LP  + Q+ L  +F   G   +  C   R R         FVD+ +E  A +A  
Sbjct: 3  LIVNYLPQDMTQEELRSLFEAIGP--IESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 76 QLNGLRFLGKVLSVERA 92
           LNG     K L V  A
Sbjct: 61 TLNGFEIRNKRLKVSYA 77

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

 Score = 39.5 bits (91), Expect = 1e-04
 Identities = 26/114 (22%), Positives = 48/114 (42%), Gaps = 4/114 (3%)

Query: 12  NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASS----VRPCSAGRLRNCVFVDFGNE 67
            ++  E   TL + +LP  + ++ L  +F  +G       VR    G+ R   FV+F +E
Sbjct: 108 RQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESE 167

Query: 68  PLASQAQMQLNGLRFLGKVLSVERASKPNEENKHKHFEAQSISSMKEAAVTRNQ 121
             A +A  +LNG    G+ L V++A   ++          +  + K +      
Sbjct: 168 ESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALL 221

Length = 306

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

 Score = 37.6 bits (88), Expect = 1e-04
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 3/73 (4%)

Query: 20 VTLLIKHLPDAIPQDTLSRIFSHYG---ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQ 76
          V L +K+L D+I  + L   FS +G   ++ V     GR +   FV F +   A++A  +
Sbjct: 2  VNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTE 61

Query: 77 LNGLRFLGKVLSV 89
          +NG    GK L V
Sbjct: 62 MNGRIIGGKPLYV 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 26/89 (29%), Positives = 45/89 (50%), Gaps = 7/89 (7%)

Query: 16  TENLVTLLIKHLPDAIPQDTLSRIFSHYG---ASSVRPCSAGRLRNCVFVDFGNEPLASQ 72
            +    L +K+L  ++ +D L  +F+ +G   +++V    +GR R   FV+F     A++
Sbjct: 175 LKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAK 234

Query: 73  AQMQLNGLRF----LGKVLSVERASKPNE 97
           A  ++NG +      GK L V RA K  E
Sbjct: 235 AVEEMNGKKIGLAKEGKKLYVGRAQKRAE 263

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

 Score = 36.4 bits (85), Expect = 3e-04
 Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 3/74 (4%)

Query: 24 IKHLPDAIPQDTLSRIFSHYGA---SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGL 80
          +K+L + +  + L  +F  YG    + V     G+ +   FV+F N   A +A  +LNG 
Sbjct: 6  VKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELNGK 65

Query: 81 RFLGKVLSVERASK 94
             GK L V RA K
Sbjct: 66 EVNGKKLYVGRAQK 79

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

 Score = 36.0 bits (83), Expect = 6e-04
 Identities = 25/77 (32%), Positives = 33/77 (42%), Gaps = 6/77 (7%)

Query: 22 LLIKHLPDAIPQDTLSRIFSHYGA----SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQL 77
          L + +LP  + +D L +IF  YG     + +R  S G  R   FV +     A  A   L
Sbjct: 3  LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 78 NGLRFLGKV--LSVERA 92
          NG    G    LSV  A
Sbjct: 63 NGTIPPGSTMPLSVRYA 79

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|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 35.8 bits (82), Expect = 6e-04
 Identities = 26/75 (34%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 22 LLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQL 77
          L++ +LP  + QD L  +FS  G    A  +R   AG      FV++ N   A +A   L
Sbjct: 4  LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 78 NGLRFLGKVLSVERA 92
          NGLR   K + V  A
Sbjct: 64 NGLRLQSKTIKVSYA 78

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|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 = 35.2 bits (81), Expect = 0.001
 Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 4/66 (6%)

Query: 33 QDTLSRIFSHYGASS----VRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS 88
          + +L ++FS YG  S    V+     R R   FV F N   A  A M +NG    G+ + 
Sbjct: 14 EQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQIR 73

Query: 89 VERASK 94
          V++A K
Sbjct: 74 VDQAGK 79

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

 Score = 34.7 bits (80), Expect = 0.002
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 8/78 (10%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASSVR----PCS--AGRLRNCVFVDFGNEPLASQAQ 74
          +L ++++ DA   D L R+F  YG   +     P      R R   +V F +   A  A 
Sbjct: 2  SLYVRNVADATRPDDLRRLFGKYGP--IVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDAL 59

Query: 75 MQLNGLRFLGKVLSVERA 92
            L+  RFLG+ + ++ A
Sbjct: 60 YYLDRTRFLGREIEIQFA 77

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

 Score = 34.7 bits (80), Expect = 0.002
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 4/75 (5%)

Query: 22 LLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQL 77
          L++ +LP  + QD +  +FS  G       +R    G+     FV++ +   A +A   L
Sbjct: 4  LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63

Query: 78 NGLRFLGKVLSVERA 92
          NGLR   K + V  A
Sbjct: 64 NGLRLQNKTIKVSYA 78

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|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 = 33.9 bits (78), Expect = 0.003
 Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 2/72 (2%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGL 80
          TL I HL   + ++ L  +F  YG   ++       R C +V       A +A  +L  +
Sbjct: 4  TLWIGHLSKKVTEEDLKNLFEEYGE--IQSIDMIPPRGCAYVCMETRQDAHRALQKLRNV 61

Query: 81 RFLGKVLSVERA 92
          +  GK + V  A
Sbjct: 62 KLAGKKIKVAWA 73

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|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 = 34.1 bits (79), Expect = 0.003
 Identities = 22/80 (27%), Positives = 31/80 (38%), Gaps = 8/80 (10%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS------AGRLRNCVFVDFGNEPLASQAQ 74
           L +  L     +  L  +FS +G   V           G  R   FV F +   A  A 
Sbjct: 3  KLFVSGLSTRTTEKELEALFSKFG--RVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60

Query: 75 MQLNGLRFLGKVLSVERASK 94
            LNG    G+V+ VE+A +
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|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 33.6 bits (77), Expect = 0.004
 Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 4/73 (5%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASS----VRPCSAGRLRNCVFVDFGNEPLASQAQMQ 76
           + I HLP    +  L + FS +G        R    G  ++  F+ F N  +A+ A   
Sbjct: 1  VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 77 LNGLRFLGKVLSV 89
          +N    +GKVL 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	121
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.81
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.77
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.75
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.74
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.74
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.72
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.68
PLN03120	260	nucleic acid binding protein; Provisional	99.66
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.64
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.64
KOG0122	270	consensus Translation initiation factor 3, subunit	99.63
PLN03213	759	repressor of silencing 3; Provisional	99.63
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.63
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.62
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.62
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.61
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.61
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.61
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.6
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.6
PLN03121	243	nucleic acid binding protein; Provisional	99.59
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.59
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.57
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.57
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.57
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.57
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.56
smart00362	72	RRM_2 RNA recognition motif.	99.56
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.53
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.53
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.53
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.51
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.51
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.51
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.5
smart00360	71	RRM RNA recognition motif.	99.49
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.49
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.49
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.48
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.47
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.47
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.46
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.45
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.45
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.43
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.4
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.39
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.39
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.38
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.38
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.37
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.33
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.32
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.31
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.29
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.28
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.25
smart00361	70	RRM_1 RNA recognition motif.	99.23
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.23
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.22
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.2
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.19
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.18
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.16
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.15
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.14
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.1
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.09
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.06
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.04
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.02
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.02
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.0
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.0
KOG0151	877	consensus Predicted splicing regulator, contains R	98.98
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.97
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.84
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.83
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.82
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.78
KOG0226	290	consensus RNA-binding proteins [General function p	98.77
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.72
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.71
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.55
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.54
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.52
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.52
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.5
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.42
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.36
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.36
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.21
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.21
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.09
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.08
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.08
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.04
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	97.99
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.81
KOG4210	285	consensus Nuclear localization sequence binding pr	97.78
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.73
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.73
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.71
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.7
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.68
KOG3152	278	consensus TBP-binding protein, activator of basal	97.49
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.48
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.45
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.43
KOG2314	698	consensus Translation initiation factor 3, subunit	97.41
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.39
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.25
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.23
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.19
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.17
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.02
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.02
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.86
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.79
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.67
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.55
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.53
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.5
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	96.21
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	96.08
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	96.06
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.05
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	95.99
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	95.94
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.91
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	95.56
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.26
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.06
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.87
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	94.54
KOG4660	549	consensus Protein Mei2, essential for commitment t	93.94
KOG2135	526	consensus Proteins containing the RNA recognition	93.66
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.63
KOG2591	684	consensus c-Mpl binding protein, contains La domai	93.49
KOG2068	327	consensus MOT2 transcription factor [Transcription	93.22
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	91.81
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	90.6
KOG4483	528	consensus Uncharacterized conserved protein [Funct	89.89
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	89.58
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	88.73
KOG4210	285	consensus Nuclear localization sequence binding pr	88.7
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	88.68
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	87.25

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

Probab=99.81  E-value=9.3e-19  Score=112.87  Aligned_cols=76  Identities=26%  Similarity=0.398  Sum_probs=70.2

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ..+++|||+|||+.+++++|+++|.+||. ..++++.   +++++|||||+|.+.++|+.|+..||+..|+|+.|+|.++
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            34789999999999999999999999999 6666654   7888999999999999999999999999999999999999

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.77  E-value=8.5e-18  Score=121.74  Aligned_cols=74  Identities=23%  Similarity=0.323  Sum_probs=69.7

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +..|||+|||+.+++++|.++|++||. .+++++.   ++.++|||||+|.+.++|..|+..|||..|+|+.|+|.++
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~  346 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFK  346 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            457999999999999999999999999 6777775   7889999999999999999999999999999999999998

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

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

Probab=99.75  E-value=9.4e-18  Score=117.99  Aligned_cols=88  Identities=22%  Similarity=0.307  Sum_probs=77.3

Q ss_pred             CCCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           12 NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        12 ~~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      +......++.|+|+|||+...+-||+.+|.+||. +.|++|. ...+||||||+|++.++|++|-.+|||..|.||+|.|
T Consensus        89 ~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEV  168 (376)
T KOG0125|consen   89 NSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEV  168 (376)
T ss_pred             cCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEE
Confidence            3444455899999999999999999999999999 8888887 5567899999999999999999999999999999999


Q ss_pred             EecCCCCcccc
Q 043634           90 ERASKPNEENK  100 (121)
Q Consensus        90 ~~a~~~~~~~~  100 (121)
                      ..+ .++..+.
T Consensus       169 n~A-TarV~n~  178 (376)
T KOG0125|consen  169 NNA-TARVHNK  178 (376)
T ss_pred             ecc-chhhccC
Confidence            999 6654443

>PF00076 RRM_1: RNA recognition motif

Probab=99.74  E-value=2.5e-17  Score=93.18  Aligned_cols=67  Identities=28%  Similarity=0.572  Sum_probs=61.4

Q ss_pred             EEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           22 LLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        22 l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      |||+|||+.+++++|+++|++||. ..+.+..  .+..+++|||+|.+.++|+.|+..++|..++|+.|+
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 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999 5565555  577889999999999999999999999999999885

(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 ....

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.74  E-value=1.9e-17  Score=119.91  Aligned_cols=78  Identities=27%  Similarity=0.471  Sum_probs=71.7

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      +.++|||+|||..+++++|+++|+.||. ..++++.   +|+++|||||+|.+.++|..||..|||..|.|+.|+|.++ 
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a-   80 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYA-   80 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEee-
Confidence            4789999999999999999999999999 6777765   6889999999999999999999999999999999999998 


Q ss_pred             CCC
Q 043634           94 KPN   96 (121)
Q Consensus        94 ~~~   96 (121)
                      .+.
T Consensus        81 ~~~   83 (352)
T TIGR01661        81 RPS   83 (352)
T ss_pred             ccc
Confidence            443

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.72  E-value=7.3e-17  Score=117.01  Aligned_cols=76  Identities=29%  Similarity=0.436  Sum_probs=70.5

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...++|||+|||+++++++|+++|..||. ..++++.   ++.++|||||+|.+.++|..|+..|++..+.++.|+|.++
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a  184 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYA  184 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecc
Confidence            34899999999999999999999999999 6666664   7888999999999999999999999999999999999998

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

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

Probab=99.68  E-value=1.1e-16  Score=104.05  Aligned_cols=73  Identities=26%  Similarity=0.371  Sum_probs=65.6

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      .++||||||+..+++.+|+.+|..||.  +.-++ .....|||||+|++..+|+.|+..|+|..|+|..|+|+.+.
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~--lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGP--LRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCc--ceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            899999999999999999999999999  43333 22457999999999999999999999999999999999984

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.66  E-value=8.4e-16  Score=106.40  Aligned_cols=74  Identities=18%  Similarity=0.250  Sum_probs=67.3

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      .++|||+|||+.+++++|+++|+.||. ..+.++..+..+|||||+|.+.++++.|+ .|+|..|.|+.|.|..+.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEEecc
Confidence            579999999999999999999999999 66777665556799999999999999999 599999999999999984

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

Probab=99.64  E-value=2e-15  Score=115.51  Aligned_cols=76  Identities=13%  Similarity=0.293  Sum_probs=70.2

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ..++|||+|||+.+++++|+++|+.||. .++++..   ++.++|||||+|.+.++|..|+..||+..|+|+.|+|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            3589999999999999999999999999 6676665   67789999999999999999999999999999999999994

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.

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

Probab=99.64  E-value=2e-15  Score=109.97  Aligned_cols=74  Identities=26%  Similarity=0.391  Sum_probs=69.4

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFL-GKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~-g~~l~v~~a   92 (121)
                      ++.||||.||+++.|++|..+|.+.|. ..++++.   +|.+||||||+|++.+.|..||+.||+.+|. |+.|.|..+
T Consensus        83 G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~S  161 (506)
T KOG0117|consen   83 GCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVS  161 (506)
T ss_pred             CceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEe
Confidence            899999999999999999999999999 7778776   8999999999999999999999999999886 888888766

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

Probab=99.63  E-value=1.8e-15  Score=102.90  Aligned_cols=77  Identities=27%  Similarity=0.463  Sum_probs=70.5

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK   94 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   94 (121)
                      .++|-|.|||.++++++|+++|.+||. ..+-+..   +|.++|||||+|.++++|.+||..|||.-++.=.|+|+|+ +
T Consensus       189 ~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws-k  267 (270)
T KOG0122|consen  189 EATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS-K  267 (270)
T ss_pred             cceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec-C
Confidence            688999999999999999999999999 5554444   9999999999999999999999999999999999999999 6


Q ss_pred             CC
Q 043634           95 PN   96 (121)
Q Consensus        95 ~~   96 (121)
                      |+
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            64

>PLN03213 repressor of silencing 3; Provisional

Probab=99.63  E-value=1.5e-15  Score=112.27  Aligned_cols=74  Identities=28%  Similarity=0.423  Sum_probs=68.3

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc-CCCcccEEEEEeCCH--HHHHHHHHHhcCCeeCCeEEEEEecCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNE--PLASQAQMQLNGLRFLGKVLSVERASK   94 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~-~~~~~g~afv~f~~~--~~a~~ai~~l~g~~i~g~~l~v~~a~~   94 (121)
                      ...||||||++.+++++|...|+.||. ..+.+++ +|  ||||||+|...  .++.+||..|||..++|+.|+|..| +
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKA-K   86 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKA-K   86 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeec-c
Confidence            689999999999999999999999999 7777877 66  89999999987  6799999999999999999999999 4


Q ss_pred             C
Q 043634           95 P   95 (121)
Q Consensus        95 ~   95 (121)
                      +
T Consensus        87 P   87 (759)
T PLN03213         87 E   87 (759)
T ss_pred             H
Confidence            4

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.63  E-value=2.8e-15  Score=85.19  Aligned_cols=67  Identities=33%  Similarity=0.538  Sum_probs=58.4

Q ss_pred             EEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           22 LLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        22 l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      |||+|||+.+++++|..+|+.||. ..+++..  .+..+++|||+|.+.++|..|+..+++..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            799999999999999999999998 5566665  466789999999999999999999999999999874

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 ....

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

Probab=99.62  E-value=7.8e-15  Score=88.09  Aligned_cols=74  Identities=26%  Similarity=0.328  Sum_probs=67.5

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +....|||+|||+.+|.++..++|++||.  ++-++   +...+|-|||.|++..+|..|++.|+|..++++.+.|.+-
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~--IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGT--IRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccc--eEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            33899999999999999999999999999  66555   5566899999999999999999999999999999999877

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

Probab=99.62  E-value=4.5e-17  Score=106.52  Aligned_cols=82  Identities=23%  Similarity=0.436  Sum_probs=73.2

Q ss_pred             CCCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEE
Q 043634           12 NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVL   87 (121)
Q Consensus        12 ~~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l   87 (121)
                      ....-..+..|||||||+..||.||.-.|++||+ ..|-+++   +|+++||||+.|+|..+..-|+..|||..|.|+.|
T Consensus        28 WH~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRti  107 (219)
T KOG0126|consen   28 WHQEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTI  107 (219)
T ss_pred             hhhhcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeE
Confidence            3444555899999999999999999999999999 6665555   99999999999999999999999999999999999


Q ss_pred             EEEecC
Q 043634           88 SVERAS   93 (121)
Q Consensus        88 ~v~~a~   93 (121)
                      +|.+..
T Consensus       108 rVDHv~  113 (219)
T KOG0126|consen  108 RVDHVS  113 (219)
T ss_pred             Eeeecc
Confidence            999873

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.61  E-value=4.7e-15  Score=107.60  Aligned_cols=76  Identities=30%  Similarity=0.426  Sum_probs=67.9

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEe
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLG--KVLSVER   91 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g--~~l~v~~   91 (121)
                      ..++|||+|||+.+++++|+++|++||. ..++++.   ++..++||||+|.+.++|++||+.||+..+.+  +.|+|.+
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            3688999999999999999999999999 5566654   77889999999999999999999999998876  6899998


Q ss_pred             cC
Q 043634           92 AS   93 (121)
Q Consensus        92 a~   93 (121)
                      +.
T Consensus       272 a~  273 (346)
T TIGR01659       272 AE  273 (346)
T ss_pred             CC
Confidence            83

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).

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

Probab=99.61  E-value=2.7e-15  Score=114.79  Aligned_cols=76  Identities=22%  Similarity=0.391  Sum_probs=69.8

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...++|||+|||+.+++++|+++|.+||. .+++++.   +|+++|||||+|.+.++|..|+..|||..|+|+.|+|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            34789999999999999999999999999 6666665   7889999999999999999999999999999999999865

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.

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

Probab=99.61  E-value=1.4e-15  Score=102.89  Aligned_cols=77  Identities=22%  Similarity=0.309  Sum_probs=66.0

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ...-++||||+|+|.+..++|+++|.+||+ ++..++.   +|+++||+||+|.|.++|.+|++.-| -.|+||+..+.+
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdGR~aNcnl   87 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PIIDGRKANCNL   87 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-Ccccccccccch
Confidence            344799999999999999999999999999 5444443   89999999999999999999986544 678999988888


Q ss_pred             cC
Q 043634           92 AS   93 (121)
Q Consensus        92 a~   93 (121)
                      |.
T Consensus        88 A~   89 (247)
T KOG0149|consen   88 AS   89 (247)
T ss_pred             hh
Confidence            74

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

Probab=99.60  E-value=9.9e-15  Score=110.39  Aligned_cols=76  Identities=20%  Similarity=0.337  Sum_probs=69.6

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ..++|||+|||..+++++|+++|..||. ..+.++.   +|.++|||||+|.+.+.|..|+..|||..|+|+.|.|.++.
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            3689999999999999999999999999 5555554   68889999999999999999999999999999999999984

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

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

Probab=99.60  E-value=5.9e-15  Score=112.60  Aligned_cols=74  Identities=24%  Similarity=0.380  Sum_probs=66.8

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFL-GKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~-g~~l~v~~a   92 (121)
                      .++|||+|||+++++++|+.+|.+||. ..++++.  +|.++|||||+|.+.++|+.||..||+..+. |+.|.|..+
T Consensus        58 ~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        58 GCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            799999999999999999999999999 6677765  7899999999999999999999999999885 777766655

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.

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.59  E-value=1.5e-14  Score=98.92  Aligned_cols=73  Identities=21%  Similarity=0.279  Sum_probs=67.4

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +.+|||+||++.+++++|+++|+.||. ..++++..+..+++|||+|.+...++.|+ .|+|..|.++.|.|...
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~   78 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRW   78 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeC
Confidence            689999999999999999999999999 77787776666789999999999999998 79999999999999876

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

Probab=99.59  E-value=9.3e-15  Score=111.93  Aligned_cols=73  Identities=26%  Similarity=0.385  Sum_probs=68.3

Q ss_pred             EEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           21 TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        21 ~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      .|||+|||..+++++|+++|++||. .+|+++.   +++++|||||+|.+.++|.+|+..+|+..+.|+.|+|.|+.
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~   78 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQ   78 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccc
Confidence            6999999999999999999999999 6777776   68889999999999999999999999999999999999874

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

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

Probab=99.57  E-value=1.5e-14  Score=99.54  Aligned_cols=80  Identities=29%  Similarity=0.473  Sum_probs=75.2

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ..++|.|.-||.++++++|+.+|...|+ +++++++   +|++-||+||.|.++.+|++||..|||..+..+.|+|+++ 
T Consensus        40 skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyA-  118 (360)
T KOG0145|consen   40 SKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYA-  118 (360)
T ss_pred             ccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEec-
Confidence            3789999999999999999999999999 8888888   8999999999999999999999999999999999999999 


Q ss_pred             CCCcc
Q 043634           94 KPNEE   98 (121)
Q Consensus        94 ~~~~~   98 (121)
                      +|..+
T Consensus       119 RPSs~  123 (360)
T KOG0145|consen  119 RPSSD  123 (360)
T ss_pred             cCChh
Confidence            77654

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

Probab=99.57  E-value=1.8e-14  Score=107.76  Aligned_cols=75  Identities=25%  Similarity=0.447  Sum_probs=69.3

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      .++|||+|||..+++++|+++|.+||. ..+.++.   +|.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            689999999999999999999999999 5666665   56889999999999999999999999999999999999974

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=99.57  E-value=1.7e-14  Score=110.44  Aligned_cols=76  Identities=32%  Similarity=0.415  Sum_probs=70.3

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ..++|||+||+..+++++|+++|++||. .+++++.  +|.++|||||+|.+.++|.+|+..|||..++|+.|.|.++.
T Consensus       284 ~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~  362 (562)
T TIGR01628       284 QGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQ  362 (562)
T ss_pred             CCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEecc
Confidence            4688999999999999999999999999 6666665  78889999999999999999999999999999999999993

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

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

Probab=99.57  E-value=1e-14  Score=91.48  Aligned_cols=85  Identities=18%  Similarity=0.301  Sum_probs=73.8

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      ++.+-.+..|||.++...++++++.+.|+.||. ..+.+-.   +|..+|||+|+|.+...|.+|+..+||..|+|+.|.
T Consensus        66 PqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~  145 (170)
T KOG0130|consen   66 PQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVS  145 (170)
T ss_pred             CccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCcee
Confidence            444555899999999999999999999999999 3333322   899999999999999999999999999999999999


Q ss_pred             EEecCCCCc
Q 043634           89 VERASKPNE   97 (121)
Q Consensus        89 v~~a~~~~~   97 (121)
                      |.|++...+
T Consensus       146 VDw~Fv~gp  154 (170)
T KOG0130|consen  146 VDWCFVKGP  154 (170)
T ss_pred             EEEEEecCC
Confidence            999974443

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

Probab=99.56  E-value=1.3e-14  Score=96.86  Aligned_cols=82  Identities=26%  Similarity=0.373  Sum_probs=74.7

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      +++.+..+.|.|-||.+.++.++|..+|.+||. ..|-+.+   ++.++|||||-|.+..+|+.|+++|+|..|+|+.|.
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            555666899999999999999999999999999 5666666   889999999999999999999999999999999999


Q ss_pred             EEecCC
Q 043634           89 VERASK   94 (121)
Q Consensus        89 v~~a~~   94 (121)
                      |+.|+.
T Consensus        87 Vq~ary   92 (256)
T KOG4207|consen   87 VQMARY   92 (256)
T ss_pred             ehhhhc
Confidence            999963

>smart00362 RRM_2 RNA recognition motif

Probab=99.56  E-value=5.3e-14  Score=78.89  Aligned_cols=70  Identities=34%  Similarity=0.598  Sum_probs=61.5

Q ss_pred             EEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           21 TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        21 ~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      +|||+|||..++.++|+++|.+||. ..+.+.. .+.++++|||+|.+.+.|..|+..+++..+.|+.+.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            4899999999999999999999999 4555554 35567999999999999999999999999999998873

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

Probab=99.53  E-value=2.2e-14  Score=89.15  Aligned_cols=74  Identities=16%  Similarity=0.255  Sum_probs=65.2

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc------CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS------AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~------~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ..+++||||||++.++|++|.++|+.+|.  |+.+.      +....|||||+|...++|..|+.-++|+.++.+.|++.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~--irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D  111 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGD--IRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRID  111 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccc--hheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeee
Confidence            34799999999999999999999999999  42222      44456999999999999999999999999999999998


Q ss_pred             ec
Q 043634           91 RA   92 (121)
Q Consensus        91 ~a   92 (121)
                      +.
T Consensus       112 ~D  113 (153)
T KOG0121|consen  112 WD  113 (153)
T ss_pred             cc
Confidence            76

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

Probab=99.53  E-value=7.2e-14  Score=96.48  Aligned_cols=77  Identities=19%  Similarity=0.398  Sum_probs=68.9

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ++.+.+|+||||||+..+++++|++.|++||. .+||+...   +||+||.|.+.+.|..||..+|+.+|.|+.++..|.
T Consensus       159 Qssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~---qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWG  235 (321)
T KOG0148|consen  159 QSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD---QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWG  235 (321)
T ss_pred             cCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc---cceEEEEecchhhHHHHHHHhcCceeCceEEEEecc
Confidence            34555999999999999999999999999999 55666543   589999999999999999999999999999999998


Q ss_pred             C
Q 043634           93 S   93 (121)
Q Consensus        93 ~   93 (121)
                      +
T Consensus       236 K  236 (321)
T KOG0148|consen  236 K  236 (321)
T ss_pred             c
Confidence            4

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.53  E-value=1.6e-13  Score=103.66  Aligned_cols=75  Identities=23%  Similarity=0.356  Sum_probs=67.5

Q ss_pred             CCccEEEecCCCC-CCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           17 ENLVTLLIKHLPD-AIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        17 ~~~~~l~V~nlp~-~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      .++++|||+|||+ .+++++|+.+|+.||. ..++++..  .+|+|||+|.+.++|..|+..|||..|.|+.|+|.+++
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~--~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~  349 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKN--KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSK  349 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeC--CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            3578999999998 6999999999999999 66666654  36899999999999999999999999999999999984

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

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

Probab=99.51  E-value=1.6e-13  Score=104.86  Aligned_cols=72  Identities=28%  Similarity=0.489  Sum_probs=64.4

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhh--CC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHY--GA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKP   95 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~--G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   95 (121)
                      .++|||+|||..+++++|+++|++|  |. ..+++     .++||||+|.+.++|.+|+..||+..|+|+.|+|.++ ++
T Consensus       233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~-----~rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~A-kp  306 (578)
T TIGR01648       233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKK-----IRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLA-KP  306 (578)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEe-----ecCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEc-cC
Confidence            6789999999999999999999999  88 33433     2579999999999999999999999999999999999 55


Q ss_pred             C
Q 043634           96 N   96 (121)
Q Consensus        96 ~   96 (121)
                      .
T Consensus       307 ~  307 (578)
T TIGR01648       307 V  307 (578)
T ss_pred             C
Confidence            3

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.

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

Probab=99.51  E-value=2e-13  Score=95.28  Aligned_cols=77  Identities=21%  Similarity=0.415  Sum_probs=71.5

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ..|=++|||+-|+.+++|..|+..|..||. ..|+++.   +|+++|||||+|....+...|.+..+|..|+|+.|.|.+
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            355799999999999999999999999999 6777776   899999999999999999999999999999999999987


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      -
T Consensus       178 E  178 (335)
T KOG0113|consen  178 E  178 (335)
T ss_pred             c
Confidence            6

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

Probab=99.51  E-value=1.6e-13  Score=102.61  Aligned_cols=74  Identities=22%  Similarity=0.316  Sum_probs=67.8

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ..++|||+|||..+++++|+++|.+||. ..++++.   ++.++|||||+|.+.++|..|+. |+|..+.|+.|.|..+
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSS  165 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeec
Confidence            3689999999999999999999999999 6677765   68889999999999999999995 9999999999999876

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.

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

Probab=99.50  E-value=1.9e-13  Score=94.10  Aligned_cols=74  Identities=32%  Similarity=0.568  Sum_probs=68.7

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ..+|||+|||..+++++|.++|..||. ..+.+..   ++..+|+|||+|.+.+++..|+..+++..+.|+.|.|.++
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~  192 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKA  192 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecc
Confidence            599999999999999999999999999 5555554   6899999999999999999999999999999999999996

>smart00360 RRM RNA recognition motif

Probab=99.49  E-value=2.4e-13  Score=75.89  Aligned_cols=67  Identities=33%  Similarity=0.580  Sum_probs=59.3

Q ss_pred             ecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           24 IKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        24 V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      |+|||..+++++|+++|.+||. ..+.+..   ++.++|+|||+|.+.+.|..|+..+++..++|+.++|+
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            6899999999999999999998 5555554   46778999999999999999999999999999998873

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

Probab=99.49  E-value=9.2e-14  Score=102.87  Aligned_cols=74  Identities=31%  Similarity=0.457  Sum_probs=70.6

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      +.+||||||+.+++++|..+|+..|. .+++++.   +|+.+||||++|.+.+++..|+..|||.++.|++|+|.++.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~   96 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYAS   96 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccc
Confidence            89999999999999999999999999 7777776   89999999999999999999999999999999999999984

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.49  E-value=2e-13  Score=103.06  Aligned_cols=73  Identities=15%  Similarity=0.177  Sum_probs=64.7

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHh--cCCeeCCeEEEEEecC
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQL--NGLRFLGKVLSVERAS   93 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l--~g~~i~g~~l~v~~a~   93 (121)
                      |+++|||+|||+.+++++|+++|++||. .++.++.   .+++|||+|.+.++|..|+..+  ++..+.|+.|+|.++.
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~---~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~   76 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP---GKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYST   76 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC---CCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecC
Confidence            4689999999999999999999999999 5555553   4689999999999999999865  7789999999999983

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).

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

Probab=99.48  E-value=9.2e-14  Score=91.47  Aligned_cols=75  Identities=24%  Similarity=0.364  Sum_probs=65.9

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ...+.|||+|||.++.+.+|+++|.+||.  |+.|.   ......||||+|++..+|+.||..-+|..++|..|+|+++.
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~--i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGR--IREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcc--eEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            34789999999999999999999999999  54444   22335799999999999999999999999999999999984

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

Probab=99.47  E-value=4.8e-14  Score=95.03  Aligned_cols=77  Identities=22%  Similarity=0.339  Sum_probs=71.0

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...++||||+|...+++.-|...|-+||. ..+.++.   ++++||||||+|...++|.+||+.||+.+|.|+.|+|.++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            34789999999999999999999999999 5566655   8899999999999999999999999999999999999999


Q ss_pred             C
Q 043634           93 S   93 (121)
Q Consensus        93 ~   93 (121)
                      +
T Consensus        88 k   88 (298)
T KOG0111|consen   88 K   88 (298)
T ss_pred             C
Confidence            4

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

Probab=99.47  E-value=2.9e-13  Score=93.56  Aligned_cols=78  Identities=22%  Similarity=0.372  Sum_probs=71.0

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ...=.-+||+.|...++.++|+..|.+||+ ...++++   +++++||+||.|...++|+.||..|||.-|++|.|+-.|
T Consensus        59 ~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNW  138 (321)
T KOG0148|consen   59 SNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNW  138 (321)
T ss_pred             cccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccc
Confidence            333578999999999999999999999999 5566666   899999999999999999999999999999999999999


Q ss_pred             cC
Q 043634           92 AS   93 (121)
Q Consensus        92 a~   93 (121)
                      +.
T Consensus       139 AT  140 (321)
T KOG0148|consen  139 AT  140 (321)
T ss_pred             cc
Confidence            94

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

Probab=99.46  E-value=2e-13  Score=89.40  Aligned_cols=76  Identities=21%  Similarity=0.332  Sum_probs=70.2

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ....+||||||+..++++.|.++|-+.|. ..+++.+   +...+||||++|.++++|+-|++.||...+-|++|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            34799999999999999999999999999 6677766   6778899999999999999999999999999999999988

>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=99.45  E-value=1.5e-12  Score=73.27  Aligned_cols=71  Identities=34%  Similarity=0.545  Sum_probs=61.9

Q ss_pred             EEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           21 TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        21 ~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      +|+|+|||..+++++|+++|..+|. ..+.+..  .+..+++|||+|.+.++|..|+..+++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999998 5555554  334578999999999999999999999999999998863

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).

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

Probab=99.45  E-value=3e-13  Score=98.71  Aligned_cols=74  Identities=27%  Similarity=0.496  Sum_probs=66.2

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCc
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNE   97 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~~~   97 (121)
                      ...|||+||+..+|++.|+.+|.+||. ..|+.+     +-||||+|.++++|.+|++.+||..|.|..|.|.+| +|..
T Consensus       259 VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~-----rDYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLA-KP~~  332 (506)
T KOG0117|consen  259 VKVLYVRNLMESTTEETLKKLFNEFGKVERVKKP-----RDYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLA-KPVD  332 (506)
T ss_pred             eeeeeeeccchhhhHHHHHHHHHhccceEEeecc-----cceeEEeecchHHHHHHHHHhcCceecCceEEEEec-CChh
Confidence            689999999999999999999999999 444443     569999999999999999999999999999999999 6544


Q ss_pred             c
Q 043634           98 E   98 (121)
Q Consensus        98 ~   98 (121)
                      +
T Consensus       333 k  333 (506)
T KOG0117|consen  333 K  333 (506)
T ss_pred             h
Confidence            4

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

Probab=99.43  E-value=6.8e-13  Score=89.46  Aligned_cols=79  Identities=30%  Similarity=0.482  Sum_probs=71.9

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHH----HHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSR----IFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~----~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      +..+..+|||.||+..+..++|+.    +|++||. +.|....+.+-+|-|||.|.+.+.|..|+..|+|..+-|+.++|
T Consensus         5 ~~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mri   84 (221)
T KOG4206|consen    5 SVNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRI   84 (221)
T ss_pred             ccCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhhe
Confidence            445666999999999999999888    9999998 66677778889999999999999999999999999999999999


Q ss_pred             EecC
Q 043634           90 ERAS   93 (121)
Q Consensus        90 ~~a~   93 (121)
                      ++|+
T Consensus        85 qyA~   88 (221)
T KOG4206|consen   85 QYAK   88 (221)
T ss_pred             eccc
Confidence            9994

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

Probab=99.40  E-value=3.8e-13  Score=93.08  Aligned_cols=83  Identities=27%  Similarity=0.388  Sum_probs=72.9

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      +.+.+|+|||-.||.+..+.+|..+|-.||- .+.++..   +..+++|+||.|++..++.+||..|||+.|+-++|+|.
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            3445899999999999999999999999999 5544333   78899999999999999999999999999999999999


Q ss_pred             ecCCCCcc
Q 043634           91 RASKPNEE   98 (121)
Q Consensus        91 ~a~~~~~~   98 (121)
                      .. +|+..
T Consensus       361 LK-RPkda  367 (371)
T KOG0146|consen  361 LK-RPKDA  367 (371)
T ss_pred             hc-Ccccc
Confidence            88 66543

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

Probab=99.39  E-value=2.4e-12  Score=97.45  Aligned_cols=75  Identities=16%  Similarity=0.304  Sum_probs=61.6

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC----------ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeE
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA----------SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKV   86 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~----------~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~   86 (121)
                      ...++|||||||+.+++++|..+|..++.          ..+..+..+..+|||||+|.+.++|..|+ .|+|..+.|+.
T Consensus       173 ~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~~~g~~  251 (509)
T TIGR01642       173 RQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAM-ALDSIIYSNVF  251 (509)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhh-cCCCeEeeCce
Confidence            33689999999999999999999998622          11223334566899999999999999999 59999999999


Q ss_pred             EEEEec
Q 043634           87 LSVERA   92 (121)
Q Consensus        87 l~v~~a   92 (121)
                      |+|...
T Consensus       252 l~v~r~  257 (509)
T TIGR01642       252 LKIRRP  257 (509)
T ss_pred             eEecCc
Confidence            999754

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

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

Probab=99.39  E-value=4.6e-13  Score=97.50  Aligned_cols=80  Identities=26%  Similarity=0.436  Sum_probs=69.7

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCe-eCC--eEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLR-FLG--KVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~-i~g--~~l~v~~a   92 (121)
                      .++||||.|+..++|.+++.+|++||. +.+.+++  .+.+||||||.|...+.|..||+.|||.. +.|  .+|.|+|+
T Consensus       124 e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFA  203 (510)
T KOG0144|consen  124 ERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFA  203 (510)
T ss_pred             chhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEec
Confidence            689999999999999999999999999 6777777  78899999999999999999999999964 444  68999999


Q ss_pred             CCCCccc
Q 043634           93 SKPNEEN   99 (121)
Q Consensus        93 ~~~~~~~   99 (121)
                       .+..++
T Consensus       204 -Dtqkdk  209 (510)
T KOG0144|consen  204 -DTQKDK  209 (510)
T ss_pred             -ccCCCc
Confidence             444443

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

Probab=99.38  E-value=9.8e-13  Score=91.75  Aligned_cols=68  Identities=28%  Similarity=0.468  Sum_probs=62.2

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+|||||||..+++.+|+.+|.+||. .++-++     +.||||..++...++.||..|||..|+|..|+|+-+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv-----KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaS   71 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIV-----KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEAS   71 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeee-----cccceEEeecccccHHHHhhcccceecceEEEEEec
Confidence            47999999999999999999999999 555555     359999999999999999999999999999999988

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

Probab=99.38  E-value=2e-12  Score=96.56  Aligned_cols=75  Identities=27%  Similarity=0.402  Sum_probs=69.2

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ...|.|+|||+.+...+|+.+|+.||. ..+.++.  .|+-+|||||+|....+|..|+..+|+..|+|++|-|.||.
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            688999999999999999999999999 6677776  55667999999999999999999999999999999999993

>PF13893 RRM_5: RNA recognition motif

Probab=99.37  E-value=6.5e-12  Score=68.37  Aligned_cols=55  Identities=35%  Similarity=0.538  Sum_probs=46.8

Q ss_pred             HHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           36 LSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        36 L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      |.++|++||. ..+.+....  +++|||+|.+.++|..|+..|||..++|+.|+|+++
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            6789999999 445554433  589999999999999999999999999999999885

(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 ....

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

Probab=99.33  E-value=3.8e-12  Score=83.50  Aligned_cols=81  Identities=19%  Similarity=0.289  Sum_probs=71.2

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-cc-EEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SS-VRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~-~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      +.++||+||.+++.+..|.++|+.||. .. .++++   +|..+||||+.|.+.+.+.+|+..+||..++.+.+.|++++
T Consensus        96 ganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~  175 (203)
T KOG0131|consen   96 GANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAF  175 (203)
T ss_pred             cccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEE
Confidence            699999999999999999999999999 32 24444   78889999999999999999999999999999999999996


Q ss_pred             CCCccc
Q 043634           94 KPNEEN   99 (121)
Q Consensus        94 ~~~~~~   99 (121)
                      +...+.
T Consensus       176 k~~~kg  181 (203)
T KOG0131|consen  176 KKDTKG  181 (203)
T ss_pred             ecCCCc
Confidence            554443

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

Probab=99.32  E-value=8.2e-12  Score=91.07  Aligned_cols=75  Identities=21%  Similarity=0.429  Sum_probs=66.4

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCe-eC--CeEEEEEe
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLR-FL--GKVLSVER   91 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~-i~--g~~l~v~~   91 (121)
                      .-++|||-||+.++|.||+.+|.+||. .+|-+++   ++.++|||||.|...++|.+|+..||... |-  ...|.|++
T Consensus        34 ~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~  113 (510)
T KOG0144|consen   34 AVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKY  113 (510)
T ss_pred             hhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecc
Confidence            689999999999999999999999999 6666666   88999999999999999999999998754 43  46889999


Q ss_pred             cC
Q 043634           92 AS   93 (121)
Q Consensus        92 a~   93 (121)
                      +.
T Consensus       114 Ad  115 (510)
T KOG0144|consen  114 AD  115 (510)
T ss_pred             cc
Confidence            94

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

Probab=99.31  E-value=1.7e-12  Score=93.19  Aligned_cols=74  Identities=23%  Similarity=0.414  Sum_probs=67.4

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .|.||||.|.+++.|+.|+..|.+||. .++-+-+   +++++|||||+|+-.+.|.-|++.|||..++|+.|+|.+-
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCC
Confidence            689999999999999999999999999 5554444   8999999999999999999999999999999999999743

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.29  E-value=6e-12  Score=93.83  Aligned_cols=73  Identities=30%  Similarity=0.467  Sum_probs=66.6

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ..||||||.+++++++|+.+|.+||. ..|.+..   +|.++||+||+|.+.++|..|+..|||++|-|+.|+|...
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v  355 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVV  355 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEe
Confidence            33999999999999999999999999 5555444   8999999999999999999999999999999999999876

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

Probab=99.28  E-value=2.5e-11  Score=90.87  Aligned_cols=74  Identities=23%  Similarity=0.372  Sum_probs=65.5

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHh-----cC-CeeCCeEEE
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQL-----NG-LRFLGKVLS   88 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l-----~g-~~i~g~~l~   88 (121)
                      ..+|||+|||+++++++|...|++||. ....++.   ++.++|+|||.|.+...+..||...     .| ..|.|+.|.
T Consensus       292 ~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lk  371 (678)
T KOG0127|consen  292 GKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLK  371 (678)
T ss_pred             cceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEe
Confidence            699999999999999999999999999 4444444   8999999999999999999999876     23 678899999


Q ss_pred             EEec
Q 043634           89 VERA   92 (121)
Q Consensus        89 v~~a   92 (121)
                      |..+
T Consensus       372 v~~A  375 (678)
T KOG0127|consen  372 VTLA  375 (678)
T ss_pred             eeec
Confidence            9988

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

Probab=99.25  E-value=5.9e-11  Score=82.06  Aligned_cols=77  Identities=23%  Similarity=0.317  Sum_probs=71.0

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ...+..|||-||.+++.|.-|-++|++||. ..|++++   +.+-+||+||++.+.++|..||..|||..++++.|.|.+
T Consensus       275 ~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsF  354 (360)
T KOG0145|consen  275 PGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSF  354 (360)
T ss_pred             CCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEE
Confidence            333899999999999999999999999999 7788887   577889999999999999999999999999999999987


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      .
T Consensus       355 K  355 (360)
T KOG0145|consen  355 K  355 (360)
T ss_pred             e
Confidence            6

>smart00361 RRM_1 RNA recognition motif

Probab=99.23  E-value=7.2e-11  Score=67.17  Aligned_cols=57  Identities=25%  Similarity=0.448  Sum_probs=48.9

Q ss_pred             HHHHHHHHh----hhCC-ccEE-E-cc--C--CCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           33 QDTLSRIFS----HYGA-SSVR-P-CS--A--GRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        33 ~~~L~~~f~----~~G~-~~~~-~-~~--~--~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      +++|+++|.    +||. .++. + +.  +  +.++|+|||+|.+.++|..|+..|||..+.|+.|++
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            578888998    9999 5553 2 22  3  788999999999999999999999999999999876

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

Probab=99.23  E-value=6.7e-11  Score=91.41  Aligned_cols=77  Identities=19%  Similarity=0.385  Sum_probs=68.2

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCc
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNE   97 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~~~   97 (121)
                      ++|||||.|+..+++.||..+|..||. .+|.++.   +++||||.+....+|++|+.+|....+.++.|+|.|+.....
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~---~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~  497 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP---PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGP  497 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeecc---CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCc
Confidence            699999999999999999999999999 5555543   479999999999999999999999999999999999954443


Q ss_pred             c
Q 043634           98 E   98 (121)
Q Consensus        98 ~   98 (121)
                      +
T Consensus       498 k  498 (894)
T KOG0132|consen  498 K  498 (894)
T ss_pred             c
Confidence            3

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

Probab=99.22  E-value=5.6e-11  Score=87.06  Aligned_cols=71  Identities=31%  Similarity=0.468  Sum_probs=65.9

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ..|||.||++.++..+|.++|+.||. +++++..  .| ++|| ||+|.+++.|..||+.+||..+.|++|.|...
T Consensus        77 ~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~  150 (369)
T KOG0123|consen   77 SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLF  150 (369)
T ss_pred             ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeec
Confidence            33999999999999999999999999 8887777  45 7899 99999999999999999999999999999887

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.20  E-value=9.1e-11  Score=86.03  Aligned_cols=74  Identities=22%  Similarity=0.336  Sum_probs=66.3

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHh-hhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFS-HYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~-~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+.+||.|||+++...+|+++|. +.|+ ..|.++.  +|+.+|||.|+|.+++.+++|++.||.+.+.|+.|.|+..
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd  121 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKED  121 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEecc
Confidence            45699999999999999999997 5677 5565555  8999999999999999999999999999999999999865

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

Probab=99.19  E-value=4.1e-10  Score=76.35  Aligned_cols=79  Identities=25%  Similarity=0.413  Sum_probs=64.5

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCc----ccEEEEEeCCHHHHHHHHHHhcCCeeC---CeEEEEE
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRL----RNCVFVDFGNEPLASQAQMQLNGLRFL---GKVLSVE   90 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~----~g~afv~f~~~~~a~~ai~~l~g~~i~---g~~l~v~   90 (121)
                      .++|||.+||.++...+|..+|..|.. +...+-.+++.    +.+||++|.+...|.+|+..|||..++   +..|+++
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiE  113 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIE  113 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEee
Confidence            699999999999999999999999866 33322223332    369999999999999999999999887   7899999


Q ss_pred             ecCCCCcc
Q 043634           91 RASKPNEE   98 (121)
Q Consensus        91 ~a~~~~~~   98 (121)
                      ++ +.+.+
T Consensus       114 lA-KSNtK  120 (284)
T KOG1457|consen  114 LA-KSNTK  120 (284)
T ss_pred             eh-hcCcc
Confidence            99 44333

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.18  E-value=6.7e-11  Score=84.73  Aligned_cols=78  Identities=19%  Similarity=0.312  Sum_probs=71.9

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      .+|-..|||.-|.+.+++++|+-+|+.||. .++.+++   +|.+-.||||+|.+.+++++|.-+|+..-|+++.|+|.+
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            445789999999999999999999999999 7777776   899999999999999999999999999999999999998


Q ss_pred             cC
Q 043634           92 AS   93 (121)
Q Consensus        92 a~   93 (121)
                      +.
T Consensus       316 SQ  317 (479)
T KOG0415|consen  316 SQ  317 (479)
T ss_pred             hh
Confidence            73

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.16  E-value=4e-11  Score=91.76  Aligned_cols=75  Identities=27%  Similarity=0.394  Sum_probs=69.5

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      .++|+|+|||+..+..+++.+|..||. .+++++.   .+.++|||||+|-+..+|.+|+..|.++.+.|+.|.++|++
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~  691 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAK  691 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhc
Confidence            689999999999999999999999999 6677776   45679999999999999999999999999999999999994

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

Probab=99.15  E-value=3e-10  Score=80.98  Aligned_cols=81  Identities=26%  Similarity=0.411  Sum_probs=64.9

Q ss_pred             CCCCCCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHh-cCCeeCCeEEEEE
Q 043634           12 NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQL-NGLRFLGKVLSVE   90 (121)
Q Consensus        12 ~~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l-~g~~i~g~~l~v~   90 (121)
                      .+++...-++|||++|-..+++.+|++.|.+||.  ++.+..-..++||||+|.+.+.|+.|..+. +-..|+|++|+|.
T Consensus       221 epPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGe--irsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~  298 (377)
T KOG0153|consen  221 EPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGE--IRSIRILPRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIK  298 (377)
T ss_pred             CCCcccceeEEEecccccchhHHHHHHHHhhcCC--eeeEEeecccccceeeehhhHHHHHHHHhhcceeeecceEEEEE
Confidence            3444455799999999999999999999999999  444442223479999999999999777544 6678899999999


Q ss_pred             ecCCC
Q 043634           91 RASKP   95 (121)
Q Consensus        91 ~a~~~   95 (121)
                      |. ++
T Consensus       299 Wg-~~  302 (377)
T KOG0153|consen  299 WG-RP  302 (377)
T ss_pred             eC-CC
Confidence            99 55

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

Probab=99.14  E-value=9.7e-11  Score=81.28  Aligned_cols=75  Identities=24%  Similarity=0.391  Sum_probs=67.5

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeC---CeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFL---GKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~---g~~l~v~~a   92 (121)
                      .++||||-|...-+|+|++.+|..||. .++.+++  .|.++||+||.|.+..+|..||..|||..-+   ...|.|+++
T Consensus        19 drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~A   98 (371)
T KOG0146|consen   19 DRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKFA   98 (371)
T ss_pred             chhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEec
Confidence            799999999999999999999999999 7777777  7888999999999999999999999996544   367899999


Q ss_pred             C
Q 043634           93 S   93 (121)
Q Consensus        93 ~   93 (121)
                      .
T Consensus        99 D   99 (371)
T KOG0146|consen   99 D   99 (371)
T ss_pred             c
Confidence            3

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

Probab=99.10  E-value=1.1e-10  Score=81.58  Aligned_cols=72  Identities=21%  Similarity=0.339  Sum_probs=64.8

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ....++|+||||.+.++..+|+..|.+||. ..+.++     ++|+||.|+-.++|..|+..|++.++.|++++|+.+
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv-----kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~s  147 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV-----KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLS  147 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeee-----cceeEEEEeeccchHHHHhcccccccccceeeeeee
Confidence            345899999999999999999999999999 444443     479999999999999999999999999999999988

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

Probab=99.09  E-value=4.1e-10  Score=85.09  Aligned_cols=75  Identities=23%  Similarity=0.346  Sum_probs=66.4

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      +++|||.+|+..+.-.+|+.+|++||. .-.+++-   +..-++|+||++.+..+|.+||..||.+.|+|+.|.|+.++
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            689999999999999999999999999 4334443   44457899999999999999999999999999999999995

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

Probab=99.06  E-value=6e-10  Score=81.70  Aligned_cols=70  Identities=23%  Similarity=0.280  Sum_probs=64.9

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ..||||   +.+++..|.++|+++|. .++++++ .+ +-|||||.|.+..+|++|+..+|...+.|+.++|.|+.
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~   73 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDAT-SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQ   73 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecCC-ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhc
Confidence            368999   99999999999999999 8888888 53 88999999999999999999999999999999999983

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.04  E-value=1.1e-09  Score=73.16  Aligned_cols=79  Identities=20%  Similarity=0.374  Sum_probs=67.8

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-c-cEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-S-SVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~-~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      +.......+|++.+|..+.+..+..+|.++|. . .+++-+   +|.++|||||+|.+.+.|.-|-+.||+.-++++.|.
T Consensus        44 p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~  123 (214)
T KOG4208|consen   44 PEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLE  123 (214)
T ss_pred             CccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheee
Confidence            33444788999999999999999999999955 3 333323   899999999999999999999999999999999999


Q ss_pred             EEec
Q 043634           89 VERA   92 (121)
Q Consensus        89 v~~a   92 (121)
                      +.+-
T Consensus       124 c~vm  127 (214)
T KOG4208|consen  124 CHVM  127 (214)
T ss_pred             eEEe
Confidence            8877

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

Probab=99.02  E-value=8.4e-10  Score=79.59  Aligned_cols=77  Identities=14%  Similarity=0.319  Sum_probs=69.5

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK   94 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   94 (121)
                      -..|||..+.++.+++||+..|..||. ..+.+-+   .+.++||+|++|.+..+...||..||-+.++|+.|+|..+..
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vT  289 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  289 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccC
Confidence            478999999999999999999999999 6666666   567899999999999999999999999999999999998854


Q ss_pred             C
Q 043634           95 P   95 (121)
Q Consensus        95 ~   95 (121)
                      |
T Consensus       290 P  290 (544)
T KOG0124|consen  290 P  290 (544)
T ss_pred             C
Confidence            4

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.02  E-value=1e-09  Score=80.62  Aligned_cols=75  Identities=21%  Similarity=0.275  Sum_probs=65.7

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ....|+|+|+|||+++|...|++-|..||. +...++..|+++|  .|.|.+.++|++|+..|+|..+.|+.|.|.+.
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhhccCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            344799999999999999999999999999 4444555787766  89999999999999999999999999999863

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.00  E-value=1.4e-09  Score=83.47  Aligned_cols=74  Identities=23%  Similarity=0.279  Sum_probs=64.8

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CC----CcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AG----RLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~----~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ++|||.||++.++.++|...|...|. .++++..  .+    .+.|||||+|.+.++|.+|+..|+|+.|+|+.|.|+++
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            45999999999999999999999999 5555554  22    23499999999999999999999999999999999998


Q ss_pred             C
Q 043634           93 S   93 (121)
Q Consensus        93 ~   93 (121)
                      .
T Consensus       596 ~  596 (725)
T KOG0110|consen  596 E  596 (725)
T ss_pred             c
Confidence            3

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=99.00  E-value=2.7e-09  Score=73.83  Aligned_cols=76  Identities=24%  Similarity=0.350  Sum_probs=66.5

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccE--EEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSV--RPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK   94 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~--~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   94 (121)
                      .++|+|.|||+.+.++||+++|..||. ..+  .+-..|.+.|.|-|.|...++|.+|+..+||..++|+.+++.....
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            599999999999999999999999987 222  2222888899999999999999999999999999999999988743

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

Probab=98.98  E-value=2.7e-09  Score=82.15  Aligned_cols=75  Identities=27%  Similarity=0.409  Sum_probs=68.7

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc------CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS------AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~------~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      .+++||+||++.++++.|-..|+.||. .++++++      ....+.|+||.|-+..++++|++.|+|..+.+..+++.|
T Consensus       174 TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~gW  253 (877)
T KOG0151|consen  174 TTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLGW  253 (877)
T ss_pred             ccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeecc
Confidence            799999999999999999999999999 7788777      344567999999999999999999999999999999999


Q ss_pred             cC
Q 043634           92 AS   93 (121)
Q Consensus        92 a~   93 (121)
                      ++
T Consensus       254 gk  255 (877)
T KOG0151|consen  254 GK  255 (877)
T ss_pred             cc
Confidence            83

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.97  E-value=3.9e-09  Score=75.42  Aligned_cols=76  Identities=24%  Similarity=0.296  Sum_probs=67.9

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-c--------cEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeE
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-S--------SVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKV   86 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~--------~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~   86 (121)
                      .++.|||+|||..+|.+++..+|+++|. .        .|++-+  .|..+|=|.+.|.-.+++.-|+..|++..+.|+.
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            3788999999999999999999999997 2        144444  7888999999999999999999999999999999


Q ss_pred             EEEEecC
Q 043634           87 LSVERAS   93 (121)
Q Consensus        87 l~v~~a~   93 (121)
                      |+|+.|+
T Consensus       213 ~rVerAk  219 (382)
T KOG1548|consen  213 LRVERAK  219 (382)
T ss_pred             EEEehhh
Confidence            9999995

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

Probab=98.84  E-value=5.5e-09  Score=78.41  Aligned_cols=71  Identities=35%  Similarity=0.482  Sum_probs=63.3

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      ..+..+|+|-|||..+++++|..+|+.||+  |+-+. +-..+|..||+|-|..+|++|++.|++..+.|+.|+
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGe--ir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGE--IREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcc--hhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            444789999999999999999999999999  54454 556679999999999999999999999999999887

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

Probab=98.83  E-value=5e-09  Score=71.20  Aligned_cols=70  Identities=27%  Similarity=0.404  Sum_probs=60.9

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ..+|||+||+.+.+.+|+.+|..||.  +..+.  ...||+||+|.+.-+|+.|+-.+|+..++|..+.|++++
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~--~~d~~--mk~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r   71 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGK--IPDAD--MKNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHAR   71 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccc--cccce--eecccceeccCchhhhhcccchhcCceecceeeeeeccc
Confidence            46899999999999999999999999  32222  113789999999999999999999999999999999995

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

Probab=98.82  E-value=3.7e-09  Score=75.66  Aligned_cols=78  Identities=22%  Similarity=0.288  Sum_probs=65.0

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ..+++||++|++.++++.|+..|.+||. ..+.+++   ++.++||+||+|.+.+...+++. ..-..|.|+.|.++.+ 
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~a-   82 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRA-   82 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceec-
Confidence            5799999999999999999999999999 5555544   78899999999998888877764 3347899999998888 


Q ss_pred             CCCc
Q 043634           94 KPNE   97 (121)
Q Consensus        94 ~~~~   97 (121)
                      -++.
T Consensus        83 v~r~   86 (311)
T KOG4205|consen   83 VSRE   86 (311)
T ss_pred             cCcc
Confidence            4443

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

Probab=98.78  E-value=2.2e-08  Score=74.23  Aligned_cols=73  Identities=23%  Similarity=0.354  Sum_probs=61.6

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...|||+|||++++.++|+.+|..||. ....+..   .++..+||||+|.+...+..||.+ +-..++++++.|+..
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek  364 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEK  364 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEec
Confidence            466999999999999999999999999 4433333   355559999999999999999965 478899999999977

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.77  E-value=2.3e-08  Score=69.01  Aligned_cols=78  Identities=17%  Similarity=0.305  Sum_probs=67.3

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEc---cCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPC---SAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~---~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ..+....||.|.|..+++++.|-+.|.+|-. ..-+++   ++|+++||+||.|.+..++.+|+..|+|..++.+.|++.
T Consensus       186 w~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklR  265 (290)
T KOG0226|consen  186 WDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLR  265 (290)
T ss_pred             CccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhh
Confidence            3444799999999999999999999999876 333344   499999999999999999999999999999999998875


Q ss_pred             ec
Q 043634           91 RA   92 (121)
Q Consensus        91 ~a   92 (121)
                      .+
T Consensus       266 kS  267 (290)
T KOG0226|consen  266 KS  267 (290)
T ss_pred             hh
Confidence            44

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.72  E-value=2e-07  Score=56.13  Aligned_cols=76  Identities=21%  Similarity=0.265  Sum_probs=60.1

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhh--CCccEEEc----cCCCcccEEEEEeCCHHHHHHHHHHhcCCeeC----CeEEE
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHY--GASSVRPC----SAGRLRNCVFVDFGNEPLASQAQMQLNGLRFL----GKVLS   88 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~--G~~~~~~~----~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~----g~~l~   88 (121)
                      .++|-|+|||...+.++|.+++...  |.-....+    .++.+.|||||.|.+...+..-...++|..+.    .+...
T Consensus         1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~   80 (97)
T PF04059_consen    1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCE   80 (97)
T ss_pred             CeeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEE
Confidence            4799999999999999999999754  33122111    17788999999999999999999999998775    45668


Q ss_pred             EEecCC
Q 043634           89 VERASK   94 (121)
Q Consensus        89 v~~a~~   94 (121)
                      |.+|+.
T Consensus        81 i~yAri   86 (97)
T PF04059_consen   81 ISYARI   86 (97)
T ss_pred             EehhHh
Confidence            888843

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

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

Probab=98.71  E-value=2.1e-08  Score=71.80  Aligned_cols=78  Identities=24%  Similarity=0.365  Sum_probs=64.7

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK   94 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   94 (121)
                      ..+|||++||.++++.+|++.|.+||. ..+.++.   +...+||+||+|.++++++.++ ...-..|+|+.+.|..| .
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~-~~~f~~~~gk~vevkrA-~  174 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVT-LQKFHDFNGKKVEVKRA-I  174 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceec-ccceeeecCceeeEeec-c
Confidence            459999999999999999999999997 3333333   6788999999999999988886 35668999999999999 6


Q ss_pred             CCcc
Q 043634           95 PNEE   98 (121)
Q Consensus        95 ~~~~   98 (121)
                      |+..
T Consensus       175 pk~~  178 (311)
T KOG4205|consen  175 PKEV  178 (311)
T ss_pred             chhh
Confidence            6443

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

Probab=98.55  E-value=3.3e-07  Score=68.30  Aligned_cols=76  Identities=17%  Similarity=0.212  Sum_probs=64.5

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ......|-+++|||.+|++||.++|+.++...+.+.+ +|+..|-|||+|.+.+++..|++ .+...+..+.|.|-.+
T Consensus         7 ~~~~~~vr~rGLPwsat~~ei~~Ff~~~~I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    7 GSTAFEVRLRGLPWSATEKEILDFFSNCGIENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTA   83 (510)
T ss_pred             CCcceEEEecCCCccccHHHHHHHHhcCceeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEcc
Confidence            3446788899999999999999999999985565555 69999999999999999999996 4667788888888766

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

Probab=98.54  E-value=1.3e-07  Score=71.21  Aligned_cols=76  Identities=22%  Similarity=0.432  Sum_probs=67.8

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ..+.+||++||...+++++.+++..||. ....++.   +|.++||||.+|.+......|+..|||..++++.|.|..+.
T Consensus       288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~  367 (500)
T KOG0120|consen  288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAI  367 (500)
T ss_pred             ccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhh
Confidence            3799999999999999999999999999 3333333   67899999999999999999999999999999999999984

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

Probab=98.52  E-value=2.1e-07  Score=64.39  Aligned_cols=77  Identities=16%  Similarity=0.257  Sum_probs=67.0

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ......+||+|+.+.++.++++..|..||. ..+.++.   .+..+||+||+|.+.+....++. |+|..|.|+.+.|.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeee
Confidence            334799999999999999999999999999 3344444   66789999999999999999997 999999999999987


Q ss_pred             cC
Q 043634           92 AS   93 (121)
Q Consensus        92 a~   93 (121)
                      .+
T Consensus       177 ~r  178 (231)
T KOG4209|consen  177 KR  178 (231)
T ss_pred             ee
Confidence            74

>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=98.52  E-value=6e-07  Score=52.29  Aligned_cols=70  Identities=23%  Similarity=0.379  Sum_probs=46.9

Q ss_pred             cEEEecCCCCCCCHH----HHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 043634           20 VTLLIKHLPDAIPQD----TLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK   94 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~----~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   94 (121)
                      ..|||.|||.+....    -|++++..+|.. +..+ +   .+.|++.|.+.+.|.+|.++|+|-.+-|.+|.|++...
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGk-Vl~v-~---~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~   76 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGK-VLSV-S---GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPK   76 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT---EEE------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCE-EEEE-e---CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCC
Confidence            468999999998875    466666677751 2112 3   37999999999999999999999999999999998843

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.50  E-value=4.9e-08  Score=66.16  Aligned_cols=75  Identities=23%  Similarity=0.181  Sum_probs=64.8

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +...+|||+|+...++++.|.++|-+.|. ..+.+..  .+..+ ||||.|.++.+..-|+..+||..+-+..+.+++-
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            33789999999999999999999999999 5566655  33334 9999999999999999999999999999888765

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

Probab=98.42  E-value=3.8e-06  Score=57.14  Aligned_cols=77  Identities=22%  Similarity=0.371  Sum_probs=65.6

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEEe
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFL-GKVLSVER   91 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~-g~~l~v~~   91 (121)
                      ....+...+|+.|||..++.+.|..+|.+|.. ..++++...  ++.|||+|.+...+..|...++|..|- ...+.|.+
T Consensus       141 ~~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~--~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~  218 (221)
T KOG4206|consen  141 QMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR--SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITF  218 (221)
T ss_pred             cCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC--CceeEEecchhhhhHHHhhhhccceeccCceEEecc
Confidence            33556899999999999999999999999987 678887622  479999999999999999999998887 77788877


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      +
T Consensus       219 a  219 (221)
T KOG4206|consen  219 A  219 (221)
T ss_pred             c
Confidence            6

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

Probab=98.36  E-value=5.3e-07  Score=61.46  Aligned_cols=64  Identities=23%  Similarity=0.278  Sum_probs=51.7

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFL   83 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~   83 (121)
                      -.+|||-||..+++|++|+.+|+.|.. ..+++-.. ....+||++|++.+.|..|+..|+|..|-
T Consensus       210 cstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~-~g~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  210 CSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR-GGMPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC-CCcceEeecHHHHHHHHHHHHHhhcceec
Confidence            378999999999999999999999977 32333322 22469999999999999999999987653

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.36  E-value=3.9e-06  Score=61.60  Aligned_cols=75  Identities=24%  Similarity=0.401  Sum_probs=66.3

Q ss_pred             ccEEEecCCCCC-CCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 043634           19 LVTLLIKHLPDA-IPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKP   95 (121)
Q Consensus        19 ~~~l~V~nlp~~-~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   95 (121)
                      +..|.|.||... +|.+.|..+|+-||. .+|+++.+.+  --|.|.|.|...|.-|+..|+|..|.|++|+|.+++.+
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk--d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~  373 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK--DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHT  373 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC--cceeeeecchhHHHHHHHHhhcceecCceEEEeeccCc
Confidence            588999999776 999999999999999 6777776433  68999999999999999999999999999999999643

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

Probab=98.21  E-value=1.1e-05  Score=60.44  Aligned_cols=75  Identities=17%  Similarity=0.182  Sum_probs=60.8

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-cc-EEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SS-VRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~-~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+...|-+++||+.|+++||.++|+..-. .. +.++.  .++..|-|||.|.+.+.++.|+.+ |...|+.+.|.|-.+
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehh
Confidence            45789999999999999999999987544 22 32333  667779999999999999999865 557888888888766

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.21  E-value=2.5e-06  Score=61.63  Aligned_cols=74  Identities=11%  Similarity=0.090  Sum_probs=62.6

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC---ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA---SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~---~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...+|||||-|.+|++||.+.+...|.   ..+++..   +|+++|||++...+.......++.|--..|+|+.-.|.-.
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            577999999999999999999998887   2344443   8999999999999988888999999999999987666544

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.09  E-value=8e-06  Score=58.90  Aligned_cols=78  Identities=19%  Similarity=0.323  Sum_probs=66.7

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-cc--------EEEc---cCCCcccEEEEEeCCHHHHHHHHHHhcCCeeC
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SS--------VRPC---SAGRLRNCVFVDFGNEPLASQAQMQLNGLRFL   83 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~--------~~~~---~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~   83 (121)
                      .....+|||-+||..+++++|.++|.++|. ..        +.+-   .++..++-|.|+|.|...|.+||.-+++..++
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            334799999999999999999999999987 21        1111   17888999999999999999999999999999


Q ss_pred             CeEEEEEecC
Q 043634           84 GKVLSVERAS   93 (121)
Q Consensus        84 g~~l~v~~a~   93 (121)
                      +..|+|..+.
T Consensus       143 gn~ikvs~a~  152 (351)
T KOG1995|consen  143 GNTIKVSLAE  152 (351)
T ss_pred             CCCchhhhhh
Confidence            9999999883

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

Probab=98.08  E-value=5.3e-06  Score=56.61  Aligned_cols=72  Identities=28%  Similarity=0.425  Sum_probs=61.8

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...+.+.|.+++..+...+|.+.|+.+|.  +.....  .++++||.|....++..|+..+++..+.++.|.+...
T Consensus        97 ~s~~r~~~~~~~~r~~~qdl~d~~~~~g~--~~~~~~--~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen   97 RTHFRLIVRNLSLRVSWQDLKDHFRPAGE--VTYVDA--RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             cccceeeeccchhhhhHHHHhhhhcccCC--Cchhhh--hccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence            33789999999999999999999999999  311111  4689999999999999999999999999999999544

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

Probab=98.08  E-value=6e-05  Score=55.07  Aligned_cols=78  Identities=19%  Similarity=0.293  Sum_probs=68.0

Q ss_pred             CCCCCccEEEecCCCCC-CCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           14 QETENLVTLLIKHLPDA-IPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~-~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ....+++.+.|-+|... +.-+.|..+|+.||. +.|+++++.  .|-|.|++.|....++|+..||+..+-|.+|.|..
T Consensus       282 ~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk--~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~  359 (494)
T KOG1456|consen  282 GGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK--PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCV  359 (494)
T ss_pred             CCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc--cceeEEEcCcHHHHHHHHHHhccCccccceEEEee
Confidence            44455899999999987 666789999999999 788888753  58999999999999999999999999999999998


Q ss_pred             cC
Q 043634           92 AS   93 (121)
Q Consensus        92 a~   93 (121)
                      ++
T Consensus       360 Sk  361 (494)
T KOG1456|consen  360 SK  361 (494)
T ss_pred             cc
Confidence            83

>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=98.04  E-value=1.5e-05  Score=48.80  Aligned_cols=72  Identities=21%  Similarity=0.269  Sum_probs=43.0

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCC-----eeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGL-----RFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~-----~i~g~~l~v~~a   92 (121)
                      ++.|+|.+++..++.++|+..|+.||.  |.++.-...-..|||.|.+.+.|..|+..+...     .+.+..+.++.-
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~--V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~vL   77 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGE--VAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEVL   77 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS----EEEEE--TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE--
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCC--cceEEecCCCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEEC
Confidence            357889999999999999999999998  777762222358999999999999998877544     455555555443

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=97.99  E-value=4.1e-06  Score=63.22  Aligned_cols=73  Identities=27%  Similarity=0.382  Sum_probs=65.9

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      -.++|+.-|+..++..+|+.+|+.+|. -.|++|.   ++.++|.+||+|.|..+...|| .|.|..++|.+|.|+..
T Consensus       179 ~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~s  255 (549)
T KOG0147|consen  179 QRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQLS  255 (549)
T ss_pred             HHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEeccc
Confidence            588999999999999999999999999 5566665   7788999999999999999998 79999999999999876

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.81  E-value=0.00012  Score=57.33  Aligned_cols=72  Identities=22%  Similarity=0.365  Sum_probs=63.3

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC--ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA--SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~--~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      +.|-+.|.|+.++-+||-++|..|-.  .+|++-.  .|...|-|.|.|++.+.|.+|...|++..|..+++.|.+
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            58899999999999999999999977  4455444  677789999999999999999999999999999988754

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.78  E-value=2.6e-05  Score=55.64  Aligned_cols=83  Identities=22%  Similarity=0.313  Sum_probs=66.9

Q ss_pred             CCCCccEEE-ecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           15 ETENLVTLL-IKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        15 ~~~~~~~l~-V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      ...+..++| |++++..+++++|+..|..+|. ..+++..   ++..+|+||+.|........++.. +...+.++.+.+
T Consensus       180 ~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~  258 (285)
T KOG4210|consen  180 SSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRL  258 (285)
T ss_pred             ccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCccccc
Confidence            334455666 9999999999999999999998 4444443   778899999999999998888876 778899999999


Q ss_pred             EecCCCCccc
Q 043634           90 ERASKPNEEN   99 (121)
Q Consensus        90 ~~a~~~~~~~   99 (121)
                      ... .+.++.
T Consensus       259 ~~~-~~~~~~  267 (285)
T KOG4210|consen  259 EED-EPRPKS  267 (285)
T ss_pred             ccC-CCCccc
Confidence            988 665554

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.73  E-value=0.00013  Score=52.84  Aligned_cols=74  Identities=14%  Similarity=0.300  Sum_probs=57.0

Q ss_pred             ccEEEecCCCCCCCHHH------HHHHHhhhCC-ccEEEcc-C---CCccc--EEEEEeCCHHHHHHHHHHhcCCeeCCe
Q 043634           19 LVTLLIKHLPDAIPQDT------LSRIFSHYGA-SSVRPCS-A---GRLRN--CVFVDFGNEPLASQAQMQLNGLRFLGK   85 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~------L~~~f~~~G~-~~~~~~~-~---~~~~g--~afv~f~~~~~a~~ai~~l~g~~i~g~   85 (121)
                      ..-+||-+||+.+..++      -.++|++||. ..+.+-+ +   ....+  ..||+|...++|.+||...+|..++|+
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            46789999999877765      3578999999 4443333 1   11112  349999999999999999999999999


Q ss_pred             EEEEEec
Q 043634           86 VLSVERA   92 (121)
Q Consensus        86 ~l~v~~a   92 (121)
                      .|+..+.
T Consensus       194 ~lkatYG  200 (480)
T COG5175         194 VLKATYG  200 (480)
T ss_pred             eEeeecC
Confidence            9998876

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=97.73  E-value=0.0001  Score=54.38  Aligned_cols=75  Identities=19%  Similarity=0.255  Sum_probs=61.7

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCe-EEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGK-VLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~-~l~v~~a   92 (121)
                      +|..++.+.|||..+++++|+..|..-|.. ++.-. -++.+.++++.+.+.+.|..|+-.+|...+++. -++|+++
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~-vkafkff~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFS  488 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQ-VKAFKFFQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFS  488 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCce-EEeeeecCCCcceeecccCChhHhhhhccccccccCCCCceEEEEee
Confidence            447899999999999999999999987761 22222 344567999999999999999999999998854 8899988

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

Probab=97.71  E-value=0.0001  Score=54.05  Aligned_cols=74  Identities=14%  Similarity=0.168  Sum_probs=61.8

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-cc---EEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SS---VRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~---~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...|.+++||+..+.+||.++|..|.. ..   |+++.  .|...|-|||+|.+.+.|.+|..+.+......+.|.|--+
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~  359 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPC  359 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeec
Confidence            677899999999999999999998876 32   44444  6777899999999999999998888876667888888666

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

Probab=97.70  E-value=0.00038  Score=52.63  Aligned_cols=59  Identities=17%  Similarity=0.236  Sum_probs=46.2

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc------CCCccc---EEEEEeCCHHHHHHHHHHh
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS------AGRLRN---CVFVDFGNEPLASQAQMQL   77 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~------~~~~~g---~afv~f~~~~~a~~ai~~l   77 (121)
                      .++||||+||+.++|+.|...|..||...+.+..      .-..+|   |+|+.|.++.+...-+...
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             ccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            7999999999999999999999999995555552      112345   9999999988776655443

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

Probab=97.68  E-value=8e-05  Score=57.15  Aligned_cols=78  Identities=15%  Similarity=0.239  Sum_probs=61.9

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCee---CCeEEEEEe
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRF---LGKVLSVER   91 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i---~g~~l~v~~   91 (121)
                      ...+...|||.||-+-.|..+|+.+++.-|.. |.-.+..+.+.+|||.|.+.++|.+.+..|||..+   +++.|.+.|
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~-Vee~WmDkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf  518 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGN-VEEFWMDKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADF  518 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCc-hHHHHHHHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeee
Confidence            34458999999999999999999999965441 21124455678999999999999999999999766   467788888


Q ss_pred             cC
Q 043634           92 AS   93 (121)
Q Consensus        92 a~   93 (121)
                      ..
T Consensus       519 ~~  520 (718)
T KOG2416|consen  519 VR  520 (718)
T ss_pred             cc
Confidence            74

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

Probab=97.49  E-value=9.5e-05  Score=51.40  Aligned_cols=69  Identities=22%  Similarity=0.269  Sum_probs=54.7

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---C--------CCcc----cEEEEEeCCHHHHHHHHHHhcCCe
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---A--------GRLR----NCVFVDFGNEPLASQAQMQLNGLR   81 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~--------~~~~----g~afv~f~~~~~a~~ai~~l~g~~   81 (121)
                      ....||+++||+.+...-|+.+|+.||. -.|-+-.   +        |.++    .-|+|+|.+...|..+...||+..
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            3578999999999999999999999999 3332221   1        2222    246789999999999999999999


Q ss_pred             eCCeE
Q 043634           82 FLGKV   86 (121)
Q Consensus        82 i~g~~   86 (121)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99975

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

Probab=97.48  E-value=0.00083  Score=49.28  Aligned_cols=78  Identities=26%  Similarity=0.272  Sum_probs=60.4

Q ss_pred             CCCCccEEEecCC--CCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeC--CeEEEE
Q 043634           15 ETENLVTLLIKHL--PDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFL--GKVLSV   89 (121)
Q Consensus        15 ~~~~~~~l~V~nl--p~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~--g~~l~v   89 (121)
                      +..++..|.+.=|  -+.+|.+.|..+....|. ..|.+.+  ++--.|.|+|++.+.|.+|-..|||..|-  ...|+|
T Consensus       116 s~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfk--kngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKI  193 (494)
T KOG1456|consen  116 SATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFK--KNGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKI  193 (494)
T ss_pred             CCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEe--ccceeeEEeechhHHHHHHHhhcccccccccceeEEE
Confidence            3444666666544  445899999999999999 5555544  23368999999999999999999998775  578999


Q ss_pred             EecCCC
Q 043634           90 ERASKP   95 (121)
Q Consensus        90 ~~a~~~   95 (121)
                      ++| +|
T Consensus       194 eyA-kP  198 (494)
T KOG1456|consen  194 EYA-KP  198 (494)
T ss_pred             Eec-Cc
Confidence            999 44

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

Probab=97.45  E-value=0.00013  Score=54.13  Aligned_cols=70  Identities=24%  Similarity=0.297  Sum_probs=57.2

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCC-eeCCeEEEEEec
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGL-RFLGKVLSVERA   92 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~-~i~g~~l~v~~a   92 (121)
                      .++|++||.+.++..||+.+|..... .+-.++..   .||+|+.+.+..-+.+|++.++|. .+.|+++.|...
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k---~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~s   73 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK---SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHS   73 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee---cceeeccCCchhhhhhhHHhhchhhhhcCceeeccch
Confidence            46899999999999999999975433 22333321   279999999999999999999985 688999999887

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

Probab=97.43  E-value=0.00058  Score=36.57  Aligned_cols=52  Identities=13%  Similarity=0.311  Sum_probs=38.9

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHH
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQ   74 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai   74 (121)
                      +.|-|.+.++...+..| ..|..||.  +..+.-+....+.++.|.++.+|+.|+
T Consensus         2 ~wI~V~Gf~~~~~~~vl-~~F~~fGe--I~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEEVL-EHFASFGE--IVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHHHH-HHHHhcCC--EEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            56778898888776655 48889999  544442333569999999999999874

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

Probab=97.41  E-value=0.0012  Score=50.66  Aligned_cols=74  Identities=22%  Similarity=0.291  Sum_probs=58.3

Q ss_pred             ccEEEecCCCCCCCH------HHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEE
Q 043634           19 LVTLLIKHLPDAIPQ------DTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFL-GKVLS   88 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~------~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~-g~~l~   88 (121)
                      ...|+|-|+|---..      ..|..+|+++|. ...-++.  .|..+||.|++|.+..+|..|++.|||..|+ .+.+.
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~  137 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFF  137 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceEE
Confidence            678899999875333      357788999998 4444443  5668999999999999999999999999987 56666


Q ss_pred             EEec
Q 043634           89 VERA   92 (121)
Q Consensus        89 v~~a   92 (121)
                      |...
T Consensus       138 v~~f  141 (698)
T KOG2314|consen  138 VRLF  141 (698)
T ss_pred             eehh
Confidence            6544

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

Probab=97.39  E-value=0.0012  Score=38.53  Aligned_cols=55  Identities=18%  Similarity=0.244  Sum_probs=41.7

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhc
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLN   78 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~   78 (121)
                      .+..||+ .|..+...||.++|+.||...|.++..    .-|||...+.+.+..++..+.
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~d----TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWIND----TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEEEEEECT----TEEEEEECCCHHHHHHHHHHT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEEEEEEcC----CcEEEEeecHHHHHHHHHHhc
Confidence            5667776 999999999999999999955566543    479999999999998887765

; 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.

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

Probab=97.25  E-value=0.0014  Score=42.21  Aligned_cols=57  Identities=26%  Similarity=0.419  Sum_probs=41.4

Q ss_pred             HHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCc
Q 043634           35 TLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNE   97 (121)
Q Consensus        35 ~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~~~   97 (121)
                      +|.+.|..||. .-+|++  +   +.-+|+|.+-.+|.+|+ .++|..++|+.|+|......+.
T Consensus        52 ~ll~~~~~~GevvLvRfv--~---~~mwVTF~dg~sALaal-s~dg~~v~g~~l~i~LKtpdW~  109 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFV--G---DTMWVTFRDGQSALAAL-SLDGIQVNGRTLKIRLKTPDWL  109 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEE--T---TCEEEEESSCHHHHHHH-HGCCSEETTEEEEEEE------
T ss_pred             HHHHHHHhCCceEEEEEe--C---CeEEEEECccHHHHHHH-ccCCcEECCEEEEEEeCCccHH
Confidence            68888889998 333333  2   47799999999999998 5899999999999988743343

; PDB: 1UFW_A 2DNR_A.

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=97.23  E-value=0.0019  Score=46.91  Aligned_cols=73  Identities=21%  Similarity=0.246  Sum_probs=56.6

Q ss_pred             ccEEEecCCCC----CCC-------HHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeE
Q 043634           19 LVTLLIKHLPD----AIP-------QDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKV   86 (121)
Q Consensus        19 ~~~l~V~nlp~----~~~-------~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~   86 (121)
                      .++|.+.|+=.    ..+       .++|..-..+||. .+|.+. ...+.|.+-|.|.+.+.|..||..|+|..+.|+.
T Consensus       265 ~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~-d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRq  343 (382)
T KOG1548|consen  265 DRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVY-DRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQ  343 (382)
T ss_pred             CcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEe-ccCCCceeEEEeCChHHHHHHHHHhcCeeecceE
Confidence            68888988721    223       2456666889999 333333 3345689999999999999999999999999999


Q ss_pred             EEEEec
Q 043634           87 LSVERA   92 (121)
Q Consensus        87 l~v~~a   92 (121)
                      |..+..
T Consensus       344 l~A~i~  349 (382)
T KOG1548|consen  344 LTASIW  349 (382)
T ss_pred             EEEEEe
Confidence            998877

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

Probab=97.19  E-value=0.0042  Score=34.29  Aligned_cols=54  Identities=22%  Similarity=0.328  Sum_probs=42.8

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhh----CCccEEEccCCCcccEEEEEeCCHHHHHHHHHHh
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHY----GASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQL   77 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~----G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l   77 (121)
                      +.+|+|+++.. ++.++++.+|..|    +...+.++.-    .-|-|.|.+...|.+|+..|
T Consensus         5 peavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdD----tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDD----TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecC----CcEEEEECCHHHHHHHHHcC
Confidence            57899999854 7778899999999    5566777762    25678999999999998654

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.17  E-value=0.0007  Score=54.26  Aligned_cols=77  Identities=22%  Similarity=0.327  Sum_probs=66.0

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEec
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLG--KVLSVERA   92 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g--~~l~v~~a   92 (121)
                      ...+.+.+|+++|..++....|...|..||.  ++.|.-.....|+|+.|.+...+..|+..|-|..|+|  +.++|.++
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGp--ir~Idy~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla  528 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGP--IRIIDYRHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLA  528 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCc--ceeeecccCCcceeeecccCccchhhHHHHhcCcCCCCCcccccccc
Confidence            4555899999999999999999999999999  6666523334699999999999999999999999996  57899988


Q ss_pred             C
Q 043634           93 S   93 (121)
Q Consensus        93 ~   93 (121)
                      .
T Consensus       529 ~  529 (975)
T KOG0112|consen  529 S  529 (975)
T ss_pred             c
Confidence            4

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

Probab=97.02  E-value=0.0031  Score=48.18  Aligned_cols=58  Identities=21%  Similarity=0.265  Sum_probs=45.0

Q ss_pred             HHHHHHhhhCC-ccEEEcc------CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           35 TLSRIFSHYGA-SSVRPCS------AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        35 ~L~~~f~~~G~-~~~~~~~------~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +++.-+++||. .+|.+.+      .....|..||+|.+.+++++|...|+|..+.++.+...|-
T Consensus       425 dvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYy  489 (500)
T KOG0120|consen  425 DVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYY  489 (500)
T ss_pred             HHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEec
Confidence            45555667787 4444443      1233578899999999999999999999999999988876

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

Probab=97.02  E-value=0.0028  Score=48.07  Aligned_cols=62  Identities=19%  Similarity=0.237  Sum_probs=51.0

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHh-hhCCccEEEcc------CCCcccEEEEEeCCHHHHHHHHHH
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFS-HYGASSVRPCS------AGRLRNCVFVDFGNEPLASQAQMQ   76 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~-~~G~~~~~~~~------~~~~~g~afv~f~~~~~a~~ai~~   76 (121)
                      ....++.+|||||+||.-++-.+|-.+|. -||.  |...-      -+..+|-|-|+|.+..+-.+||.+
T Consensus       364 sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGg--V~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  364 NQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGG--VLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CcccCccceEEecCCCCcchHHHHHHHHHHhcCc--eEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            34567789999999999999999999998 6998  33322      356788999999999999999864

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.86  E-value=0.0022  Score=47.79  Aligned_cols=63  Identities=29%  Similarity=0.495  Sum_probs=52.5

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccC--------C-C-------cccEEEEEeCCHHHHHHHHHHhcC
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSA--------G-R-------LRNCVFVDFGNEPLASQAQMQLNG   79 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~--------~-~-------~~g~afv~f~~~~~a~~ai~~l~g   79 (121)
                      -+.++|.+-|||.+-.-+-|.++|+.+|. ..|++|.-        + .       .+-||+|+|...+.|.+|.+.++.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            35899999999999888999999999999 77777761        1 1       256899999999999999987753

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.79  E-value=0.0061  Score=48.12  Aligned_cols=69  Identities=17%  Similarity=0.240  Sum_probs=56.8

Q ss_pred             EEEecCCCCCCCHHHHHHHHhhhCC--ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           21 TLLIKHLPDAIPQDTLSRIFSHYGA--SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        21 ~l~V~nlp~~~~~~~L~~~f~~~G~--~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .|.+.|||+.....||+.+|+....  --|+++  |...|-|||.|.+-++|..|+.+ .+..|+|-.+++-++
T Consensus         4 IIRLqnLP~tAga~DIR~FFSGL~IPdGgVHII--GGe~GeaFI~FsTDeDARlaM~k-dr~~i~g~~VrLlLS   74 (944)
T KOG4307|consen    4 IIRLQNLPMTAGASDIRTFFSGLKIPDGGVHII--GGEEGEAFIGFSTDEDARLAMTK-DRLMIHGAEVRLLLS   74 (944)
T ss_pred             EEEecCCcccccchHHHHhhcccccCCCceEEe--cccccceEEEecccchhhhhhhh-cccceecceEEEEec
Confidence            4667899999999999999987644  226776  55568999999999999998854 578899999988887

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

Probab=96.67  E-value=0.0074  Score=44.63  Aligned_cols=69  Identities=20%  Similarity=0.182  Sum_probs=50.9

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHh---hh--CCccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFS---HY--GASSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~---~~--G~~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      --.|.+++||+++++.++..+|.   ..  |.+.+.++.  .|+..|-|||.|..+++|+.|+.+ |...++.+.|.
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIE  236 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIE  236 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHH
Confidence            45677789999999999999996   22  234455554  677789999999999999999865 33444444443

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

Probab=96.55  E-value=0.0014  Score=52.33  Aligned_cols=74  Identities=20%  Similarity=0.192  Sum_probs=61.2

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...++|+|.|+..|.++|+.++...|. .+++.+.  .|+.+|.|++.|.+..++.+++....+..+.-..+.|..+
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~vs  812 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVS  812 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCcccccc
Confidence            578999999999999999999999999 5554443  7889999999999999999888777766666666666554

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

Probab=96.53  E-value=0.0022  Score=44.75  Aligned_cols=59  Identities=24%  Similarity=0.398  Sum_probs=45.4

Q ss_pred             HHHHHHHh-hhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           34 DTLSRIFS-HYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        34 ~~L~~~f~-~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +++...|. +||+ ..+.++.  ...-.|=+||.|...++|++|+..||+--+.|++|..++.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            34444455 7888 4444444  2234678899999999999999999999999999998877

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

Probab=96.50  E-value=0.018  Score=34.86  Aligned_cols=72  Identities=19%  Similarity=0.258  Sum_probs=47.7

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEc-c---------CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEE
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPC-S---------AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVL   87 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~-~---------~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l   87 (121)
                      .+-|.|=+.|+. ....+.+.|++||. .....+ .         ......+-.|+|.+..+|.+|+. -||..+.|..+
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEE
Confidence            456778888888 45668889999999 433201 0         01224688999999999999994 69999998654


Q ss_pred             -EEEec
Q 043634           88 -SVERA   92 (121)
Q Consensus        88 -~v~~a   92 (121)
                       -|.++
T Consensus        84 vGV~~~   89 (100)
T PF05172_consen   84 VGVKPC   89 (100)
T ss_dssp             EEEEE-
T ss_pred             EEEEEc
Confidence             56666

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.

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

Probab=96.21  E-value=0.041  Score=37.01  Aligned_cols=63  Identities=16%  Similarity=0.157  Sum_probs=52.2

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeC
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFL   83 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~   83 (121)
                      .-..|.|++||+..+..||++...+.|.  +.+-...+ -|++.|+|-..++..-|+..|....+.
T Consensus       114 Se~RVvVsGLp~SgSWQDLKDHmReaGd--vCfadv~r-Dg~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  114 SEYRVVVSGLPPSGSWQDLKDHMREAGD--VCFADVQR-DGVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             cceeEEEecCCCCCchHHHHHHHHhhCC--eeeeeeec-ccceeeeeeehhhHHHHHHhhcccccc
Confidence            3578999999999999999999999999  65554222 269999999999999999999876554

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=96.08  E-value=0.007  Score=47.28  Aligned_cols=72  Identities=15%  Similarity=0.110  Sum_probs=58.8

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ..++..++||+|+...+..+-++.++..+|-  |..+..   -.|||..|.+.....+|+..++...++|+.+.+..
T Consensus        36 ~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~--v~s~kr---~~fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   36 PLPPRDTVFVGNISYLVSQEFWKSILAKSGF--VPSWKR---DKFGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCCCCceeEecchhhhhhHHHHHHHHhhCCc--chhhhh---hhhcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            3444799999999999999999999999998  322221   13999999999999999999999999988876544

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

Probab=96.06  E-value=0.018  Score=42.72  Aligned_cols=73  Identities=18%  Similarity=0.336  Sum_probs=55.1

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc-C-----CCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS-A-----GRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~-~-----~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ...|.|.||.+.++.++++.+|.-.|. ..+++.- .     .-....|||.|.|...+..|. .|..+.+-++.|.|-.
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p   85 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRP   85 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEEe
Confidence            348999999999999999999999999 4444433 1     122459999999998888775 5666777777766654


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      .
T Consensus        86 ~   86 (479)
T KOG4676|consen   86 Y   86 (479)
T ss_pred             c
Confidence            4

>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=96.05  E-value=0.0063  Score=40.57  Aligned_cols=75  Identities=15%  Similarity=0.158  Sum_probs=46.8

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhh-hCCc-cEEEcc--------CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCC---
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSH-YGAS-SVRPCS--------AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLG---   84 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~-~G~~-~~~~~~--------~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g---   84 (121)
                      ...+|-|++||+.++++++...++. ++.. ......        .......|||.|.+.+++..-...++|..+.+   
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            3679999999999999999987776 5552 111111        11224689999999999888888999976643   


Q ss_pred             --eEEEEEec
Q 043634           85 --KVLSVERA   92 (121)
Q Consensus        85 --~~l~v~~a   92 (121)
                        ....|++|
T Consensus        86 ~~~~~~VE~A   95 (176)
T PF03467_consen   86 NEYPAVVEFA   95 (176)
T ss_dssp             -EEEEEEEE-
T ss_pred             CCcceeEEEc
Confidence              23456666

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.

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

Probab=95.99  E-value=0.00042  Score=55.15  Aligned_cols=64  Identities=22%  Similarity=0.314  Sum_probs=52.0

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEc-c--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeC
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPC-S--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFL   83 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~-~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~   83 (121)
                      .++||+||+..+.+.+|...|..+|. ..+++. .  .++.+|+||+.|...+.+.+|+....+..++
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            68899999999999999999999988 433333 2  7888999999999999999988655544333

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

Probab=95.94  E-value=0.013  Score=40.96  Aligned_cols=59  Identities=22%  Similarity=0.375  Sum_probs=49.4

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-cc-EEEcc-CCCcccEEEEEeCCHHHHHHHHHHhc
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SS-VRPCS-AGRLRNCVFVDFGNEPLASQAQMQLN   78 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~-~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~   78 (121)
                      ..|||.||+..++.+.|...|+.||. .. |.++. .++..+-++|.|.....+..|....+
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhc
Confidence            88999999999999999999999999 33 33333 66667899999999999888887764

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=95.91  E-value=0.037  Score=39.69  Aligned_cols=59  Identities=27%  Similarity=0.285  Sum_probs=44.2

Q ss_pred             HHHHHHHhhhCC-ccEEEcc---C-CCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           34 DTLSRIFSHYGA-SSVRPCS---A-GRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        34 ~~L~~~f~~~G~-~~~~~~~---~-~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ++++.-+.+||. ..|.+..   . -.....-||+|...++|..|+..|||..++|+.++..+-
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheec
Confidence            467777889998 3332222   1 122346799999999999999999999999999887655

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=95.56  E-value=0.052  Score=38.84  Aligned_cols=49  Identities=16%  Similarity=0.241  Sum_probs=39.3

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHH
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEP   68 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~   68 (121)
                      .+-||++|||+++...||+..+.+.+....++-+.|. +|-||+.|.+..
T Consensus       330 ~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswkg~-~~k~flh~~~~~  378 (396)
T KOG4410|consen  330 KTDIKLTNLSRDIRVKDLKSELRKRECTPMSISWKGH-FGKCFLHFGNRK  378 (396)
T ss_pred             ccceeeccCccccchHHHHHHHHhcCCCceeEeeecC-CcceeEecCCcc
Confidence            5789999999999999999999998873344444553 579999998753

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

Probab=95.26  E-value=0.095  Score=35.24  Aligned_cols=58  Identities=28%  Similarity=0.327  Sum_probs=42.7

Q ss_pred             CHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhc--CCeeCCeEEEEEec
Q 043634           32 PQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLN--GLRFLGKVLSVERA   92 (121)
Q Consensus        32 ~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~--g~~i~g~~l~v~~a   92 (121)
                      ....|+.+|..|+. .....+.+   -+...|.|.+.+.|.+|...|+  +..++|..+++.++
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s---FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~   68 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS---FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFG   68 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT---TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE--
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC---CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEc
Confidence            34789999999998 44444432   3578899999999999999999  99999999999988

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.

>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=95.06  E-value=0.21  Score=28.34  Aligned_cols=68  Identities=24%  Similarity=0.347  Sum_probs=37.8

Q ss_pred             EEec-CCCCCCCHHHHHHHHhhhCC---ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           22 LLIK-HLPDAIPQDTLSRIFSHYGA---SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        22 l~V~-nlp~~~~~~~L~~~f~~~G~---~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +||. +--..++..+|..++...+.   ..+-.+.-  ...|+||+... ..+..++..|++..+.|++++|+.|
T Consensus         3 l~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I--~~~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen    3 LFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDI--FDNFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             EEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE---SS-EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             EEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEE--eeeEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            4443 33345788889999987644   33434431  12589999865 5788899999999999999999865

; PDB: 2G0C_A 3MOJ_B.

>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=94.87  E-value=0.47  Score=29.24  Aligned_cols=66  Identities=23%  Similarity=0.266  Sum_probs=45.2

Q ss_pred             ccEEEecCCCCC-CCHHHHHHHHhhhCC--ccEEEccCCC-cccEEEEEeCCHHHHHHHHHHhcCCeeCC
Q 043634           19 LVTLLIKHLPDA-IPQDTLSRIFSHYGA--SSVRPCSAGR-LRNCVFVDFGNEPLASQAQMQLNGLRFLG   84 (121)
Q Consensus        19 ~~~l~V~nlp~~-~~~~~L~~~f~~~G~--~~~~~~~~~~-~~g~afv~f~~~~~a~~ai~~l~g~~i~g   84 (121)
                      ++.+.+=-.|+. ++.++|..+.+.+-.  ..+++++.+. ++--+.+.|.+...|+.=...+||..++.
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            444554445555 555566555555555  4567777443 56577899999999999999999987763

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=94.54  E-value=0.0083  Score=48.41  Aligned_cols=74  Identities=15%  Similarity=0.185  Sum_probs=57.7

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ..+||+|||+..+++.+|+..|..+|. ..|.+-.  -+....|+|+.|.+...+..|...+.+..|..-.+++.+.
T Consensus       372 trTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  372 TRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            689999999999999999999999999 4443332  3344469999999999999998888887776444444433

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

Probab=93.94  E-value=0.084  Score=40.69  Aligned_cols=44  Identities=14%  Similarity=0.147  Sum_probs=34.9

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhcCCeeC---C-eEEEEEecCCCC
Q 043634           53 AGRLRNCVFVDFGNEPLASQAQMQLNGLRFL---G-KVLSVERASKPN   96 (121)
Q Consensus        53 ~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~---g-~~l~v~~a~~~~   96 (121)
                      +..+.|||||.|.+.+.+....+++||+.+.   + +...+.||+.+.
T Consensus       427 nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYArIQG  474 (549)
T KOG4660|consen  427 NKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYARIQG  474 (549)
T ss_pred             cccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhhhhc
Confidence            6677899999999999999999999997553   4 445788885443

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=93.66  E-value=0.076  Score=40.32  Aligned_cols=72  Identities=15%  Similarity=0.226  Sum_probs=55.2

Q ss_pred             cEEEecCCCCCCC-HHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 043634           20 VTLLIKHLPDAIP-QDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKP   95 (121)
Q Consensus        20 ~~l~V~nlp~~~~-~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   95 (121)
                      +.+-+.-.|+... ..+|...|.+||.  +..+-.+.+.-.|.|+|.+..+|-.|. +.++..|+++-|+|-|- .+
T Consensus       373 s~l~lek~~~glnt~a~ln~hfA~fG~--i~n~qv~~~~~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~wh-np  445 (526)
T KOG2135|consen  373 SPLALEKSPFGLNTIADLNPHFAQFGE--IENIQVDYSSLHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLFWH-NP  445 (526)
T ss_pred             chhhhhccCCCCchHhhhhhhhhhcCc--cccccccCchhhheeeeeccccccchh-ccccceecCceeEEEEe-cC
Confidence            4455555566644 4789999999999  555554555568999999988886664 57899999999999988 44

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.63  E-value=0.82  Score=29.64  Aligned_cols=71  Identities=21%  Similarity=0.380  Sum_probs=48.2

Q ss_pred             CCCccEEEecCCCCCCCH-HH---HHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           16 TENLVTLLIKHLPDAIPQ-DT---LSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~-~~---L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      .+|..+|.|+=|..++.. +|   +..-++.||. .+|..+  |  +.-|.|.|.|..+|=.|+.+++. ..-|..+...
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c--G--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCs  157 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC--G--RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCS  157 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec--C--CceEEEEehhhHHHHHHHHhhcC-CCCCceEEee
Confidence            345678888877666543 34   4455567899 454443  3  46899999999999999988875 4445555544


Q ss_pred             e
Q 043634           91 R   91 (121)
Q Consensus        91 ~   91 (121)
                      |
T Consensus       158 W  158 (166)
T PF15023_consen  158 W  158 (166)
T ss_pred             c
Confidence            3

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=93.49  E-value=0.16  Score=39.47  Aligned_cols=67  Identities=18%  Similarity=0.325  Sum_probs=49.1

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhh--hCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcC--CeeCCeEEE
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSH--YGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNG--LRFLGKVLS   88 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~--~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g--~~i~g~~l~   88 (121)
                      .+|.|.++-||..+..++++.+|..  +-. .++.+-.+    .-=||+|.+..+|..|.+.|..  .+|.|+.|.
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N----~nWyITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN----DNWYITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec----CceEEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            3799999999999999999999965  222 23333222    1338999999999999887754  456676653

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=93.22  E-value=0.029  Score=40.64  Aligned_cols=74  Identities=15%  Similarity=0.266  Sum_probs=53.4

Q ss_pred             ccEEEecCCCCCCCHHHHH---HHHhhhCC-ccEEEcc-C----CC-cccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           19 LVTLLIKHLPDAIPQDTLS---RIFSHYGA-SSVRPCS-A----GR-LRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~---~~f~~~G~-~~~~~~~-~----~~-~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      ...+||-+|+.....+.+.   ..|.+||. .++..-. .    +. ...-++|+|...++|..||..++|..+.|+.++
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            4678888999886555433   46777887 4443333 1    11 123479999999999999999999999999877


Q ss_pred             EEec
Q 043634           89 VERA   92 (121)
Q Consensus        89 v~~a   92 (121)
                      ..+.
T Consensus       157 a~~g  160 (327)
T KOG2068|consen  157 ASLG  160 (327)
T ss_pred             HhhC
Confidence            6666

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=91.81  E-value=0.59  Score=33.81  Aligned_cols=69  Identities=19%  Similarity=0.233  Sum_probs=49.3

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeE-EEEEec
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKV-LSVERA   92 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~-l~v~~a   92 (121)
                      .=|-|-+.|+.-.. -|...|.+||.  |.-...+.+..+-+|.|....+|++||. .+|..|+|.. |-|+.+
T Consensus       198 ~WVTVfGFppg~~s-~vL~~F~~cG~--Vvkhv~~~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpC  267 (350)
T KOG4285|consen  198 TWVTVFGFPPGQVS-IVLNLFSRCGE--VVKHVTPSNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPC  267 (350)
T ss_pred             ceEEEeccCccchh-HHHHHHHhhCe--eeeeecCCCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeec
Confidence            44555577776554 46678999999  4333333444699999999999999995 5899998754 467665

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=90.60  E-value=1.9  Score=32.93  Aligned_cols=66  Identities=23%  Similarity=0.311  Sum_probs=55.6

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC--ccEEEccCCCc-ccEEEEEeCCHHHHHHHHHHhcCCeeCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA--SSVRPCSAGRL-RNCVFVDFGNEPLASQAQMQLNGLRFLG   84 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~--~~~~~~~~~~~-~g~afv~f~~~~~a~~ai~~l~g~~i~g   84 (121)
                      ++.|.|=.+|..++..||..+...+-.  ..+++++.|.. +=-..|.|.+..+|..=...+||..++.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            789999999999999999999998765  56888885543 3356899999999999999999987763

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.89  E-value=1.6  Score=32.97  Aligned_cols=55  Identities=18%  Similarity=0.214  Sum_probs=46.3

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC--ccEEEccCCCcccEEEEEeCCHHHHHHHHHH
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA--SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQ   76 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~--~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~   76 (121)
                      -.+.|-|-+.|.....+||..+|+.|+.  -.|+|+..    .++|..|.+...|..|+..
T Consensus       390 lpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDd----thalaVFss~~~AaeaLt~  446 (528)
T KOG4483|consen  390 LPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDD----THALAVFSSVNRAAEALTL  446 (528)
T ss_pred             ccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeec----ceeEEeecchHHHHHHhhc
Confidence            4799999999999999999999999988  45666543    4899999999998888753

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

Probab=89.58  E-value=0.014  Score=43.77  Aligned_cols=74  Identities=19%  Similarity=0.321  Sum_probs=61.1

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+++-|+|+|+....+.|..++..||. ..+..+.+.......-++|...+.+..||..++|..+....++|.|.
T Consensus        80 srk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~Yi  154 (584)
T KOG2193|consen   80 SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYI  154 (584)
T ss_pred             hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccC
Confidence            577999999999999999999999999 55544444333345567899999999999999999999998888876

>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=88.73  E-value=2.8  Score=23.38  Aligned_cols=55  Identities=13%  Similarity=0.221  Sum_probs=42.7

Q ss_pred             CCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           30 AIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        30 ~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      .++..+++.-+..|+-  .+++..   +..=||.|.+..+|+++....+|..+.+..+.+
T Consensus        11 ~~~v~d~K~~Lr~y~~--~~I~~d---~tGfYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW--DRIRDD---RTGFYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc--ceEEec---CCEEEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            4778899999999987  333321   123489999999999999999999888777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=88.70  E-value=0.35  Score=34.75  Aligned_cols=70  Identities=16%  Similarity=0.105  Sum_probs=53.7

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      .+++|++++.+.+.+.+...++..+|. .......   ...+++++++.|...+.+..++.......+.+..+.
T Consensus        88 ~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~  161 (285)
T KOG4210|consen   88 SSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGE  161 (285)
T ss_pred             cccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhcccccccccc
Confidence            689999999999999988899989887 3333322   667889999999999999999865443455554443

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

Probab=88.68  E-value=0.045  Score=40.66  Aligned_cols=65  Identities=14%  Similarity=0.044  Sum_probs=50.3

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeE
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKV   86 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~   86 (121)
                      ..+++|++|+..+...++-.+|..+|.  +.+-.  .+....+|-+.|....+...|+ .++|..+.-+.
T Consensus       151 rRt~~v~sl~~~~~l~e~~e~f~r~Ge--v~ya~~ask~~s~~c~~sf~~qts~~hal-r~~gre~k~qh  217 (479)
T KOG4676|consen  151 RRTREVQSLISAAILPESGESFERKGE--VSYAHTASKSRSSSCSHSFRKQTSSKHAL-RSHGRERKRQH  217 (479)
T ss_pred             Hhhhhhhcchhhhcchhhhhhhhhcch--hhhhhhhccCCCcchhhhHhhhhhHHHHH-Hhcchhhhhhh
Confidence            578999999999999999999999999  43333  5555667889999888887787 45666655333

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=87.25  E-value=0.52  Score=38.46  Aligned_cols=70  Identities=21%  Similarity=0.204  Sum_probs=53.7

Q ss_pred             EEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCee--CCeEEEEEecC
Q 043634           21 TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRF--LGKVLSVERAS   93 (121)
Q Consensus        21 ~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i--~g~~l~v~~a~   93 (121)
                      +.++-|.+-..+...|..+|+.||. .+.+.++   .-..|.|+|...+.|..|++.++|.++  .|-+.+|.+++
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr---~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak  372 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLR---DLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAK  372 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheecc---cccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecc
Confidence            3444555567788889999999999 4444443   235899999999999999999999764  46678898884

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	121
2cpx_A	115	Solution Structure Of Rna Binding Domain In Hypothe		7e-04
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		9e-04
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		9e-04

>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical Protein Flj11016 Length = 115

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 4/74 (5%)
Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS----AGRLRNCVFVDFGNEPLASQAQMQ 76
            L +K+L   + +  L  +F+ +      P       GR+R   F+ F N+ +A QA   
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86
Query: 77  LNGLRFLGKVLSVE 90
           +NG +  GK+L +E
Sbjct: 87  VNGYKLYGKILVIE 100

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 38.5 bits (88), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 39/81 (48%), Gaps = 5/81 (6%)
Query: 22 LLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQL 77
          L++ +LP  + QD L  +FS  G    A  +R   AG      FV++     A +A   L
Sbjct: 5  LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 78 NGLRFLGKVLSVERASKPNEE 98
          NGLR   K + V  A +P+ E
Sbjct: 65 NGLRLQSKTIKVSYA-RPSSE 84

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 38.5 bits (88), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 39/81 (48%), Gaps = 5/81 (6%)
Query: 22 LLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQL 77
          L++ +LP  + QD L  +FS  G    A  +R   AG      FV++     A +A   L
Sbjct: 5  LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 78 NGLRFLGKVLSVERASKPNEE 98
          NGLR   K + V  A +P+ E
Sbjct: 65 NGLRLQSKTIKVSYA-RPSSE 84

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	121
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-11
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	7e-11
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-11
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-10
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	6e-10
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	6e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	7e-10
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-10
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-06
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	9e-10
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-09
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-09
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-09
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-09
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-07
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	5e-09
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-09
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-09
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	5e-04
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-09
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	6e-09
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-08
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	5e-04
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-05
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-08
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-08
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-08
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-08
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-04
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-08
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	8e-08
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	5e-08
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-08
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-06
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-06
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-07
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-07
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-07
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-07
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-07
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-07
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	7e-06
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-07
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-07
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-07
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-07
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-07
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	5e-07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	5e-07
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	6e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	6e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-07
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	7e-07
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	7e-07
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	8e-07
1x4e_A	85	RNA binding motif, single-stranded interacting pro	8e-07
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-07
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-04
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	8e-07
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	9e-07
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-06
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-06
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-06
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-06
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-06
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-06
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-06
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-06
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-06
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-06
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-06
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-06
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-06
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-06
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-06
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-06
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-06
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	8e-04
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	5e-06
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-06
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	9e-06
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-05
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-05
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-05
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-05
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-05
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-05
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-05
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-05
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-05
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-05
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-05
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	4e-05
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-05
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-05
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	4e-05
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	5e-05
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	7e-05
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	7e-05
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	7e-05
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	8e-05
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	8e-05
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	8e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-04
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-04
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-04
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-04
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-04
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-04
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-04
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-04
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	3e-04
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-04
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-04
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-04
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	4e-04
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	4e-04
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	4e-04
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	6e-04
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	6e-04
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	7e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	8e-04
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	8e-04
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	9e-04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	9e-04

>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 = 55.7 bits (135), Expect = 1e-11
 Identities = 20/103 (19%), Positives = 46/103 (44%), Gaps = 4/103 (3%)

Query: 9   GPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEP 68
           G         +  L +++L + + ++ L + FS +G          +L++  F+ F    
Sbjct: 1   GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLE----RVKKLKDYAFIHFDERD 56

Query: 69  LASQAQMQLNGLRFLGKVLSVERASKPNEENKHKHFEAQSISS 111
            A +A  ++NG    G+ + +  A  P+++ K +  + Q+ S 
Sbjct: 57  GAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASG 99

>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 = 53.8 bits (130), Expect = 7e-11
 Identities = 23/96 (23%), Positives = 46/96 (47%), Gaps = 4/96 (4%)

Query: 7   DSGPQNKQETENLVTLL-IKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFG 65
            SG    ++T + V +L +++L  +  ++ + + F++    +V      ++R+  FV F 
Sbjct: 2   SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAV--ERVKKIRDYAFVHFS 59

Query: 66  NEPLASQAQMQLNGLRFLGKVLSVERASKPNEENKH 101
           N   A +A   LNG    G  + V  A KP +++  
Sbjct: 60  NREDAVEAMKALNGKVLDGSPIEVTLA-KPVDKDSS 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 = 54.0 bits (130), Expect = 8e-11
 Identities = 16/74 (21%), Positives = 26/74 (35%), Gaps = 2/74 (2%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGL 80
           +L K+LP       +   FS +G+  +             V+F     A +A   L   
Sbjct: 12 VILAKNLPAGTLAAEIQETFSRFGS--LGRVLLPEGGITAIVEFLEPLEARKAFRHLAYS 69

Query: 81 RFLGKVLSVERASK 94
          +F    L +E A  
Sbjct: 70 KFHHVPLYLEWAPI 83

>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 = 52.4 bits (126), Expect = 2e-10
 Identities = 16/72 (22%), Positives = 24/72 (33%), Gaps = 3/72 (4%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGL 80
           +L+K+LP       +  +   Y           R +   FV   N   A  A    +  
Sbjct: 7  GILVKNLPQDSNCQEVHDLLKDYDLKYCY---VDRNKRTAFVTLLNGEQAQNAIQMFHQY 63

Query: 81 RFLGKVLSVERA 92
           F GK L V+  
Sbjct: 64 SFRGKDLIVQLQ 75

>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 = 52.5 bits (126), Expect = 6e-10
 Identities = 22/102 (21%), Positives = 41/102 (40%), Gaps = 10/102 (9%)

Query: 10  PQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASS---------VRPCSAGRLRNCV 60
            ++ +  E    + +K+L   + +  L  IF  Y   S         +R    GR++   
Sbjct: 36  FRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQA 95

Query: 61  FVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENKHK 102
           F+   NE  A++A  + NG    GK + V+ A +     +  
Sbjct: 96  FIGLPNEKAAAKALKEANGYVLFGKPMVVQFA-RSARPKQDP 136

>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 = 51.1 bits (123), Expect = 6e-10
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 5/82 (6%)

Query: 21 TLLIKHLPDAIPQDTLSR----IFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQM 75
          T+ I +L + I +D L +    IFS +G    +    + ++R   FV F     A+ A  
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 69

Query: 76 QLNGLRFLGKVLSVERASKPNE 97
           + G  F  K + ++ A   ++
Sbjct: 70 SMQGFPFYDKPMRIQYAKTDSD 91

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

 Score = 51.5 bits (124), Expect = 7e-10
 Identities = 18/93 (19%), Positives = 37/93 (39%), Gaps = 6/93 (6%)

Query: 6   FDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDF 64
                  ++   +   L ++  P  + +  L+ IF  +G    V+      L    FV+F
Sbjct: 18  GSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVK-----ILNGFAFVEF 72

Query: 65  GNEPLASQAQMQLNGLRFLGKVLSVERASKPNE 97
                A++A  +++G  F  + L V  +  P +
Sbjct: 73  EEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK 105

>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 = 52.6 bits (127), Expect = 7e-10
 Identities = 23/85 (27%), Positives = 34/85 (40%), Gaps = 4/85 (4%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPC---SAGRLRNCVFVDFGNEPLASQAQMQ 76
            L++ +LP  +    L  +F   G  ++ R       G      FVDF +E  + +A   
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 77  LNGLRFLGKVLSVERASKPNEENKH 101
           LNG+    K L V  A    E  K 
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 = 41.8 bits (99), Expect = 6e-06
 Identities = 26/88 (29%), Positives = 36/88 (40%), Gaps = 6/88 (6%)

Query: 11  QNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVDFGN 66
           +   E+     L + +LP  I  D L  IF  YG     + +R    GR R   FV +  
Sbjct: 81  RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNK 140

Query: 67  EPLASQAQMQLNGLRFLG--KVLSVERA 92
              A +A   LN +   G  + LSV  A
Sbjct: 141 REEAQEAISALNNVIPEGGSQPLSVRLA 168

>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 = 51.2 bits (123), Expect = 9e-10
 Identities = 22/102 (21%), Positives = 36/102 (35%), Gaps = 5/102 (4%)

Query: 3   TAPFDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRN 58
           T        +++E      L I HLP       L ++F  +G    A           + 
Sbjct: 9   TQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC 68

Query: 59  CVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENK 100
             FV + N   A  A   +NG +   K L V+   +   ++K
Sbjct: 69  FGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK-RSKNDSK 109

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 51.4 bits (123), Expect = 1e-09
 Identities = 16/111 (14%), Positives = 39/111 (35%), Gaps = 9/111 (8%)

Query: 1   MATAPFDSGPQNKQETENLVTLLIKHLPDAIPQDTLSR----IFSHYGA-SSVRPCSAGR 55
           M +    S P + + ++    +LI ++   +P++ L      + S  G    +    +  
Sbjct: 14  MDSPDLGSTPPHTEPSQ---VVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDD 70

Query: 56  LRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA-SKPNEENKHKHFE 105
                ++ F  +  A        G  F G  L +  + +  ++  +    E
Sbjct: 71  NSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAEDGSLE 121

>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 = 50.8 bits (122), Expect = 1e-09
 Identities = 21/90 (23%), Positives = 36/90 (40%), Gaps = 3/90 (3%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNG 79
            L I++LP  I  + +  IF  YG    +R  +    R   +V + +   A  A   L+G
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSG 69

Query: 80  LRFLGKVLSVERAS--KPNEENKHKHFEAQ 107
                + L V   +  +  ++   K  E Q
Sbjct: 70  FNVSNRYLVVLYYNANRAFQKMDTKKKEEQ 99

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 50.5 bits (121), Expect = 1e-09
 Identities = 19/90 (21%), Positives = 36/90 (40%), Gaps = 5/90 (5%)

Query: 2  ATAPFDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCV 60
          ++    S P+ ++       L I+++P  +  + L  +   YG   S    +       V
Sbjct: 2  SSGSSGSVPKRQRIR----KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVV 57

Query: 61 FVDFGNEPLASQAQMQLNGLRFLGKVLSVE 90
           V + ++  A QA  +LNG +     L V 
Sbjct: 58 NVTYSSKDQARQALDKLNGFQLENFTLKVA 87

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 50.2 bits (120), Expect = 2e-09
 Identities = 20/94 (21%), Positives = 32/94 (34%), Gaps = 1/94 (1%)

Query: 2  ATAPFDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVF 61
          ++     G    +       + + +LP       L R     G+  +R    G  R   F
Sbjct: 2  SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGP-RRRAF 60

Query: 62 VDFGNEPLASQAQMQLNGLRFLGKVLSVERASKP 95
          + + +   A QA   L GLR     L V  A + 
Sbjct: 61 LHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94

>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 = 52.3 bits (126), Expect = 2e-09
 Identities = 17/86 (19%), Positives = 30/86 (34%), Gaps = 3/86 (3%)

Query: 11 QNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLA 70
            +++  N   +LI+ LP  +    +  + S Y       C   + +   FV   N   A
Sbjct: 14 HTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKY---CFVDKYKGTAFVTLLNGEQA 70

Query: 71 SQAQMQLNGLRFLGKVLSVERASKPN 96
            A    +  R   + LSV+      
Sbjct: 71 EAAINAFHQSRLRERELSVQLQPTDA 96

>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 = 49.2 bits (118), Expect = 3e-08
 Identities = 23/112 (20%), Positives = 40/112 (35%), Gaps = 9/112 (8%)

Query: 11  QNKQETENLV---TLLIKHLPDAIPQ-DTLSRIFSHYGA-SSVR--PCSAGRLRNCVFVD 63
              Q T  L+    L +  LP      D L R  S   + +  +      G+L+    ++
Sbjct: 173 DAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLE 232

Query: 64  FGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENKH--KHFEAQSISSMK 113
           +    +A +AQ Q +GL   G  L V   +              AQ+ +  +
Sbjct: 233 YETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQATALNR 284

>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 = 46.1 bits (110), Expect = 4e-07
 Identities = 15/87 (17%), Positives = 30/87 (34%), Gaps = 4/87 (4%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQ 76
            L + +LP ++ Q     +   +G       V     G+ +   F ++  +  A++A+  
Sbjct: 97  LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156

Query: 77  LNGLRFLGKVLSVERASKPNEENKHKH 103
           L G     + L V             H
Sbjct: 157 LLGKPLGPRTLYVHWTDAGQLTPALLH 183

>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 = 49.7 bits (119), Expect = 5e-09
 Identities = 21/105 (20%), Positives = 42/105 (40%), Gaps = 8/105 (7%)

Query: 6   FDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-----AGRLRNCV 60
           FDSG    +  E    LL+ +L   +    +  +F+ +G  +++  +     +GR     
Sbjct: 22  FDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFG--TLKKAAVDYDRSGRSLGTA 79

Query: 61  FVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENKHKHFE 105
            V F     A +A  Q  G+   G+ + ++       + +H H  
Sbjct: 80  DVHFERRADALKAMKQYKGVPLDGRPMDIQLV-ASQIDLEHHHHH 123

>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 = 50.3 bits (121), Expect = 5e-09
 Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 1/85 (1%)

Query: 10  PQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPL 69
            ++ ++     TLL K+L   I +D L  +F             G+ +   +++F +E  
Sbjct: 90  GRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-EIRLVSQDGKSKGIAYIEFKSEAD 148

Query: 70  ASQAQMQLNGLRFLGKVLSVERASK 94
           A +   +  G    G+ +S+    +
Sbjct: 149 AEKNLEEKQGAEIDGRSVSLYYTGE 173

>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 = 50.3 bits (121), Expect = 6e-09
 Identities = 20/85 (23%), Positives = 35/85 (41%), Gaps = 4/85 (4%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPC---SAGRLRNCVFVDFGNEPLASQAQMQ 76
            L++ +LP  + Q+    +F   G   S +       G+     FV++ +   A +A   
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 77  LNGLRFLGKVLSVERASKPNEENKH 101
           LNGLR   K + V  A   +   + 
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 = 36.4 bits (85), Expect = 5e-04
 Identities = 20/88 (22%), Positives = 34/88 (38%), Gaps = 6/88 (6%)

Query: 11  QNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVDFGN 66
           +    +     L +  LP  + Q  L ++FS YG    +  +     G  R   F+ F  
Sbjct: 80  RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDK 139

Query: 67  EPLASQAQMQLNG--LRFLGKVLSVERA 92
              A +A   LNG       + ++V+ A
Sbjct: 140 RIEAEEAIKGLNGQKPSGATEPITVKFA 167

>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 = 49.2 bits (118), Expect = 6e-09
 Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 5/84 (5%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGASS----VRPCSAGRLRNCVFVDFGNEPLASQAQMQ 76
            L +K+L   + +  L  +F+ +              GR+R   F+ F N+ +A QA   
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 77  LNGLRFLGKVLSVERASKPNEENK 100
           +NG +  GK+L +E   K  ++  
Sbjct: 87  VNGYKLYGKILVIEFG-KNKKQRS 109

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 48.9 bits (117), Expect = 6e-09
 Identities = 22/94 (23%), Positives = 31/94 (32%), Gaps = 4/94 (4%)

Query: 3   TAPFDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRN 58
           +A   +    + E      L I HLP       L+  F  +G    A           + 
Sbjct: 24  SAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKC 83

Query: 59  CVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA 92
             FV F N   A  A   +NG +   K L V+  
Sbjct: 84  FGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>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 = 49.5 bits (119), Expect = 1e-08
 Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 6/87 (6%)

Query: 20  VTLLIKHLPDAIPQDTLSRIFSHYGA-SSV-----RPCSAGRLRNCVFVDFGNEPLASQA 73
           + + +  +P    +  L  +F  YGA   +     R  +  + + C FV F     A +A
Sbjct: 4   IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63

Query: 74  QMQLNGLRFLGKVLSVERASKPNEENK 100
           Q  L+ ++ L  +    +    + E  
Sbjct: 64  QNALHNMKVLPGMHHPIQMKPADSEKN 90

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 36.8 bits (86), Expect = 5e-04
 Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 10/90 (11%)

Query: 11  QNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPC-----SAGRLRNCVFVDFG 65
             K        L I  +     ++ +  +FS +G   +  C       G  R C FV F 
Sbjct: 87  SEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFG--QIEECRILRGPDGLSRGCAFVTFT 144

Query: 66  NEPLASQAQMQLNGLRFL---GKVLSVERA 92
              +A  A   ++  + +      + V+ A
Sbjct: 145 TRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>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 = 50.3 bits (119), Expect = 1e-08
 Identities = 20/98 (20%), Positives = 38/98 (38%), Gaps = 5/98 (5%)

Query: 21  TLLIKHLPDAIPQDTLSR----IFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQM 75
           T+ I +L + I +D L +    IFS +G    +    + ++R   FV F     A+ A  
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 70

Query: 76  QLNGLRFLGKVLSVERASKPNEENKHKHFEAQSISSMK 113
            + G  F  K + ++ A   ++               +
Sbjct: 71  SMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKR 108

>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 = 41.4 bits (96), Expect = 2e-05
 Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 2/75 (2%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGL 80
            L + +LP+   +  LS +F+ +          GR  +  FV+F NE  A  A+  L G 
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-HDIAFVEFDNEVQAGAARDALQGF 267

Query: 81  RFL-GKVLSVERASK 94
           +      + +  A K
Sbjct: 268 KITQNNAMKISFAKK 282

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 47.8 bits (114), Expect = 2e-08
 Identities = 13/89 (14%), Positives = 29/89 (32%), Gaps = 6/89 (6%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPC---SAGRLRNCVFVDFGNEPLASQAQMQ 76
            +    L D + +  L  +   YG    V         +      V F +   A +    
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 77  LNGLRFLGKVLSVERASKPNEENKHKHFE 105
           L+    +G ++  +       + + K++E
Sbjct: 68  LHLTSVMGNIIHAQLD--IKGQQRMKYYE 94

>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 = 46.8 bits (112), Expect = 3e-08
 Identities = 26/92 (28%), Positives = 44/92 (47%), Gaps = 3/92 (3%)

Query: 11  QNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVR-PCSAGRLRNCVFVDFGNEP 68
            ++     +V L +K+L D I  + L + FS +G  +S +     GR +   FV F +  
Sbjct: 7   GDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPE 66

Query: 69  LASQAQMQLNGLRFLGKVLSVERASKPNEENK 100
            A++A  ++NG     K L V  A +  EE +
Sbjct: 67  EATKAVTEMNGRIVATKPLYVALA-QRKEERQ 97

>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 = 46.9 bits (112), Expect = 3e-08
 Identities = 20/92 (21%), Positives = 37/92 (40%), Gaps = 3/92 (3%)

Query: 7  DSGPQNKQET-ENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFG 65
           SG    ++T      L + +LP  I ++ + ++F  YG          + +   F+   
Sbjct: 2  SSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYG--KAGEVFIHKDKGFGFIRLE 59

Query: 66 NEPLASQAQMQLNGLRFLGKVLSVERASKPNE 97
             LA  A+++L+ +   GK L V  A     
Sbjct: 60 TRTLAEIAKVELDNMPLRGKQLRVRFACHSAS 91

>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 = 48.5 bits (116), Expect = 4e-08
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 2/87 (2%)

Query: 10 PQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPL 69
             ++       L + +LP  I ++   R+F  YG          R R   F+   +  L
Sbjct: 13 KPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYG--EPSEVFINRDRGFGFIRLESRTL 70

Query: 70 ASQAQMQLNGLRFLGKVLSVERASKPN 96
          A  A+ +L+G     + L +  A+   
Sbjct: 71 AEIAKAELDGTILKSRPLRIRFATHGA 97

>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 = 37.4 bits (87), Expect = 3e-04
 Identities = 21/88 (23%), Positives = 37/88 (42%), Gaps = 11/88 (12%)

Query: 22  LLIKHLPDAIPQDTLSRIFSHYGASSVRPC-----SAGRLRNCVFVDFGNEPLASQAQMQ 76
           L +K+L   +  + L + FS +G   V          GR     FV+F  +P A +A  +
Sbjct: 99  LTVKNLSPVVSNELLEQAFSQFG--PVEKAVVVVDDRGRATGKGFVEFAAKPPARKALER 156

Query: 77  LNGLRFLG----KVLSVERASKPNEENK 100
                FL     + + VE   + ++E+ 
Sbjct: 157 CGDGAFLLTTTPRPVIVEPMEQFDDEDG 184

>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 = 48.1 bits (115), Expect = 5e-08
 Identities = 17/107 (15%), Positives = 38/107 (35%), Gaps = 10/107 (9%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYG---------ASSVRPCSAGRLRNCVFVDFGNEPLAS 71
            L + ++P  I ++ +   F+             + V      + +N  F++F +    +
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 72  QAQMQLNGLRFLGKVLSVERASKPNEENKHKHFEAQSISSMKEAAVT 118
           QA M  +G+ F G+ L + R              +  +  +    V 
Sbjct: 66  QA-MAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVP 111

>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 = 47.3 bits (113), Expect = 8e-08
 Identities = 21/98 (21%), Positives = 44/98 (44%), Gaps = 4/98 (4%)

Query: 4   APFDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNC 59
           + +  G  +    ++   L I  LP+ +  D +  + + +G     + V+  + G  +  
Sbjct: 99  SVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGY 158

Query: 60  VFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNE 97
            F ++ +  +  QA   LNG++   K L V+RAS   +
Sbjct: 159 AFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK 196

>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 = 46.1 bits (110), Expect = 5e-08
 Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 4/86 (4%)

Query: 16  TENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQM 75
           +  +  L I +L  A+  D L ++F                    FVD+ ++  A +A  
Sbjct: 5   SSGMNKLYIGNLSPAVTADDLRQLFGDRKL--PLAGQVLLKSGYAFVDYPDQNWAIRAIE 62

Query: 76  QLNG-LRFLGKVLSVERASKPNEENK 100
            L+G +   GK++ V+ +    +   
Sbjct: 63  TLSGKVELHGKIMEVDYS-VSKKLRS 87

>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 = 47.6 bits (114), Expect = 6e-08
 Identities = 16/92 (17%), Positives = 33/92 (35%), Gaps = 10/92 (10%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGASS---------VRPCSAGRLRNCVFVDFGNEPLAS 71
            L + ++P  I ++ +   F+               V      + +N  F++F +    +
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 72  QAQMQLNGLRFLGKVLSVERASKPNEENKHKH 103
           QA M  +G+ F G+ L + R            
Sbjct: 66  QA-MAFDGIIFQGQSLKIRRPHDYQPLPGAHK 96

>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 = 45.7 bits (109), Expect = 3e-07
 Identities = 22/88 (25%), Positives = 40/88 (45%), Gaps = 4/88 (4%)

Query: 10  PQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVDFG 65
           P + Q       L I  LP+ +  D +  + + +G     + V+  + G  +   F ++ 
Sbjct: 85  PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV 144

Query: 66  NEPLASQAQMQLNGLRFLGKVLSVERAS 93
           +  +  QA   LNG++   K L V+RAS
Sbjct: 145 DINVTDQAIAGLNGMQLGDKKLLVQRAS 172

>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 = 47.3 bits (113), Expect = 1e-07
 Identities = 20/98 (20%), Positives = 38/98 (38%), Gaps = 8/98 (8%)

Query: 5   PFDSGPQNKQETENLVTLLIKHLPDAIPQ-DTLSRIFSHYGA-SSVR----PCSAGRLRN 58
           P +   +    T     ++I++L   +   + L   F  +G+   +              
Sbjct: 196 PLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNC 255

Query: 59  CVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA-SKP 95
           C F+ F N+  A +A +Q+N      + +SV  A  KP
Sbjct: 256 CAFMVFENKDSAERA-LQMNRSLLGNREISVSLADKKP 292

>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 = 44.6 bits (106), Expect = 1e-06
 Identities = 17/92 (18%), Positives = 35/92 (38%), Gaps = 4/92 (4%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYG--ASSVRPCSA--GRLRNCVFVDFGNEPLASQAQMQ 76
           TL + + P +  Q  +  +       A S+R  S      R   ++D  ++  A     +
Sbjct: 119 TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 178

Query: 77  LNGLRFLGKVLSVERASKPNEENKHKHFEAQS 108
           LNGL+  G  L  + ++   +  +      + 
Sbjct: 179 LNGLKIEGYTLVTKVSNPLEKSKRTDSATLEG 210

>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 = 44.6 bits (106), Expect = 1e-06
 Identities = 15/78 (19%), Positives = 30/78 (38%), Gaps = 3/78 (3%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGA-SSVR-PCSAGRLRNCVFVDFGNEPLASQAQMQLN 78
           T+L+K+LP +  Q+ + + F H G    V    S  +      ++F     A  A  + +
Sbjct: 43  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTH 102

Query: 79  GLRFLGKVLSVERASKPN 96
                   + V   ++  
Sbjct: 103 K-VVGQNEIIVSHLTECT 119

>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 = 45.3 bits (108), Expect = 1e-07
 Identities = 18/98 (18%), Positives = 42/98 (42%), Gaps = 5/98 (5%)

Query: 7   DSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFV 62
                  +  ++  T+ + +L +   +  L  +F  +G+ S +        G+ +   F+
Sbjct: 3   SGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFI 62

Query: 63  DFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENK 100
            F     A++A   ++G  +   +L+VE A KP+  + 
Sbjct: 63  SFHRREDAARAIAGVSGFGYDHLILNVEWA-KPSTNSG 99

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 44.9 bits (107), Expect = 2e-07
 Identities = 23/96 (23%), Positives = 40/96 (41%), Gaps = 5/96 (5%)

Query: 8  SGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVR-PC--SAGRLRNCVFVD 63
          S   +  + + ++TL + +L      D+L R+F  YG    V  P        R   FV 
Sbjct: 2  SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61

Query: 64 FGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEEN 99
          F +   A  A+  ++G    G+ L V+ A +    +
Sbjct: 62 FHDRRDAQDAEAAMDGAELDGRELRVQVA-RYGRRD 96

>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 = 45.4 bits (108), Expect = 2e-07
 Identities = 20/93 (21%), Positives = 33/93 (35%), Gaps = 5/93 (5%)

Query: 1  MATAPFDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNC 59
          M+      GP    +      + + +LP  I    +  +F  YGA   +   +       
Sbjct: 8  MSGGGVIRGPAGNNDC----RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPF 63

Query: 60 VFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA 92
           FV+F +   A  A    +G  + G  L VE  
Sbjct: 64 AFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP 96

>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 = 45.0 bits (107), Expect = 2e-07
 Identities = 20/93 (21%), Positives = 41/93 (44%), Gaps = 7/93 (7%)

Query: 6   FDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-----AGRLRNCV 60
           FDSG       E    LL+ +L   +    +  +F+ +G  +++  +     +GR     
Sbjct: 16  FDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFG--TLKKAAVHYDRSGRSLGTA 73

Query: 61  FVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS 93
            V F  +  A +A  Q NG+   G+ ++++  +
Sbjct: 74  DVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 106

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 44.6 bits (106), Expect = 2e-07
 Identities = 13/70 (18%), Positives = 26/70 (37%), Gaps = 4/70 (5%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNG 79
          T  I ++P    +  L  +F ++G     +       + C F+ +     A+   + L  
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILDFK---HYPEKGCCFIKYDTHEQAAVCIVALAN 85

Query: 80 LRFLGKVLSV 89
            F G+ L  
Sbjct: 86 FPFQGRNLRT 95

>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 = 44.6 bits (106), Expect = 3e-07
 Identities = 21/84 (25%), Positives = 32/84 (38%), Gaps = 7/84 (8%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGA-SSVR------PCSAGRLRNCVFVDFGNEPLASQA 73
           L IK+L  +  ++TL  +FS  GA  S                   FV++     A +A
Sbjct: 7  GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

Query: 74 QMQLNGLRFLGKVLSVERASKPNE 97
            QL G    G  L V  + +  +
Sbjct: 67 LKQLQGHTVDGHKLEVRISERATK 90

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 45.8 bits (109), Expect = 3e-07
 Identities = 17/95 (17%), Positives = 38/95 (40%), Gaps = 4/95 (4%)

Query: 7   DSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPC---SAGRLRNCVFV 62
            S  Q +     +  + +  +   + +DT+ + F+ +G   S+         + +   FV
Sbjct: 16  GSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFV 75

Query: 63  DFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNE 97
           ++     A  A  Q+N +   G+ + V R S   +
Sbjct: 76  EYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQ 110

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 42.3 bits (100), Expect = 7e-06
 Identities = 16/93 (17%), Positives = 35/93 (37%), Gaps = 4/93 (4%)

Query: 7   DSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFV 62
               Q  +E      + +  +   +  D +  +F  +G    A+  R  + G+ +   F+
Sbjct: 113 PIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFI 172

Query: 63  DFGNEPLASQAQMQLNGLRFLGKVLSVERASKP 95
           ++     +  A   +N     G+ L V +A  P
Sbjct: 173 EYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205

>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 = 44.2 bits (105), Expect = 3e-07
 Identities = 20/94 (21%), Positives = 34/94 (36%), Gaps = 5/94 (5%)

Query: 10  PQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS---AGRLRNCVFVDFGN 66
           P    E+     L I +L        L    S   A +         G  R   +VDF +
Sbjct: 8   PVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFES 67

Query: 67  EPLASQAQMQLNGLRFLGKVLSVERASKPNEENK 100
                +A ++L GL+  G  + +E+  K  +  +
Sbjct: 68  AEDLEKA-LELTGLKVFGNEIKLEKP-KGRDGTR 99

>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 = 44.2 bits (105), Expect = 3e-07
 Identities = 19/86 (22%), Positives = 36/86 (41%), Gaps = 3/86 (3%)

Query: 8  SGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSA-GRLRNCVFVDFGN 66
            P   ++     TLL K+L   I +D L  +F       +R  S  G+ +   +++F +
Sbjct: 5  EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDAL--EIRLVSQDGKSKGIAYIEFKS 62

Query: 67 EPLASQAQMQLNGLRFLGKVLSVERA 92
          E  A +   +  G    G+ +S+   
Sbjct: 63 EADAEKNLEEKQGAEIDGRSVSLYYT 88

>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 = 44.2 bits (105), Expect = 3e-07
 Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 4/89 (4%)

Query: 8  SGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDF 64
          SG    QE  +  T+ + +L   + ++ L  +F   G  + V  C    G+ ++  FV F
Sbjct: 6  SGMFPAQEEAD-RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCF 64

Query: 65 GNEPLASQAQMQLNGLRFLGKVLSVERAS 93
           +    S A   LNG+R  G+ ++V   S
Sbjct: 65 KHPESVSYAIALLNGIRLYGRPINVSGPS 93

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 45.6 bits (108), Expect = 4e-07
 Identities = 21/103 (20%), Positives = 42/103 (40%), Gaps = 8/103 (7%)

Query: 6   FDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-----AGRLRNCV 60
           FDSG    +  E    LL+ +L   +    +  +F+ +G  +++  +     +GR     
Sbjct: 75  FDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFG--TLKKAAVDYDRSGRSLGTA 132

Query: 61  FVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENKHKH 103
            V F     A +A  Q  G+   G+ + ++       + +H H
Sbjct: 133 DVHFERRADALKAMKQYKGVPLDGRPMDIQLV-ASQIDLEHHH 174

>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 = 43.8 bits (104), Expect = 4e-07
 Identities = 23/93 (24%), Positives = 35/93 (37%), Gaps = 5/93 (5%)

Query: 7  DSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGN 66
           S  + +   +   TL +      +    L   FS +G  ++   S    RNC FV +  
Sbjct: 4  GSSGERRAPRKG-NTLYVYGED--MTPTLLRGAFSPFG--NIIDLSMDPPRNCAFVTYEK 58

Query: 67 EPLASQAQMQLNGLRFLGKVLSVERASKPNEEN 99
             A QA  +LNG +     L V  A K    +
Sbjct: 59 MESADQAVAELNGTQVESVQLKVNIARKQPMLD 91

>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 = 43.4 bits (103), Expect = 5e-07
 Identities = 19/83 (22%), Positives = 32/83 (38%), Gaps = 5/83 (6%)

Query: 9  GPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNE 67
             +  E + + TL +  L D I +  L   F  +G   ++        + C F+ F   
Sbjct: 2  SSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTIT-VVQR--QQCAFIQFATR 58

Query: 68 PLASQA-QMQLNGLRFLGKVLSV 89
            A  A +   N L   G+ L+V
Sbjct: 59 QAAEVAAEKSFNKLIVNGRRLNV 81

>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 = 44.4 bits (105), Expect = 5e-07
 Identities = 26/94 (27%), Positives = 39/94 (41%), Gaps = 5/94 (5%)

Query: 10  PQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFG 65
            Q   E + L  L++ ++P  + +  L ++F  YG   SV+        + R   FV F 
Sbjct: 33  TQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQ 92

Query: 66  NEPLASQAQMQLNGLRFLGKVLSVERASKPNEEN 99
           +   A QA   LNG   L K L V  A     + 
Sbjct: 93  SGSSAQQAIAGLNGFNILNKRLKVALA-ASGHQR 125

>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 = 43.9 bits (104), Expect = 6e-07
 Identities = 24/88 (27%), Positives = 37/88 (42%), Gaps = 3/88 (3%)

Query: 15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLAS 71
          E ++   L I  L     +  L  +F  +G  S V        + R   F+ F N   A 
Sbjct: 3  EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAK 62

Query: 72 QAQMQLNGLRFLGKVLSVERASKPNEEN 99
           A   +NG    GK + VE+A KP+ ++
Sbjct: 63 NAAKDMNGKSLHGKAIKVEQAKKPSFQS 90

>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 = 43.4 bits (103), Expect = 6e-07
 Identities = 17/98 (17%), Positives = 36/98 (36%), Gaps = 13/98 (13%)

Query: 8  SGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSA------------GR 55
              +   ++N  T+ ++ L + +  ++++  F   G       +             G+
Sbjct: 3  HHHHHHSHSDNN-TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK 61

Query: 56 LRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS 93
          L+    V F + P A  A    +G  F G  + V  A+
Sbjct: 62 LKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT 99

>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 = 43.4 bits (103), Expect = 6e-07
 Identities = 16/81 (19%), Positives = 35/81 (43%), Gaps = 5/81 (6%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGASSVR----PCSAGRLRNCVFVDFGNEPLASQAQMQ 76
           T  + +LP  + ++++   F     S+VR    P +  RL+   + +F +      A + 
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA-LS 79

Query: 77  LNGLRFLGKVLSVERASKPNE 97
           LN      + + V+ A +  +
Sbjct: 80  LNEESLGNRRIRVDVADQAQD 100

>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 = 43.4 bits (103), Expect = 7e-07
 Identities = 20/102 (19%), Positives = 37/102 (36%), Gaps = 10/102 (9%)

Query: 2  ATAPFDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA---SSVRPCSAGRLRN 58
          ++    S  +  ++      L +  L     ++ + R+F  +G     +V     G  + 
Sbjct: 2  SSGSSGSESRGGRDR----KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKG 57

Query: 59 CVFVDFGNEPLASQAQMQLNG---LRFLGKVLSVERASKPNE 97
          C FV F +   A  A   L+G   +      L V+ A    E
Sbjct: 58 CAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKE 99

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

 Score = 43.4 bits (103), Expect = 7e-07
 Identities = 22/91 (24%), Positives = 42/91 (46%), Gaps = 3/91 (3%)

Query: 8  SGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDF 64
          SG      +     L I  LP +  ++ L  I   +G    +R  +  AG+ +   +V++
Sbjct: 6  SGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEY 65

Query: 65 GNEPLASQAQMQLNGLRFLGKVLSVERASKP 95
           NE  ASQA M+++G+     ++ V  ++  
Sbjct: 66 ENESQASQAVMKMDGMTIKENIIKVAISNSG 96

>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 = 43.0 bits (102), Expect = 8e-07
 Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 5/74 (6%)

Query: 27  LPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKV 86
           LP    +  +  +F  YG   V       ++N  FV   ++  A  A   L+  +  G  
Sbjct: 16  LPREATEQEIRSLFEQYG--KVL--ECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLHGVN 71

Query: 87  LSVERASKPNEENK 100
           ++VE + K   +  
Sbjct: 72  INVEAS-KNKSKAS 84

>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 = 42.9 bits (102), Expect = 8e-07
 Identities = 15/76 (19%), Positives = 26/76 (34%), Gaps = 4/76 (5%)

Query: 22 LLIKHLPDAIPQDTLSRIFSHYGA-SSVRP---CSAGRLRNCVFVDFGNEPLASQAQMQL 77
          L I+ L        L ++   YG   S +     +  + +   FVDF +   A +A   L
Sbjct: 8  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

Query: 78 NGLRFLGKVLSVERAS 93
                 ++      S
Sbjct: 68 KASGVQAQMAKQSGPS 83

>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 = 44.4 bits (106), Expect = 8e-07
 Identities = 18/87 (20%), Positives = 37/87 (42%), Gaps = 3/87 (3%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPC--SAGRLRNCVFVDFGNEPLASQAQMQL 77
            L + +L  AI +D L + F   G  ++++       +  N  FV++     A+ A   L
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 78  NGLRFLGKVLSVERASKPNEENKHKHF 104
           NG +    ++ +  A +  + +    F
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDDTF 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 = 38.3 bits (90), Expect = 1e-04
 Identities = 17/91 (18%), Positives = 33/91 (36%), Gaps = 4/91 (4%)

Query: 8   SGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVD 63
           +    +  +++   L +  L   +  +TL   F  +        +     G  R   FV 
Sbjct: 76  AFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVS 135

Query: 64  FGNEPLASQAQMQLNGLRFLGKVLSVERASK 94
           F ++  A  A   + G    G+ L +  A+K
Sbjct: 136 FTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166

>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 = 43.0 bits (102), Expect = 8e-07
 Identities = 13/69 (18%), Positives = 27/69 (39%), Gaps = 4/69 (5%)

Query: 27 LPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLG-- 84
          L        L+R F  +G+  +R     +  +  ++ + +   A  A  ++ G    G  
Sbjct: 25 LGPNTSLAALAREFDRFGS--IRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPD 82

Query: 85 KVLSVERAS 93
          + L V+ A 
Sbjct: 83 RRLRVDFAK 91

>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 = 43.1 bits (102), Expect = 9e-07
 Identities = 21/100 (21%), Positives = 38/100 (38%), Gaps = 7/100 (7%)

Query: 7   DSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVR----PCSAGRLRNCVF 61
                   + +    +L++++P    Q  +  +FS +G   +VR        G  R   F
Sbjct: 3   SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62

Query: 62  VDFGNEPLASQAQMQL-NGLRFLGKVLSVERASKPNEENK 100
           VDF  +  A +A   L +     G+ L +E A       +
Sbjct: 63  VDFITKQDAKKAFNALCHSTHLYGRRLVLEWA-DSEVTVQ 101

>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 = 43.4 bits (103), Expect = 1e-06
 Identities = 21/88 (23%), Positives = 35/88 (39%), Gaps = 2/88 (2%)

Query: 22  LLIKHLPDAIPQDTLSRIFSHYGA-SSVR-PCSAGRLRNCVFVDFGNEPLASQAQMQLNG 79
           + IK+L  +I    L   FS +G   S +  C     +   FV F  +  A +A  ++NG
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67

Query: 80  LRFLGKVLSVERASKPNEENKHKHFEAQ 107
           +    + + V R     E        A+
Sbjct: 68  MLLNDRKVFVGRFKSRKEREAELGARAK 95

>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 = 44.5 bits (105), Expect = 1e-06
 Identities = 20/90 (22%), Positives = 35/90 (38%), Gaps = 4/90 (4%)

Query: 21  TLLIKHL-PDAIPQDTLSRIFSHYGASSVRPCSAGR-LRNCVFVDFGNEPLASQAQMQLN 78
            LL+ +L P+ +   +L  +F  YG   V+        +    V   +   A  A   LN
Sbjct: 5   VLLVSNLNPERVTPQSLFILFGVYG--DVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62

Query: 79  GLRFLGKVLSVERASKPNEENKHKHFEAQS 108
           G +  GK + +  +   N +   +  E Q 
Sbjct: 63  GHKLHGKPIRITLSKHQNVQLPREGQEDQG 92

>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 = 42.7 bits (101), Expect = 1e-06
 Identities = 17/96 (17%), Positives = 33/96 (34%), Gaps = 6/96 (6%)

Query: 4  APFDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYG--ASSVRPC--SAGRLRNC 59
          +   SG  + +       + ++++P  +  D +   F  Y     SV       G     
Sbjct: 2  SSGSSGASSGKPGPT--IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGE 59

Query: 60 VFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKP 95
            V F +   A+ A + LN      + + +   S P
Sbjct: 60 AMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP 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 = 42.6 bits (101), Expect = 1e-06
 Identities = 14/71 (19%), Positives = 24/71 (33%), Gaps = 4/71 (5%)

Query: 27 LPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKV 86
          +        L   F  YG   V       +++  FV       A +A   L+   F GK 
Sbjct: 18 ISPTCTNQELRAKFEEYGP--VI--ECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQGKR 73

Query: 87 LSVERASKPNE 97
          + V+ ++    
Sbjct: 74 MHVQLSTSRLR 84

>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 = 42.6 bits (101), Expect = 1e-06
 Identities = 17/84 (20%), Positives = 37/84 (44%), Gaps = 5/84 (5%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGASSVR----PCSAGRLRNCVFVDFGNEPLASQAQMQ 76
           T  + +LP  + ++++   F     S+VR    P +  RL+   + +F +      A + 
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA-LS 75

Query: 77  LNGLRFLGKVLSVERASKPNEENK 100
           LN      K + V+ A +  +++ 
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKDS 99

>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 = 42.2 bits (100), Expect = 2e-06
 Identities = 13/85 (15%), Positives = 25/85 (29%), Gaps = 11/85 (12%)

Query: 27  LPDAIPQDTLSRIFSHYGASSVRPCSA--------GRLRNCVFVDFGNEPLASQAQMQLN 78
           L      + L+      G + +             G+ +    V  G+E  + +    L 
Sbjct: 9   LTWWTTDEDLTEAVHSLGVNDIL--EIKFFENRANGQSKGFALVGVGSEASSKKLMDLLP 66

Query: 79  GLRFLGKVLSVERASKPNEENKHKH 103
                G+   V  +    E + H H
Sbjct: 67  KRELHGQNPVVTPS-NKLEHHHHHH 90

>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 = 42.2 bits (100), Expect = 2e-06
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 26 HLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGK 85
          ++  A     L  +F   G   V  C    +++  FV    E  A  A  QLNG    GK
Sbjct: 16 NVSAACTSQELRSLFERRGR--VIECDV--VKDYAFVHMEKEADAKAAIAQLNGKEVKGK 71

Query: 86 VLSVERASKPNEEN 99
           ++VE ++K  +++
Sbjct: 72 RINVELSTKGQKKS 85

>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 = 42.4 bits (100), Expect = 2e-06
 Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 4/68 (5%)

Query: 28  PDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVL 87
              + +  +  IFS YG   V  CS    +   FV + NE  A  A +  NG    G+ L
Sbjct: 37  TALVKKSDVETIFSKYG--RVAGCSV--HKGYAFVQYSNERHARAAVLGENGRVLAGQTL 92

Query: 88  SVERASKP 95
            +  A +P
Sbjct: 93  DINMAGEP 100

>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 = 43.8 bits (103), Expect = 2e-06
 Identities = 20/90 (22%), Positives = 35/90 (38%), Gaps = 4/90 (4%)

Query: 21  TLLIKHL-PDAIPQDTLSRIFSHYGASSVRPCSAGR-LRNCVFVDFGNEPLASQAQMQLN 78
            LL+ +L P+ +   +L  +F  YG   V+        +    V   +   A  A   LN
Sbjct: 36  VLLVSNLNPERVTPQSLFILFGVYG--DVQRVKILFNKKENALVQMADGNQAQLAMSHLN 93

Query: 79  GLRFLGKVLSVERASKPNEENKHKHFEAQS 108
           G +  GK + +  +   N +   +  E Q 
Sbjct: 94  GHKLHGKPIRITLSKHQNVQLPREGQEDQG 123

>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 = 42.2 bits (100), Expect = 2e-06
 Identities = 20/96 (20%), Positives = 39/96 (40%), Gaps = 8/96 (8%)

Query: 9   GPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDF 64
           G      +     L +++L     ++ L ++FS YG  S +         + +   FV F
Sbjct: 1   GSSGSSGS---GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57

Query: 65  GNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENK 100
                A +A  +++G  F G++L V  +    +E  
Sbjct: 58  MFPEHAVKAYAEVDGQVFQGRMLHVLPS-TIKKEAS 92

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 20/95 (21%), Positives = 34/95 (35%), Gaps = 2/95 (2%)

Query: 11  QNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVR-PCSAGRLRNCVFVDFGNEP 68
                   +  + IK+L  +I    L   FS +G   S +  C     +   FV F  + 
Sbjct: 95  DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQE 154

Query: 69  LASQAQMQLNGLRFLGKVLSVERASKPNEENKHKH 103
            A +A  ++NG+    + + V R     E      
Sbjct: 155 AAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELG 189

>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 = 43.4 bits (103), Expect = 3e-06
 Identities = 20/105 (19%), Positives = 36/105 (34%), Gaps = 5/105 (4%)

Query: 4   APFDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPC---SAGRLRNC 59
            P  S   +   +  + +L +  L   + +  L   FS  G   S+R C      R    
Sbjct: 1   GPLGSMNPS-APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGY 59

Query: 60  VFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENKHKHF 104
            +V+F     A +A   +N     GK + +  + +     K    
Sbjct: 60  AYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVG 104

>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 = 41.8 bits (99), Expect = 2e-06
 Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 5/83 (6%)

Query: 20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVR----PCSAGRLRNCVFVDFGNEPLASQAQ 74
            + I  L   + +D +  IFS YG    +            +   +V+F N   A +A 
Sbjct: 5  TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64

Query: 75 MQLNGLRFLGKVLSVERASKPNE 97
            ++G +  G+ ++      P  
Sbjct: 65 KHMDGGQIDGQEITATAVLAPWP 87

>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 = 42.3 bits (100), Expect = 2e-06
 Identities = 18/95 (18%), Positives = 28/95 (29%), Gaps = 7/95 (7%)

Query: 8  SGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-----AGRLRNCVFV 62
                Q      T+ + +L   +    L  +FS  G   V          G+ R    V
Sbjct: 4  GSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAG--VVVRADILEDKDGKSRGIGTV 61

Query: 63 DFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNE 97
           F     A QA    NG     + + V+   +   
Sbjct: 62 TFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALP 96

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 42.4 bits (100), Expect = 2e-06
 Identities = 18/100 (18%), Positives = 40/100 (40%), Gaps = 13/100 (13%)

Query: 13  KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSA------------GRLRNCV 60
           +  ++N  T+ ++ L + +  ++++  F   G       +             G+L+   
Sbjct: 2   QDNSDN-NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60

Query: 61  FVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENK 100
            V F + P A  A    +G  F G  + V  A++  + N+
Sbjct: 61  TVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNR 100

>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 = 41.9 bits (99), Expect = 3e-06
 Identities = 16/95 (16%), Positives = 32/95 (33%), Gaps = 6/95 (6%)

Query: 4  APFDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYG--ASSVRPC--SAGRLRNC 59
          +   SG  + +       + ++++P  +  D +   F  Y     SV       G     
Sbjct: 2  SSGSSGSSSGKPGPT--VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGE 59

Query: 60 VFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK 94
            V F +   A+ A + LN      + + +   S 
Sbjct: 60 AMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPSS 94

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 41.9 bits (99), Expect = 3e-06
 Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 2/75 (2%)

Query: 22  LLIKHLPDAIPQDTLSRIFSHYGA-SSVR-PCSAGRLRNCVFVDFGNEPLASQAQMQLNG 79
           L + ++P       L ++F  +G    V    +    +   FV F N   A +A+ +L+G
Sbjct: 32  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 91

Query: 80  LRFLGKVLSVERASK 94
               G+ + V  A+ 
Sbjct: 92  TVVEGRKIEVNNATA 106

>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 = 43.2 bits (101), Expect = 3e-06
 Identities = 18/103 (17%), Positives = 37/103 (35%), Gaps = 4/103 (3%)

Query: 21  TLLIKHL-PDAIPQDTLSRIFSHYGASSVRPCSAGR-LRNCVFVDFGNEPLASQAQMQLN 78
            L++  L    +  D +  +F  YG  +V      +       V+  +     +A   LN
Sbjct: 6   VLMVYGLDQSKMNCDRVFNVFCLYG--NVEKVKFMKSKPGAAMVEMADGYAVDRAITHLN 63

Query: 79  GLRFLGKVLSVERASKPNEENKHKHFEAQSISSMKEAAVTRNQ 121
                G+ ++V  + +P       +       S K+ + +RN 
Sbjct: 64  NNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNN 106

>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 = 36.6 bits (84), Expect = 8e-04
 Identities = 8/78 (10%), Positives = 20/78 (25%), Gaps = 4/78 (5%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGASS----VRPCSAGRLRNCVFVDFGNEPLASQAQMQ 76
            L   + P  + ++    I    G                 +   +++ ++  A +    
Sbjct: 125 VLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGF 184

Query: 77  LNGLRFLGKVLSVERASK 94
           LN  +            K
Sbjct: 185 LNHYQMKNPNGPYPYTLK 202

>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 = 41.6 bits (98), Expect = 5e-06
 Identities = 21/106 (19%), Positives = 38/106 (35%), Gaps = 13/106 (12%)

Query: 7   DSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSA------------G 54
            S     ++++N   + ++ L D++  D L+  F   G   +   +             G
Sbjct: 4   GSSGDPDEDSDN-SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETG 62

Query: 55  RLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENK 100
           + +    V + + P A  A    +G  F G  L V  A K    N 
Sbjct: 63  KPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 108

>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 = 41.1 bits (97), Expect = 5e-06
 Identities = 21/96 (21%), Positives = 39/96 (40%), Gaps = 3/96 (3%)

Query: 8   SGPQNKQETENLVT-LLIKHLPDAIPQDTLSRIFSHYGA-SSVR-PCSAGRLRNCVFVDF 64
           SG     E+++    L + ++P       L ++F  +G    V    +    +   FV F
Sbjct: 3   SGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTF 62

Query: 65  GNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENK 100
            N   A +A+ +L+G    G+ + V  A+     N 
Sbjct: 63  ENSADADRAREKLHGTVVEGRKIEVNNATARVMTNS 98

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

 Score = 40.4 bits (95), Expect = 9e-06
 Identities = 19/68 (27%), Positives = 28/68 (41%), Gaps = 3/68 (4%)

Query: 26 HLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLG 84
          +L     +  L R FS+YG   +R    A       FV+F +   A  A   L+G    G
Sbjct: 7  NLGTGAGKGELERAFSYYG--PLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICG 64

Query: 85 KVLSVERA 92
            + VE +
Sbjct: 65 SRVRVELS 72

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 40.3 bits (95), Expect = 1e-05
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 4/82 (4%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQL 77
          T  + +LP    Q  +  IF      SVR        + +   +V+F       +A +  
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEA-LTY 75

Query: 78 NGLRFLGKVLSVERASKPNEEN 99
          +G     + L V+ A    ++ 
Sbjct: 76 DGALLGDRSLRVDIAEGRKQDK 97

>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 = 40.5 bits (95), Expect = 1e-05
 Identities = 13/90 (14%), Positives = 32/90 (35%), Gaps = 9/90 (10%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGA--SSVR----PCSAGRLRNCVFVDFGNEPLASQA- 73
            L I  +P    ++ +    +        V          + R   FV++ +   A+ A 
Sbjct: 10  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69

Query: 74  -QMQLNGLRFLGKVLSVERASKPNEENKHK 102
            ++    ++  G  ++V+ A +P  +    
Sbjct: 70  RKLMPGRIQLWGHQIAVDWA-EPEIDVDED 98

>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 = 40.3 bits (95), Expect = 1e-05
 Identities = 18/96 (18%), Positives = 30/96 (31%), Gaps = 6/96 (6%)

Query: 8  SGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVD 63
          SG      T+    L +  L + +    L   F  +G              + R   FV+
Sbjct: 3  SGSSGMATTKR--VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60

Query: 64 FGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEEN 99
          F     A+ A   +N     G+ + V  A     + 
Sbjct: 61 FELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKE 96

>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 = 40.0 bits (94), Expect = 2e-05
 Identities = 14/70 (20%), Positives = 26/70 (37%), Gaps = 4/70 (5%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNG 79
          T+    +   +    + + FS +G    +R       +   FV F     A+ A + +NG
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF---PEKGYSFVRFSTHESAAHAIVSVNG 83

Query: 80 LRFLGKVLSV 89
              G V+  
Sbjct: 84 TTIEGHVVKC 93

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 39.9 bits (94), Expect = 2e-05
 Identities = 16/85 (18%), Positives = 27/85 (31%), Gaps = 3/85 (3%)

Query: 11  QNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPC--SAGRLRNCVFVDFGNE 67
             KQ+ ++   L I +LP ++ +  L  +   +G   S R    S+G  R   F    + 
Sbjct: 17  MAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMEST 76

Query: 68  PLASQAQMQLNGLRFLGKVLSVERA 92
                     NG             
Sbjct: 77  EKCEAVIGHFNGKFIKTPPGVSAPT 101

>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 = 40.9 bits (95), Expect = 2e-05
 Identities = 14/95 (14%), Positives = 29/95 (30%), Gaps = 6/95 (6%)

Query: 8   SGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPC------SAGRLRNCVF 61
           +       T   + L I +L      + L+      G + +         + G+ +    
Sbjct: 57  APNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFAL 116

Query: 62  VDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPN 96
           V  G+E  + +    L      G+   V   +K  
Sbjct: 117 VGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQF 151

>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 = 39.6 bits (93), Expect = 2e-05
 Identities = 20/106 (18%), Positives = 36/106 (33%), Gaps = 12/106 (11%)

Query: 8   SGPQN-KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFV 62
           SG      +     T+ I++L     ++ L  +   +G    VR          + C F 
Sbjct: 3   SGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFA 62

Query: 63  DFGNEPLASQAQMQLN------GLRFLGKVLSVERASKPNEENKHK 102
            F  +  A +     +      GL+  G+ L V+ A    +E    
Sbjct: 63  QFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLA-VTRDEAASG 107

>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 = 39.5 bits (93), Expect = 2e-05
 Identities = 20/92 (21%), Positives = 39/92 (42%), Gaps = 2/92 (2%)

Query: 11  QNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNEP 68
              ++     TL + +L   + +  + ++FS  G   S +  +         FV+F    
Sbjct: 7   GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHR 66

Query: 69  LASQAQMQLNGLRFLGKVLSVERASKPNEENK 100
            A+ A   +NG + LGK + V  A+ P+ +  
Sbjct: 67  DAAAALAAMNGRKILGKEVKVNWATTPSSQKS 98

>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 = 40.2 bits (94), Expect = 2e-05
 Identities = 18/87 (20%), Positives = 35/87 (40%), Gaps = 3/87 (3%)

Query: 10  PQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEP 68
             ++        + + +L +   +  L R F +YG   +R    A       FV+F +  
Sbjct: 64  HMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYG--PLRSVWVARNPPGFAFVEFEDPR 121

Query: 69  LASQAQMQLNGLRFLGKVLSVERASKP 95
            A+ A  +L+G    G  + VE ++  
Sbjct: 122 DAADAVRELDGRTLCGCRVRVELSNGE 148

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

 Score = 39.1 bits (92), Expect = 3e-05
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 5/78 (6%)

Query: 24 IKHLPDAIPQDTLSRIFSHYGA-SSVR-PCSAGRLRNCVFVDFGNEPLASQAQMQLNGLR 81
          +++LP       L   F+  G           G+ + C  V F +  +A +A   +NG++
Sbjct: 13 VRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMK 72

Query: 82 FLGKVLSV---ERASKPN 96
            G+ + V     AS P+
Sbjct: 73 LSGREIDVRIDRNASGPS 90

>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 = 40.2 bits (94), Expect = 3e-05
 Identities = 24/95 (25%), Positives = 39/95 (41%), Gaps = 5/95 (5%)

Query: 12  NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVR-PC--SAGRLRNCVFVDFGNE 67
           +  + E + +L + +L      DTL R+F  YG    V  P        R   FV F ++
Sbjct: 63  HHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDK 122

Query: 68  PLASQAQMQLNGLRFLGKVLSVERAS-KPNEENKH 101
             A  A   ++G    G+ L V+ A      ++ H
Sbjct: 123 RDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSHH 157

>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 = 38.6 bits (90), Expect = 4e-05
 Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 10/74 (13%)

Query: 27 LPDAIPQDTLSRIFSHYGASS---------VRPCSAGRLRNCVFVDFGNEPLASQAQMQL 77
          +P  I ++ +   F+               V      + +N  F++F +    +QA M  
Sbjct: 14 IPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA-MAF 72

Query: 78 NGLRFLGKVLSVER 91
          +G+ F G+ L + R
Sbjct: 73 DGIIFQGQSLKIRR 86

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

 Score = 38.9 bits (91), Expect = 4e-05
 Identities = 12/83 (14%), Positives = 26/83 (31%), Gaps = 4/83 (4%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYG---ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQL 77
           ++ IK  P     D +       G      +R       +  +FV F +   A +  ++ 
Sbjct: 13  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF-VET 71

Query: 78  NGLRFLGKVLSVERASKPNEENK 100
            G ++    L +        +  
Sbjct: 72  PGQKYKETDLLILFKDDYFAKKN 94

>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 = 38.8 bits (91), Expect = 4e-05
 Identities = 21/95 (22%), Positives = 37/95 (38%), Gaps = 5/95 (5%)

Query: 8   SGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVD 63
                ++ +   + L +  L   I +D L  IF  +G   S++       GR +   F+ 
Sbjct: 15  MANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFIT 74

Query: 64  FGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEE 98
           F +   A +A  QLNG    G+ + V        +
Sbjct: 75  FSDSECAKKALEQLNGFELAGRPMKVGHV-TERTD 108

>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 = 38.8 bits (91), Expect = 4e-05
 Identities = 21/97 (21%), Positives = 43/97 (44%), Gaps = 6/97 (6%)

Query: 8   SGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVD 63
           SGP +++  +   T+ +  L + + +  L  +F   G   +         G+ +   FV+
Sbjct: 6   SGPISERNQDA--TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE 63

Query: 64  FGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENK 100
           F +E  A  A   ++ ++  GK + V +AS  N+   
Sbjct: 64  FLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLS 100

>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 = 38.4 bits (90), Expect = 5e-05
 Identities = 16/79 (20%), Positives = 32/79 (40%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGL 80
          TL++ +L  +  ++TL  +F       V     G+ +   F++F +   A +A    N  
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKR 76

Query: 81 RFLGKVLSVERASKPNEEN 99
             G+ + +E        N
Sbjct: 77 EIEGRAIRLELQGPRGSPN 95

>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 = 38.6 bits (90), Expect = 5e-05
 Identities = 17/102 (16%), Positives = 36/102 (35%), Gaps = 5/102 (4%)

Query: 11  QNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYG--ASSVRPC--SAGRLRNCVFVDFGN 66
                    V   I ++P +I +  + +         ++V     + G+      V F N
Sbjct: 7   GEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKN 66

Query: 67  EPLASQAQMQLNGLRFLGKVLSVERASKPNEENKHKHFEAQS 108
           E  A ++  +L+  +  G+   V   +  +     K+  AQ 
Sbjct: 67  EDDARKS-ERLHRKKLNGREAFVHVVTLEDMREIEKNPPAQG 107

>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 = 38.5 bits (90), Expect = 7e-05
 Identities = 21/97 (21%), Positives = 37/97 (38%), Gaps = 4/97 (4%)

Query: 8   SGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVD 63
                K++T N   + +  L   I  + +   F+ +G  S  R       G+ +   FV 
Sbjct: 4   GSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVS 63

Query: 64  FGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENK 100
           F N+  A  A  Q+ G    G+ +    A++     K
Sbjct: 64  FFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPK 100

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 38.6 bits (90), Expect = 7e-05
 Identities = 23/92 (25%), Positives = 36/92 (39%), Gaps = 8/92 (8%)

Query: 7   DSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS------AGRLRNCV 60
            S  +   + E + +L + +L      DTL R+F  YG   V              R   
Sbjct: 35  MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYG--RVGDVYIPRDRYTKESRGFA 92

Query: 61  FVDFGNEPLASQAQMQLNGLRFLGKVLSVERA 92
           FV F ++  A  A   ++G    G+ L V+ A
Sbjct: 93  FVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124

>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 = 37.5 bits (88), Expect = 7e-05
 Identities = 14/70 (20%), Positives = 23/70 (32%), Gaps = 4/70 (5%)

Query: 27 LPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRF 82
          L + +    L   F  +G              + R   FV+F     A+ A   +N    
Sbjct: 15 LAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL 74

Query: 83 LGKVLSVERA 92
           G+ + V  A
Sbjct: 75 FGRTIRVNLA 84

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

 Score = 38.6 bits (90), Expect = 8e-05
 Identities = 15/95 (15%), Positives = 26/95 (27%), Gaps = 4/95 (4%)

Query: 2   ATAPFDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLR 57
                     +         L +  L + +    L   F  +G              + R
Sbjct: 46  VDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 105

Query: 58  NCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA 92
              FV+F     A+ A   +N     G+ + V  A
Sbjct: 106 GFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>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 = 38.1 bits (89), Expect = 8e-05
 Identities = 20/79 (25%), Positives = 29/79 (36%), Gaps = 17/79 (21%)

Query: 22 LLIKHLP-DAIPQDTLSRIFSHYGASSVRPCSAGRLRNCV------FVDFGNEPLASQAQ 74
          L I +LP   + ++ L RIFS YG           +          F+ F N      A 
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYG----------HIMQINIKNAFGFIQFDNPQSVRDAI 74

Query: 75 MQLNGLRFLGKVLSVERAS 93
             +     GK L +E +S
Sbjct: 75 EXESQEMNFGKKLILEVSS 93

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

 Score = 38.0 bits (89), Expect = 8e-05
 Identities = 16/66 (24%), Positives = 21/66 (31%), Gaps = 16/66 (24%)

Query: 36 LSRIFSHYGASSVRPCSAGRLRNCV------FVDFGNEPLASQAQMQLNGLRFLGKVLSV 89
          L RIFS YG           +          F+ F N      A    +     GK L +
Sbjct: 28 LFRIFSPYG----------HIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLIL 77

Query: 90 ERASKP 95
          E +S  
Sbjct: 78 EVSSSN 83

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 12/72 (16%), Positives = 22/72 (30%), Gaps = 4/72 (5%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQA--QMQLN 78
           + I+ L D + +  L      +G   +        +    V+F +   A  A      N
Sbjct: 23 VVHIRGLIDGVVEADLVEALQEFG--PISYVVVMPKKRQALVEFEDVLGACNAVNYAADN 80

Query: 79 GLRFLGKVLSVE 90
           +   G    V 
Sbjct: 81 QIYIAGHPAFVN 92

>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 = 37.5 bits (87), Expect = 1e-04
 Identities = 8/86 (9%), Positives = 25/86 (29%), Gaps = 4/86 (4%)

Query: 7  DSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGN 66
               +  +      + ++ L +++ +  L      +G  ++        +    V+F N
Sbjct: 3  SGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFG--TICYVMMMPFKRQALVEFEN 60

Query: 67 EPLASQA--QMQLNGLRFLGKVLSVE 90
             A +         +   G+     
Sbjct: 61 IDSAKECVTFAADVPVYIAGQQAFFN 86

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 37.6 bits (87), Expect = 2e-04
 Identities = 16/94 (17%), Positives = 30/94 (31%), Gaps = 10/94 (10%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGASSVRPC------SAGRLRNCVFVDFGNEPLASQAQ 74
            + +           L ++    G   V         + G+ +    V   +E    +  
Sbjct: 57  AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116

Query: 75  MQLNGLRFLGKVLSVERASKPNEENKHKHFEAQS 108
             L G    G+ + V  A++ N       FEAQ+
Sbjct: 117 ELLPGKVLNGEKVDVRPATRQNL----SQFEAQA 146

>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 = 37.4 bits (87), Expect = 2e-04
 Identities = 21/108 (19%), Positives = 39/108 (36%), Gaps = 12/108 (11%)

Query: 7   DSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS------AGRLRNCV 60
           + GPQ   E      L +  + +   ++ +   F+ YG   ++          G L+   
Sbjct: 13  EPGPQRSVEG---WILFVTGVHEEATEEDIHDKFAEYG--EIKNIHLNLDRRTGYLKGYT 67

Query: 61  FVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENKHKHFEAQS 108
            V++     A  A   LNG   +G+ +SV+         K K    + 
Sbjct: 68  LVEYETYKEAQAAMEGLNGQDLMGQPISVDWC-FVRGPPKGKRRGGRR 114

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 36.4 bits (85), Expect = 2e-04
 Identities = 16/86 (18%), Positives = 36/86 (41%), Gaps = 9/86 (10%)

Query: 27  LPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRF 82
           +P    ++ +  + S+ G   +++       GR +   F++F +   ++ A   LNG + 
Sbjct: 10  IPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 69

Query: 83  LGKVLSVERA-----SKPNEENKHKH 103
             + L    +     S  + E+ H H
Sbjct: 70  GSRFLKCGYSSNSDISGVSLEHHHHH 95

>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 = 36.4 bits (85), Expect = 3e-04
 Identities = 19/77 (24%), Positives = 30/77 (38%), Gaps = 5/77 (6%)

Query: 27 LPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRF 82
          L   I +D L  IF  +G   ++        GR +   F+ F +   A +A  QLNG   
Sbjct: 13 LHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFEL 72

Query: 83 LGKVLSVERASKPNEEN 99
           G+ + V        + 
Sbjct: 73 AGRPMRVGHV-TERLDG 88

>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 = 36.3 bits (85), Expect = 3e-04
 Identities = 16/75 (21%), Positives = 27/75 (36%), Gaps = 5/75 (6%)

Query: 27 LPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRF 82
          L   +  +TL   F  + +  S         G  R   FV F ++  A  A   + G   
Sbjct: 9  LNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDL 68

Query: 83 LGKVLSVERAS-KPN 96
           G+ L +  A+   +
Sbjct: 69 NGRPLRINWAAKLEH 83

>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 = 37.9 bits (87), Expect = 3e-04
 Identities = 12/78 (15%), Positives = 24/78 (30%), Gaps = 4/78 (5%)

Query: 24  IKHLPDAIPQDTLSRIFSHYG---ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGL 80
           IK  P     D +       G      +R       +  +FV F +   A +  ++  G 
Sbjct: 114 IKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF-VETPGQ 172

Query: 81  RFLGKVLSVERASKPNEE 98
           ++    L +        +
Sbjct: 173 KYKETDLLILFKDDYFAK 190

>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 = 37.1 bits (86), Expect = 3e-04
 Identities = 19/109 (17%), Positives = 40/109 (36%), Gaps = 15/109 (13%)

Query: 4   APFDSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS------AGRLR 57
              + GPQ   E      L +  + +   +D +   F  YG   ++          G  +
Sbjct: 60  DELEPGPQRSVEG---WILFVTSIHEEAQEDEIQEKFCDYG--EIKNIHLNLDRRTGFSK 114

Query: 58  NCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV----ERASKPNEENKHK 102
               V++     A  A+  LNG   +G+ + V     +  K  ++++ +
Sbjct: 115 GYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSEKR 163

>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 = 36.0 bits (84), Expect = 3e-04
 Identities = 12/69 (17%), Positives = 28/69 (40%), Gaps = 6/69 (8%)

Query: 33 QDTLSRIFSHYGA-SSVR-PC--SAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS 88
           + L   F   G+ + V   C   +G  +   +++F ++     + + L+   F G+ + 
Sbjct: 20 AEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS-LALDESLFRGRQIK 78

Query: 89 VERASKPNE 97
          V    + N 
Sbjct: 79 VIPK-RTNR 86

>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 = 36.6 bits (85), Expect = 3e-04
 Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 8/92 (8%)

Query: 7   DSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS------AGRLRNCV 60
                N+   +    L +  L     +  L  +FS YG   +   S      + R R   
Sbjct: 34  SRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYG--PIADVSIVYDQQSRRSRGFA 91

Query: 61  FVDFGNEPLASQAQMQLNGLRFLGKVLSVERA 92
           FV F N   A +A+ + NG+   G+ + V+ +
Sbjct: 92  FVYFENVDDAKEAKERANGMELDGRRIRVDFS 123

>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 = 36.1 bits (84), Expect = 4e-04
 Identities = 20/97 (20%), Positives = 34/97 (35%), Gaps = 6/97 (6%)

Query: 7   DSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVR-PC--SAGRLRNCVFV 62
           +       E  +  T+    L   I    L   FS  G    VR     ++ R +   +V
Sbjct: 13  EPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYV 72

Query: 63  DFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEEN 99
           +F        A + L G R LG  + V+ + +  +  
Sbjct: 73  EFCEIQSVPLA-IGLTGQRLLGVPIIVQAS-QAEKNR 107

>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 = 36.1 bits (84), Expect = 4e-04
 Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 4/69 (5%)

Query: 33 QDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS 88
          + +L ++FS YG  S V         R R   FV F N   A  A M +NG    G+ + 
Sbjct: 26 EQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIR 85

Query: 89 VERASKPNE 97
          V++A K ++
Sbjct: 86 VDQAGKSSD 94

>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 = 35.6 bits (83), Expect = 4e-04
 Identities = 22/86 (25%), Positives = 35/86 (40%), Gaps = 4/86 (4%)

Query: 12 NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNE 67
          N+   +    L +  L     +  L  +FS YG  + V       + R R   FV F N 
Sbjct: 8  NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67

Query: 68 PLASQAQMQLNGLRFLGKVLSVERAS 93
            A +A+ + NG+   G+ + V   S
Sbjct: 68 DDAKEAKERANGMELDGRRIRVSGPS 93

>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 = 35.7 bits (83), Expect = 5e-04
 Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 4/70 (5%)

Query: 27 LPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRF 82
          LP ++  + L RIFS YG    V         + +   F+ F ++  A      +N  + 
Sbjct: 24 LPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQL 83

Query: 83 LGKVLSVERA 92
           G+V+    A
Sbjct: 84 FGRVIKASIA 93

>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 = 35.9 bits (83), Expect = 6e-04
 Identities = 12/89 (13%), Positives = 33/89 (37%), Gaps = 3/89 (3%)

Query: 8  SGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPC--SAGRLRNCVFVDFG 65
          S  +      + + + +  +P +  ++ +   F      +V       GR      V F 
Sbjct: 5  SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGNGLVKFL 64

Query: 66 NEPLASQAQMQLNGLRFLGKVLSVERASK 94
          +     +A ++ N +  + + + V  A++
Sbjct: 65 SPQDTFEA-LKRNRMLMIQRYVEVSPATE 92

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 36.2 bits (83), Expect = 6e-04
 Identities = 13/80 (16%), Positives = 31/80 (38%), Gaps = 1/80 (1%)

Query: 1  MATAPFDSGPQNKQETENLVTLL-IKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNC 59
          +A +            ++ V  + +++L   +  D L +IFS +G            +  
Sbjct: 9  LAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ 68

Query: 60 VFVDFGNEPLASQAQMQLNG 79
            + + +   A  A++ L+G
Sbjct: 69 ALLQYADPVSAQHAKLSLDG 88

>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 = 35.2 bits (82), Expect = 7e-04
 Identities = 16/83 (19%), Positives = 35/83 (42%), Gaps = 9/83 (10%)

Query: 27  LPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRF 82
           L  +   + +  +FS +G   +V+        + +   FV+   E   S+A  +L+   F
Sbjct: 9   LVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDF 67

Query: 83  LGKVLSV----ERASKPNEENKH 101
           +G+ + V     + S  +  + H
Sbjct: 68  MGRTIRVTEANPKKSLEHHHHHH 90

>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 = 35.7 bits (82), Expect = 8e-04
 Identities = 20/111 (18%), Positives = 38/111 (34%), Gaps = 7/111 (6%)

Query: 8   SGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFS----HYGASSVRPC--SAGRLRNCVF 61
           SG     E      + ++ LP +   + +    S    H G + V       GR     F
Sbjct: 6   SGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAF 65

Query: 62  VDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNEENKHKHFEAQSISSM 112
           V+  +E     A ++ +      + + V ++ +   +   KH    S S  
Sbjct: 66  VELESEDDVKLA-LKKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGP 115

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 35.4 bits (82), Expect = 8e-04
 Identities = 17/97 (17%), Positives = 39/97 (40%), Gaps = 7/97 (7%)

Query: 8  SGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVD 63
          S   +  +  + + L I  +P  + +  L  +F  +G     + ++    G  + C F+ 
Sbjct: 2  SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61

Query: 64 FGNEPLASQAQMQLNG---LRFLGKVLSVERASKPNE 97
          +     A +AQ  L+    L  + + + V+ A   + 
Sbjct: 62 YCERESALKAQSALHEQKTLPGMNRPIQVKPADSESR 98

>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 = 35.2 bits (81), Expect = 9e-04
 Identities = 11/90 (12%), Positives = 29/90 (32%), Gaps = 4/90 (4%)

Query: 7  DSGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGN 66
               +K +      L I+ LP  + +  +  +   +G   V      + +N  F++   
Sbjct: 3  SGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFG--KVTNILMLKGKNQAFLELAT 60

Query: 67 EPLASQA--QMQLNGLRFLGKVLSVERASK 94
          E  A                + + ++ ++ 
Sbjct: 61 EEAAITMVNYYSAVTPHLRNQPIYIQYSNH 90

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 35.3 bits (82), Expect = 9e-04
 Identities = 21/106 (19%), Positives = 36/106 (33%), Gaps = 11/106 (10%)

Query: 12  NKQETENLVTLLIKHLPDAIPQDTLSRIFS-HYGASSVRPC-----SAGRLRNCVFVDFG 65
           +   +    +L +  L   +    L   F   Y   S R         G  +   FV F 
Sbjct: 2   SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYP--SCRGGKVVLDQTGVSKGYGFVKFT 59

Query: 66  NEPLASQAQMQLNGLRFLG-KVLSVERASKPNEENKHKHFEAQSIS 110
           +E    +A  +  G   LG K + +  A    + ++ K  E+   S
Sbjct: 60  DELEQKRALTECQGAVGLGSKPVRLSVAIP--KASRVKPVESGPSS 103

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	121
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.9
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.87
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.87
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.87
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.87
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.86
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.86
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.86
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.86
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.86
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.86
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.86
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.86
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.86
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.86
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.86
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.85
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.85
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.85
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.85
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.85
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.85
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.85
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.85
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.85
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.85
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.85
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.85
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.85
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.85
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.85
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.85
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.85
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.85
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.85
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.85
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.85
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.85
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.84
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.84
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.84
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.84
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.84
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.84
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.84
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.84
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.84
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.84
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.84
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.84
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.84
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.84
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.84
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.84
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.84
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.84
2div_A	99	TRNA selenocysteine associated protein; structural	99.83
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.83
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.83
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.83
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.83
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.83
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.83
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.83
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.83
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.82
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.82
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.82
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.82
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.82
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.82
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.82
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.82
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.82
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.82
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.82
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.82
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.82
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.82
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.82
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.82
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.82
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.82
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.82
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.82
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.82
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.82
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.82
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.82
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.82
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.82
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.82
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.82
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.81
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.81
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.81
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.81
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.81
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.81
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.81
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.81
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.81
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.81
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.81
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.81
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.81
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.81
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.81
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.81
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.81
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.81
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.8
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.8
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.8
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.8
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.8
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.8
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.8
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.8
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.8
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.8
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.79
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.79
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.79
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.79
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.79
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.79
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.79
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.79
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.78
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.78
1x5p_A	97	Negative elongation factor E; structure genomics,	99.78
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.78
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.78
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.77
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.77
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.77
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.77
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.77
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.77
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.77
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.76
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.76
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.76
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.75
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.75
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.61
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.75
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.75
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.75
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.74
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.74
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.74
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.74
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.74
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.74
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.74
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.74
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.73
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.73
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.73
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.73
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.73
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.73
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.72
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.72
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.71
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.71
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.71
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.7
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.7
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.69
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.69
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.69
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.69
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.69
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.68
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.68
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.67
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.66
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.66
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.66
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.66
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.66
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.65
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.65
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.65
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.65
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.64
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.63
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.63
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.63
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.63
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.63
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.61
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.6
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.56
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.54
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.53
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.52
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.44
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.43
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.36
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.28
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.26
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.1
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.94
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.46
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	98.19
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.1
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.77
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.74
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.73
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.12
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.7
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	95.84
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.63
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	95.38
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.31
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.24

>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=99.90  E-value=2e-23  Score=125.92  Aligned_cols=77  Identities=32%  Similarity=0.475  Sum_probs=71.2

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      .+++|||+|||+.+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|.+|+..|||..++|+.|+|.+| 
T Consensus        18 ~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           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA-   96 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC-
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe-
Confidence            3789999999999999999999999999 6676665   6889999999999999999999999999999999999999 


Q ss_pred             CC
Q 043634           94 KP   95 (121)
Q Consensus        94 ~~   95 (121)
                      +|
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            54

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

Probab=99.87  E-value=1.5e-21  Score=119.82  Aligned_cols=76  Identities=16%  Similarity=0.176  Sum_probs=71.1

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|.+|+..|||..++|+.|+|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45889999999999999999999999999 6676665   6889999999999999999999999999999999999999

>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=99.87  E-value=4.6e-21  Score=118.04  Aligned_cols=82  Identities=24%  Similarity=0.333  Sum_probs=73.4

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ...+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+..||+..|+|+.|+|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3344799999999999999999999999999 6777665   68889999999999999999999999999999999999


Q ss_pred             ecCCCCc
Q 043634           91 RASKPNE   97 (121)
Q Consensus        91 ~a~~~~~   97 (121)
                      ++ .++.
T Consensus       101 ~a-~~~~  106 (115)
T 2cpz_A          101 LK-RSKN  106 (115)
T ss_dssp             CC-CCSC
T ss_pred             Ec-CCCC
Confidence            99 4443

>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=99.87  E-value=1.5e-21  Score=120.50  Aligned_cols=75  Identities=24%  Similarity=0.342  Sum_probs=69.4

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      .++|||+|||+.+++++|+++|++||. .+++++. .+.++|||||+|.+.++|..|+..|||..|+|+.|+|.++.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            678999999999999999999999999 6677766 56678999999999999999999999999999999999993

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.87  E-value=9e-22  Score=116.91  Aligned_cols=79  Identities=23%  Similarity=0.377  Sum_probs=69.4

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhC-C-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHh-cCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYG-A-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQL-NGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G-~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l-~g~~i~g~~l~v~~a   92 (121)
                      +.+|||+|||+.+++++|+++|++|| . ..++++.   +|.++|||||+|.+.++|.+|++.+ ++..++|+.|+|.++
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            36899999999999999999999999 5 6677765   6889999999999999999999877 567899999999999


Q ss_pred             CCCCcc
Q 043634           93 SKPNEE   98 (121)
Q Consensus        93 ~~~~~~   98 (121)
                       .++.+
T Consensus        81 -~~~~~   85 (91)
T 2lxi_A           81 -DPKPK   85 (91)
T ss_dssp             -CSCCC
T ss_pred             -CCCCC
Confidence             55443

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

Probab=99.86  E-value=7.8e-21  Score=116.95  Aligned_cols=85  Identities=24%  Similarity=0.356  Sum_probs=74.7

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      .....+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+..|||..|+|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (115)
T 2dgo_A            9 KKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR   88 (115)
T ss_dssp             CCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            344456899999999999999999999999999 6666665   678899999999999999999999999999999999


Q ss_pred             EEecCCCCcc
Q 043634           89 VERASKPNEE   98 (121)
Q Consensus        89 v~~a~~~~~~   98 (121)
                      |.++ .++..
T Consensus        89 V~~a-~~~~~   97 (115)
T 2dgo_A           89 TNWA-TRKPP   97 (115)
T ss_dssp             EEES-SCCCC
T ss_pred             EEEc-cCCCC
Confidence            9999 44433

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

Probab=99.86  E-value=9.2e-21  Score=113.97  Aligned_cols=82  Identities=24%  Similarity=0.423  Sum_probs=73.1

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ....+.++|||+|||+.+++++|+++|.+||. ..++++.  ++.++|||||+|.+.++|..|+..|||..++|+.|+|.
T Consensus        12 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34455899999999999999999999999999 6666665  67888999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 043634           91 RASKPN   96 (121)
Q Consensus        91 ~a~~~~   96 (121)
                      ++ .++
T Consensus        92 ~a-~~~   96 (100)
T 2do4_A           92 IS-NSG   96 (100)
T ss_dssp             EC-CCC
T ss_pred             EC-CCC
Confidence            99 544

>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=99.86  E-value=1.9e-20  Score=114.31  Aligned_cols=80  Identities=23%  Similarity=0.310  Sum_probs=72.3

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ....+.++|||+|||+.+++++|+++|++||. ..+.+...+.++|||||+|.+.++|..|+..||+..|+|+.|+|.++
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   96 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            34445899999999999999999999999999 66666667778899999999999999999999999999999999999


Q ss_pred             C
Q 043634           93 S   93 (121)
Q Consensus        93 ~   93 (121)
                      +
T Consensus        97 ~   97 (109)
T 1x4a_A           97 R   97 (109)
T ss_dssp             C
T ss_pred             c
Confidence            3

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.86  E-value=5.3e-21  Score=114.55  Aligned_cols=76  Identities=22%  Similarity=0.347  Sum_probs=69.3

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC---ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCC----eeCCeE
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA---SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGL----RFLGKV   86 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~---~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~----~i~g~~   86 (121)
                      ..-.+|||+|||+.+|+++|+++|++||.   ..++++.   +|.++|||||+|.+.++|.+|++.|||.    .|+|+.
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            34789999999999999999999999995   4577766   7899999999999999999999999996    599999


Q ss_pred             EEEEec
Q 043634           87 LSVERA   92 (121)
Q Consensus        87 l~v~~a   92 (121)
                      |.|++|
T Consensus        87 i~V~~A   92 (95)
T 2lkz_A           87 IGVDFA   92 (95)
T ss_dssp             EEEEEC
T ss_pred             EEEEEc
Confidence            999999

>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=99.86  E-value=2.1e-20  Score=112.94  Aligned_cols=84  Identities=21%  Similarity=0.325  Sum_probs=73.3

Q ss_pred             CCCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           12 NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        12 ~~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      ......+.++|||+|||+.+++++|+++|++||. ..++++. .+.++|||||+|.+.++|..|+..||+..|+|+.|+|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   87 (103)
T 2cq3_A            8 NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             CSCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3444555899999999999999999999999999 6666665 3447899999999999999999999999999999999


Q ss_pred             EecCCCC
Q 043634           90 ERASKPN   96 (121)
Q Consensus        90 ~~a~~~~   96 (121)
                      .++ .++
T Consensus        88 ~~a-~~~   93 (103)
T 2cq3_A           88 NNA-TAR   93 (103)
T ss_dssp             EEC-CSS
T ss_pred             EEc-ccC
Confidence            999 443

>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=99.86  E-value=2.2e-20  Score=112.88  Aligned_cols=81  Identities=23%  Similarity=0.336  Sum_probs=71.9

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      .....+.++|||+|||+.+++++|+++|++||. ..++++. .+.++|||||+|.+.++|..|+..||+..+.|+.|+|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2cqi_A            9 MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   88 (103)
T ss_dssp             CCCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEE
Confidence            334455899999999999999999999999999 6666666 44468999999999999999999999999999999999


Q ss_pred             ecC
Q 043634           91 RAS   93 (121)
Q Consensus        91 ~a~   93 (121)
                      +++
T Consensus        89 ~a~   91 (103)
T 2cqi_A           89 WAT   91 (103)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            993

>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=99.86  E-value=5.6e-21  Score=116.79  Aligned_cols=83  Identities=25%  Similarity=0.431  Sum_probs=73.8

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      +....+.++|||+|||+.+++++|+.+|++||. ..++++.   +|.++|||||+|.+.++|..|+..|||..++|+.|+
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            344455899999999999999999999999999 6666664   678899999999999999999999999999999999


Q ss_pred             EEecCCCC
Q 043634           89 VERASKPN   96 (121)
Q Consensus        89 v~~a~~~~   96 (121)
                      |.++ .++
T Consensus       100 V~~a-~~k  106 (108)
T 2jrs_A          100 VGHV-TER  106 (108)
T ss_dssp             EECS-CSS
T ss_pred             EEEc-ccC
Confidence            9999 544

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

Probab=99.86  E-value=7.9e-21  Score=115.14  Aligned_cols=82  Identities=21%  Similarity=0.304  Sum_probs=73.4

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      ....+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+..||+..|+|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            34455899999999999999999999999999 6666665   6788999999999999999999999999999999999


Q ss_pred             EecCCCC
Q 043634           90 ERASKPN   96 (121)
Q Consensus        90 ~~a~~~~   96 (121)
                      .++ .+.
T Consensus        90 ~~a-~~~   95 (105)
T 1x5u_A           90 NKA-SAH   95 (105)
T ss_dssp             EET-TTT
T ss_pred             EEC-CCC
Confidence            999 443

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

Probab=99.86  E-value=7e-21  Score=114.37  Aligned_cols=80  Identities=20%  Similarity=0.381  Sum_probs=72.1

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-cc--------EEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCC
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SS--------VRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGL   80 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~--------~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~   80 (121)
                      +....+.++|||+|||+.+++++|+++|++||. ..        ++++.   +|.++|||||+|.+.++|..|+..|||.
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            334455899999999999999999999999999 55        66665   6888999999999999999999999999


Q ss_pred             eeCCeEEEEEec
Q 043634           81 RFLGKVLSVERA   92 (121)
Q Consensus        81 ~i~g~~l~v~~a   92 (121)
                      .++|+.|+|++|
T Consensus        87 ~~~g~~l~V~~A   98 (99)
T 2la6_A           87 EFSGNPIKVSFA   98 (99)
T ss_dssp             BSSSSBCEEEEC
T ss_pred             EeCCcEEEEEec
Confidence            999999999987

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

Probab=99.86  E-value=1.3e-20  Score=115.21  Aligned_cols=86  Identities=21%  Similarity=0.377  Sum_probs=75.2

Q ss_pred             CCCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhc------CCe
Q 043634           12 NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLN------GLR   81 (121)
Q Consensus        12 ~~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~------g~~   81 (121)
                      .+....+.++|||+|||+.+++++|+.+|.+||. ..++++.   ++.++|||||+|.+.++|..|+..||      +..
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~   87 (111)
T 1x4h_A            8 LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLK   87 (111)
T ss_dssp             CCCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEE
T ss_pred             CCCcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcE
Confidence            3444556899999999999999999999999999 6666665   57889999999999999999999999      999


Q ss_pred             eCCeEEEEEecCCCCcc
Q 043634           82 FLGKVLSVERASKPNEE   98 (121)
Q Consensus        82 i~g~~l~v~~a~~~~~~   98 (121)
                      ++|+.|+|.++ .++..
T Consensus        88 ~~g~~l~v~~a-~~~~~  103 (111)
T 1x4h_A           88 LDGRQLKVDLA-VTRDE  103 (111)
T ss_dssp             SSSCEEEEECC-CCCCC
T ss_pred             EcCEEEEEEEC-CCCcc
Confidence            99999999999 54433

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

Probab=99.86  E-value=1.2e-20  Score=113.81  Aligned_cols=79  Identities=19%  Similarity=0.296  Sum_probs=72.3

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ...+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+..||+..|+|+.|+|.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3445899999999999999999999999999 6777765   57889999999999999999999999999999999999


Q ss_pred             ecC
Q 043634           91 RAS   93 (121)
Q Consensus        91 ~a~   93 (121)
                      +++
T Consensus        88 ~a~   90 (102)
T 2cqb_A           88 LAK   90 (102)
T ss_dssp             ECC
T ss_pred             eCC
Confidence            993

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

Probab=99.85  E-value=1.1e-20  Score=112.79  Aligned_cols=79  Identities=19%  Similarity=0.298  Sum_probs=72.1

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccE-EEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSV-RPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~-~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      .+.++|||+|||+.+++++|+++|++||. ..+ +++.   ++.++|||||+|.+.++|..|+..|||..++|+.|+|.+
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            45899999999999999999999999999 666 7765   678899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 043634           92 ASKPN   96 (121)
Q Consensus        92 a~~~~   96 (121)
                      + .++
T Consensus        83 a-~~~   86 (96)
T 1x5t_A           83 A-FKK   86 (96)
T ss_dssp             S-CCC
T ss_pred             e-ccc
Confidence            9 443

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

Probab=99.85  E-value=9.4e-21  Score=114.49  Aligned_cols=81  Identities=22%  Similarity=0.436  Sum_probs=73.1

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      +..+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+..|||..|+|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            4455899999999999999999999999999 6666664   67889999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 043634           91 RASKPN   96 (121)
Q Consensus        91 ~a~~~~   96 (121)
                      ++ .++
T Consensus        91 ~a-~~~   95 (103)
T 2cq0_A           91 WA-KPS   95 (103)
T ss_dssp             ES-SCC
T ss_pred             EC-CCC
Confidence            99 443

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

Probab=99.85  E-value=1.3e-20  Score=112.16  Aligned_cols=81  Identities=26%  Similarity=0.346  Sum_probs=72.9

Q ss_pred             CCCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEE
Q 043634           12 NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVL   87 (121)
Q Consensus        12 ~~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l   87 (121)
                      ......+.++|||+|||+.+++++|+++|++||. ..+.++.   ++.++|||||+|.+.++|..|+..|||..++|+.|
T Consensus         8 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   87 (95)
T 2cqc_A            8 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI   87 (95)
T ss_dssp             CCCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            3444566899999999999999999999999999 6666654   57889999999999999999999999999999999


Q ss_pred             EEEec
Q 043634           88 SVERA   92 (121)
Q Consensus        88 ~v~~a   92 (121)
                      +|.++
T Consensus        88 ~v~~a   92 (95)
T 2cqc_A           88 RVSGP   92 (95)
T ss_dssp             EEECC
T ss_pred             EEEec
Confidence            99998

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

Probab=99.85  E-value=2e-20  Score=114.75  Aligned_cols=83  Identities=22%  Similarity=0.368  Sum_probs=73.7

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-c--------cEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCC
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-S--------SVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGL   80 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~--------~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~   80 (121)
                      .....+.++|||+|||+.+++++|+++|.+||. .        .++++.   ++.++|||||+|.+.++|..|+..|||.
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            344556899999999999999999999999999 5        466665   6788999999999999999999999999


Q ss_pred             eeCCeEEEEEecCCCC
Q 043634           81 RFLGKVLSVERASKPN   96 (121)
Q Consensus        81 ~i~g~~l~v~~a~~~~   96 (121)
                      .|+|+.|+|.++ .++
T Consensus        89 ~~~g~~l~V~~a-~~~  103 (113)
T 2cpe_A           89 DFQGSKLKVSLA-RKK  103 (113)
T ss_dssp             EETTEECEEECS-SCC
T ss_pred             ccCCCEEEEEEC-CCC
Confidence            999999999999 443

>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=99.85  E-value=8.2e-21  Score=111.32  Aligned_cols=76  Identities=22%  Similarity=0.336  Sum_probs=69.4

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+.++|||+|||..+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+..|||..++|+.|+|.++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            34789999999999999999999999999 6666655   6788999999999999999999999999999999999999

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

Probab=99.85  E-value=1.2e-20  Score=113.82  Aligned_cols=79  Identities=29%  Similarity=0.388  Sum_probs=72.5

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ...+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+..||+..++|+.|+|.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3455899999999999999999999999999 7777776   67789999999999999999999999999999999999


Q ss_pred             ecC
Q 043634           91 RAS   93 (121)
Q Consensus        91 ~a~   93 (121)
                      +++
T Consensus        88 ~a~   90 (102)
T 1x5s_A           88 QAG   90 (102)
T ss_dssp             EEE
T ss_pred             ECC
Confidence            993

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

Probab=99.85  E-value=1.4e-20  Score=111.85  Aligned_cols=78  Identities=23%  Similarity=0.395  Sum_probs=71.2

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ...+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+..||+..++|+.|+|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   91 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS   91 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            3445899999999999999999999999999 6676665   57789999999999999999999999999999999999


Q ss_pred             ec
Q 043634           91 RA   92 (121)
Q Consensus        91 ~a   92 (121)
                      ++
T Consensus        92 ~a   93 (94)
T 2e5h_A           92 IA   93 (94)
T ss_dssp             EC
T ss_pred             ec
Confidence            98

>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=99.85  E-value=1.8e-20  Score=112.49  Aligned_cols=80  Identities=23%  Similarity=0.357  Sum_probs=72.3

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ..+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+..|||..++|+.|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            355899999999999999999999999999 5666655   678899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 043634           92 ASKPN   96 (121)
Q Consensus        92 a~~~~   96 (121)
                      + .++
T Consensus        85 a-~~~   88 (99)
T 1whw_A           85 S-TIK   88 (99)
T ss_dssp             C-CCC
T ss_pred             c-CCC
Confidence            9 443

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

Probab=99.85  E-value=1e-20  Score=114.36  Aligned_cols=81  Identities=26%  Similarity=0.422  Sum_probs=72.8

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      ++...+.++|||+|||+.+++++|+++|++||. ..+.++.   ++.++|||||+|.+.++|..|+..|||..++|+.|+
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            344555899999999999999999999999999 5666665   578899999999999999999999999999999999


Q ss_pred             EEecC
Q 043634           89 VERAS   93 (121)
Q Consensus        89 v~~a~   93 (121)
                      |.+++
T Consensus        87 V~~a~   91 (103)
T 2dnm_A           87 VQVAR   91 (103)
T ss_dssp             EEECS
T ss_pred             EEECC
Confidence            99994

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

Probab=99.85  E-value=1.1e-20  Score=114.19  Aligned_cols=83  Identities=29%  Similarity=0.411  Sum_probs=73.6

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      .....+.++|||+|||+.+++++|+++|++||. ..++++. ++.++|||||+|.+.++|..|+..|||..++|+.|+|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2d9p_A            9 RITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVA   88 (103)
T ss_dssp             CCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            344456899999999999999999999999999 5666655 67889999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 043634           91 RASKPN   96 (121)
Q Consensus        91 ~a~~~~   96 (121)
                      ++ .++
T Consensus        89 ~a-~~~   93 (103)
T 2d9p_A           89 LA-QRK   93 (103)
T ss_dssp             EC-SSC
T ss_pred             Ee-ccc
Confidence            99 443

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

Probab=99.85  E-value=1.8e-20  Score=114.67  Aligned_cols=80  Identities=21%  Similarity=0.326  Sum_probs=72.4

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      .....+.++|||+|||..+++++|+++|++||. ..++++. .+.++|||||+|.+.++|..|+..|||..++|+.|+|.
T Consensus        23 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            334445899999999999999999999999999 7788776 45578999999999999999999999999999999999


Q ss_pred             ec
Q 043634           91 RA   92 (121)
Q Consensus        91 ~a   92 (121)
                      ++
T Consensus       103 ~a  104 (109)
T 2err_A          103 NA  104 (109)
T ss_dssp             EC
T ss_pred             EC
Confidence            99

>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=99.85  E-value=1.3e-20  Score=109.60  Aligned_cols=76  Identities=22%  Similarity=0.292  Sum_probs=69.5

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKP   95 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   95 (121)
                      ++|||+|||+.+++++|+++|++||. ..+.++.   ++.++|||||+|.+.++|..|+..|||..++|+.|+|.++ .+
T Consensus         2 ~~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            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA-AK   80 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC-CC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEec-Cc
Confidence            68999999999999999999999999 6666664   6888999999999999999999999999999999999999 44


Q ss_pred             C
Q 043634           96 N   96 (121)
Q Consensus        96 ~   96 (121)
                      +
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.85  E-value=1.7e-20  Score=113.62  Aligned_cols=78  Identities=22%  Similarity=0.348  Sum_probs=71.0

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCC---eEEEE
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLG---KVLSV   89 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g---~~l~v   89 (121)
                      ..+.++|||+|||+.+++++|+.+|++||. ..++++.  ++.++|||||+|.+.++|..|+..|||..+.|   +.|+|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            345899999999999999999999999999 6666665  67889999999999999999999999999998   99999


Q ss_pred             EecC
Q 043634           90 ERAS   93 (121)
Q Consensus        90 ~~a~   93 (121)
                      .+++
T Consensus        92 ~~a~   95 (105)
T 2dnh_A           92 KFAD   95 (105)
T ss_dssp             EESC
T ss_pred             EECc
Confidence            9993

>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=99.85  E-value=1.4e-20  Score=109.92  Aligned_cols=76  Identities=20%  Similarity=0.314  Sum_probs=69.9

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+..|||..++|+.|+|+++
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45899999999999999999999999999 5566554   6778999999999999999999999999999999999988

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

Probab=99.85  E-value=1.3e-20  Score=112.27  Aligned_cols=80  Identities=25%  Similarity=0.393  Sum_probs=72.2

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+..|||..++|+.|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            45899999999999999999999999999 6666665   5788999999999999999999999999999999999999


Q ss_pred             CCCCc
Q 043634           93 SKPNE   97 (121)
Q Consensus        93 ~~~~~   97 (121)
                       .++.
T Consensus        83 -~~~~   86 (95)
T 2dnz_A           83 -TERL   86 (95)
T ss_dssp             -SCCC
T ss_pred             -cccc
Confidence             4443

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

Probab=99.85  E-value=2.1e-20  Score=112.17  Aligned_cols=79  Identities=23%  Similarity=0.365  Sum_probs=71.4

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ..+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+. +|+..++|+.|+|.+
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEE
Confidence            445899999999999999999999999999 6677765   57889999999999999999998 999999999999999


Q ss_pred             cCCCC
Q 043634           92 ASKPN   96 (121)
Q Consensus        92 a~~~~   96 (121)
                      + .++
T Consensus        86 a-~~~   89 (99)
T 2dgs_A           86 A-EPR   89 (99)
T ss_dssp             C-CCC
T ss_pred             C-CCC
Confidence            9 443

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

Probab=99.85  E-value=1.7e-20  Score=112.13  Aligned_cols=75  Identities=16%  Similarity=0.299  Sum_probs=69.7

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      |.++|||+|||..+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|..|+..|||..++|+.|+|.++
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   79 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYS   79 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEc
Confidence            4689999999999999999999999999 6666665   5788999999999999999999999999999999999999

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

Probab=99.85  E-value=1.9e-20  Score=112.77  Aligned_cols=77  Identities=18%  Similarity=0.280  Sum_probs=70.8

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...+.++|||+|||+.+++++|+++|.+||.  |+++.  ++.++|||||+|.+.++|..|+..||+..|+|+.|+|.++
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~--v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   88 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATF--IKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQ   88 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSE--EECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCE--EEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEc
Confidence            4455899999999999999999999999998  66665  7788999999999999999999999999999999999999


Q ss_pred             C
Q 043634           93 S   93 (121)
Q Consensus        93 ~   93 (121)
                      +
T Consensus        89 ~   89 (101)
T 2fc9_A           89 G   89 (101)
T ss_dssp             S
T ss_pred             C
Confidence            3

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

Probab=99.85  E-value=6.2e-21  Score=120.13  Aligned_cols=83  Identities=24%  Similarity=0.283  Sum_probs=73.7

Q ss_pred             CCCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-cc--EEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCC----e
Q 043634           12 NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SS--VRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGL----R   81 (121)
Q Consensus        12 ~~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~--~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~----~   81 (121)
                      .+....+.++|||+|||+.+++++|+++|.+||. ..  ++++.   +|.++|||||+|.+. +|..|+..|||.    .
T Consensus        16 ~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~   94 (131)
T 2m2b_A           16 EPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLT   94 (131)
T ss_dssp             CCCCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCcc
Confidence            3444456899999999999999999999999999 55  67776   788999999999999 999999999999    9


Q ss_pred             eCCeEEEEEecCCCC
Q 043634           82 FLGKVLSVERASKPN   96 (121)
Q Consensus        82 i~g~~l~v~~a~~~~   96 (121)
                      ++|+.|+|.++ .++
T Consensus        95 ~~gr~l~V~~a-~~~  108 (131)
T 2m2b_A           95 IDGKTINVEFA-KGS  108 (131)
T ss_dssp             GGGCCCCCEEC-CCS
T ss_pred             CCCEEEEEEEC-CCC
Confidence            99999999999 443

>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=99.85  E-value=1.7e-20  Score=112.33  Aligned_cols=79  Identities=15%  Similarity=0.178  Sum_probs=70.3

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ....++|||+|||+.+++++|+++|.+||. ..+.++.   ++.++|||||+|.+.++|..|+..|||..|+|+.|+|.+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            344799999999999999999999999999 4444443   788899999999999999999999999999999999999


Q ss_pred             cCC
Q 043634           92 ASK   94 (121)
Q Consensus        92 a~~   94 (121)
                      +..
T Consensus        92 a~~   94 (98)
T 2cqp_A           92 GSG   94 (98)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            943

>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=99.85  E-value=1.6e-20  Score=114.67  Aligned_cols=80  Identities=19%  Similarity=0.363  Sum_probs=72.2

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      +....+.++|||+|||+.+++++|+.+|++||. ..+.++.   +|.++|||||+|.+.++|..|+..|||..++|+.|+
T Consensus        20 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   99 (110)
T 1oo0_B           20 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ   99 (110)
T ss_dssp             BCCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            334455899999999999999999999999999 6666664   678899999999999999999999999999999999


Q ss_pred             EEec
Q 043634           89 VERA   92 (121)
Q Consensus        89 v~~a   92 (121)
                      |.++
T Consensus       100 V~~a  103 (110)
T 1oo0_B          100 VDWC  103 (110)
T ss_dssp             EEES
T ss_pred             EEEc
Confidence            9999

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

Probab=99.85  E-value=1.1e-20  Score=116.77  Aligned_cols=77  Identities=26%  Similarity=0.318  Sum_probs=70.5

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ..+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+..|||..++|+.|+|++
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            344799999999999999999999999999 6677765   678899999999999999999999999999999999998


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      +
T Consensus       117 a  117 (118)
T 2khc_A          117 K  117 (118)
T ss_dssp             C
T ss_pred             c
Confidence            7

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

Probab=99.84  E-value=1.3e-20  Score=111.66  Aligned_cols=78  Identities=19%  Similarity=0.359  Sum_probs=71.5

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ..+.++|||+|||+.+++++|+++|++||. ..++++. ++.++|||||+|.+.++|..|+..||+..++|+.|+|.+++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   84 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR   84 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            345899999999999999999999999999 6666665 78889999999999999999999999999999999999993

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

Probab=99.84  E-value=1.2e-20  Score=118.52  Aligned_cols=79  Identities=18%  Similarity=0.254  Sum_probs=71.0

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHH----HHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLS----RIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~----~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      ....+.++|||+|||+.+++++|+    .+|++||. ..+.+..++.++|||||+|.+.++|..|+..|||..+.|+.|+
T Consensus        24 ~~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           24 PHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             CCCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            344568999999999999999876    69999999 5666666788999999999999999999999999999999999


Q ss_pred             EEec
Q 043634           89 VERA   92 (121)
Q Consensus        89 v~~a   92 (121)
                      |.++
T Consensus       104 V~~a  107 (127)
T 2a3j_A          104 ITFS  107 (127)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9999

>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=99.84  E-value=3.6e-20  Score=112.38  Aligned_cols=79  Identities=19%  Similarity=0.435  Sum_probs=71.9

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCee---CCeEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRF---LGKVL   87 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i---~g~~l   87 (121)
                      ...+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+..||+..+   +|+.|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            3455899999999999999999999999999 6777766   588899999999999999999999999988   89999


Q ss_pred             EEEecC
Q 043634           88 SVERAS   93 (121)
Q Consensus        88 ~v~~a~   93 (121)
                      +|.++.
T Consensus        89 ~v~~a~   94 (106)
T 2dgp_A           89 QVKPAD   94 (106)
T ss_dssp             EEEECC
T ss_pred             EEEECC
Confidence            999993

>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=99.84  E-value=2.6e-21  Score=114.53  Aligned_cols=73  Identities=16%  Similarity=0.212  Sum_probs=66.2

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhC--C-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYG--A-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G--~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+|||+|||+.+++++|+++|++||  . ..++++.   +|.++|||||+|.+.++|.+|+..|||..++|+.|+|.++
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~   80 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPS   80 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEEC
Confidence            5799999999999999999999999  7 6677665   7889999999999999999999999999999999999999

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

Probab=99.84  E-value=1.3e-20  Score=114.30  Aligned_cols=80  Identities=20%  Similarity=0.356  Sum_probs=72.0

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      +....+.++|||+|||+.+++++|+.+|++||. ..+.++.   +|.++|||||+|.+.++|..|+..|||..++|+.|+
T Consensus        17 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   96 (106)
T 1p27_B           17 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS   96 (106)
T ss_dssp             BCCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEE
Confidence            333445799999999999999999999999999 6666654   588899999999999999999999999999999999


Q ss_pred             EEec
Q 043634           89 VERA   92 (121)
Q Consensus        89 v~~a   92 (121)
                      |.++
T Consensus        97 V~~a  100 (106)
T 1p27_B           97 VDWC  100 (106)
T ss_dssp             EEES
T ss_pred             EEee
Confidence            9999

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

Probab=99.84  E-value=6e-20  Score=112.73  Aligned_cols=81  Identities=21%  Similarity=0.198  Sum_probs=72.7

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      .....+.++|||+|||+.+++++|+++|.+||. ..++++.  ++.++|||||+|.+.++|..|+..||+..|+|+.|+|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   88 (114)
T 2do0_A            9 LQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHV   88 (114)
T ss_dssp             CCCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEE
Confidence            344455899999999999999999999999999 5666655  6778999999999999999999999999999999999


Q ss_pred             EecC
Q 043634           90 ERAS   93 (121)
Q Consensus        90 ~~a~   93 (121)
                      .+++
T Consensus        89 ~~a~   92 (114)
T 2do0_A           89 KMDE   92 (114)
T ss_dssp             EECS
T ss_pred             EEcc
Confidence            9994

>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=99.84  E-value=5.5e-20  Score=110.01  Aligned_cols=79  Identities=18%  Similarity=0.129  Sum_probs=69.9

Q ss_pred             CCccEEEecCCCCCCCHHHHH----HHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           17 ENLVTLLIKHLPDAIPQDTLS----RIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~----~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ...++|||+|||+.+++++|+    ++|++||. ..++++.....+|||||+|.+.++|..|+..|||..++|+.|+|.+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~   86 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSL   86 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            447999999999999999999    99999999 6677775222289999999999999999999999999999999999


Q ss_pred             cCCCC
Q 043634           92 ASKPN   96 (121)
Q Consensus        92 a~~~~   96 (121)
                      + .++
T Consensus        87 a-~~~   90 (96)
T 2dgx_A           87 A-TGA   90 (96)
T ss_dssp             C-CCS
T ss_pred             c-CCC
Confidence            9 444

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

Probab=99.84  E-value=4.8e-20  Score=111.94  Aligned_cols=83  Identities=25%  Similarity=0.394  Sum_probs=72.7

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc----CCCcccEEEEEeCCHHHHHHHHHHh-cCCeeCCeE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS----AGRLRNCVFVDFGNEPLASQAQMQL-NGLRFLGKV   86 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~----~~~~~g~afv~f~~~~~a~~ai~~l-~g~~i~g~~   86 (121)
                      .....+.++|||+|||+.+++++|+++|++||. ..++++.    ++.++|||||+|.+.++|..|+..| |+..|+|+.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~   88 (107)
T 2cph_A            9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRR   88 (107)
T ss_dssp             SCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCB
T ss_pred             cccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCE
Confidence            334455899999999999999999999999999 5666643    5677899999999999999999999 999999999


Q ss_pred             EEEEecCCCC
Q 043634           87 LSVERASKPN   96 (121)
Q Consensus        87 l~v~~a~~~~   96 (121)
                      |+|.++ .++
T Consensus        89 l~v~~a-~~~   97 (107)
T 2cph_A           89 LVLEWA-DSE   97 (107)
T ss_dssp             CEEEEC-CCC
T ss_pred             EEEEeC-CCC
Confidence            999999 443

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

Probab=99.84  E-value=7.2e-20  Score=112.82  Aligned_cols=81  Identities=20%  Similarity=0.303  Sum_probs=72.6

Q ss_pred             CCCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEE
Q 043634           12 NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVL   87 (121)
Q Consensus        12 ~~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l   87 (121)
                      ......+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|.+|+..+++ .|+|+.|
T Consensus        10 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l   88 (116)
T 2cqd_A           10 GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKA   88 (116)
T ss_dssp             CCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEEC
T ss_pred             CCcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEE
Confidence            3444556899999999999999999999999999 6677766   578899999999999999999999998 8999999


Q ss_pred             EEEecC
Q 043634           88 SVERAS   93 (121)
Q Consensus        88 ~v~~a~   93 (121)
                      +|.++.
T Consensus        89 ~V~~a~   94 (116)
T 2cqd_A           89 NVNLAY   94 (116)
T ss_dssp             EEEEST
T ss_pred             EEEEcc
Confidence            999993

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

Probab=99.84  E-value=2.9e-20  Score=110.71  Aligned_cols=79  Identities=25%  Similarity=0.428  Sum_probs=71.2

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ....+.++|||+|||+.+++++|+++|++||. ..++++.  .+.++|||||+|.+.++|..|+..||+..++|+.|+|.
T Consensus        11 ~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           11 AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             -CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            34455899999999999999999999999999 6666665  67788999999999999999999999999999999999


Q ss_pred             ec
Q 043634           91 RA   92 (121)
Q Consensus        91 ~a   92 (121)
                      ++
T Consensus        91 ~a   92 (95)
T 2ywk_A           91 GP   92 (95)
T ss_dssp             CC
T ss_pred             Ec
Confidence            98

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

Probab=99.84  E-value=2.1e-20  Score=111.54  Aligned_cols=82  Identities=22%  Similarity=0.326  Sum_probs=71.8

Q ss_pred             CCCCCCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           12 NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        12 ~~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ......+.++|||+|||+.+++++|+++|++||.  ++.+. ++.++|||||+|.+.++|..|+..|||..++|+.|+|.
T Consensus         9 ~~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~--v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   86 (96)
T 1fjc_A            9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDALE--IRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEE--ECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             ccccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCc--EEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3344456899999999999999999999999998  43334 78889999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 043634           91 RASKPN   96 (121)
Q Consensus        91 ~a~~~~   96 (121)
                      ++ .++
T Consensus        87 ~a-~~~   91 (96)
T 1fjc_A           87 YT-GEK   91 (96)
T ss_dssp             EC-SSS
T ss_pred             Ec-CCC
Confidence            99 443

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

Probab=99.84  E-value=6.3e-20  Score=116.29  Aligned_cols=79  Identities=32%  Similarity=0.489  Sum_probs=71.4

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      +..+.++|||+|||+.+++++|+++|+.||. ..++++.   ++.++|||||+|.+.++|.+|+..|||..|+|+.|+|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3344799999999999999999999999999 6666665   67889999999999999999999999999999999999


Q ss_pred             ecC
Q 043634           91 RAS   93 (121)
Q Consensus        91 ~a~   93 (121)
                      +++
T Consensus       118 ~a~  120 (139)
T 1u6f_A          118 LAA  120 (139)
T ss_dssp             ESS
T ss_pred             ECC
Confidence            993

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

Probab=99.84  E-value=3.2e-20  Score=111.88  Aligned_cols=83  Identities=25%  Similarity=0.358  Sum_probs=72.4

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      .....+.++|||+|||+.+++++|+++|+.|+.  ++++.   ++.++|||||+|.+.++|..|+..||+..|+|+.|+|
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~--~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   86 (102)
T 2fc8_A            9 NARSQPSKTLFVKGLSEDTTEETLKESFDGSVR--ARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL   86 (102)
T ss_dssp             SSSSCCCSSEEEECCCTTCCHHHHHHTSTTCSE--EEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCCEEEEeCCCCccCHHHHHHHhcCCeE--EEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            344556899999999999999999999998876  55554   7788999999999999999999999999999999999


Q ss_pred             EecCCCCcc
Q 043634           90 ERASKPNEE   98 (121)
Q Consensus        90 ~~a~~~~~~   98 (121)
                      .++ .++..
T Consensus        87 ~~a-~~~~~   94 (102)
T 2fc8_A           87 DWA-KPKGE   94 (102)
T ss_dssp             EEC-CCCCS
T ss_pred             EEe-cCCCC
Confidence            999 54433

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

Probab=99.84  E-value=2.4e-20  Score=113.36  Aligned_cols=76  Identities=12%  Similarity=0.190  Sum_probs=67.0

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcC--CeeCCeEEEEEe
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNG--LRFLGKVLSVER   91 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g--~~i~g~~l~v~~   91 (121)
                      +..+.++|||+|||+.+++++|+++|++||. ..++++..   +|||||+|.+.++|..|+..|++  ..+.|+.|+|.+
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~---kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~   88 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG---KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF   88 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC---CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            3456899999999999999999999999999 55665543   79999999999999999998864  789999999999


Q ss_pred             cC
Q 043634           92 AS   93 (121)
Q Consensus        92 a~   93 (121)
                      ++
T Consensus        89 A~   90 (105)
T 1sjq_A           89 SN   90 (105)
T ss_dssp             CS
T ss_pred             cC
Confidence            93

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

Probab=99.84  E-value=4.9e-20  Score=111.38  Aligned_cols=81  Identities=22%  Similarity=0.294  Sum_probs=71.2

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ....+.++|||+|||+.+++++|+++|++||...++++.   ++.++|||||+|.+.++|..|+ .||+..|+|+.|+|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~gi~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTTTSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCCceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            334558999999999999999999999999755566655   6888999999999999999999 899999999999999


Q ss_pred             ecCCCC
Q 043634           91 RASKPN   96 (121)
Q Consensus        91 ~a~~~~   96 (121)
                      ++ .++
T Consensus        89 ~a-~~~   93 (103)
T 2dng_A           89 IA-EGR   93 (103)
T ss_dssp             EC-CCC
T ss_pred             Ee-cCC
Confidence            99 443

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

Probab=99.84  E-value=3.7e-20  Score=112.49  Aligned_cols=80  Identities=20%  Similarity=0.297  Sum_probs=72.1

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      .....+.++|||+|||+.+++++|+++|++||. ..++++.  ++.++|||||+|.+.++|..|+..|||..++|+.|+|
T Consensus        23 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V  102 (107)
T 3ulh_A           23 GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI  102 (107)
T ss_dssp             -CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            344556899999999999999999999999999 6666665  7788999999999999999999999999999999999


Q ss_pred             Eec
Q 043634           90 ERA   92 (121)
Q Consensus        90 ~~a   92 (121)
                      .++
T Consensus       103 ~~a  105 (107)
T 3ulh_A          103 QLV  105 (107)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            988

>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=99.84  E-value=1.4e-20  Score=112.52  Aligned_cols=78  Identities=28%  Similarity=0.426  Sum_probs=70.2

Q ss_pred             CCCCccEEEecCCCCCCCHHHHH----HHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLS----RIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~----~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      +..+.++|||+|||+.+++++|+    .+|++||. ..+.++.+|.++|||||+|.+.++|..|+..|||..++|+.|+|
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   83 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEE
Confidence            34568999999999999999999    99999999 55666557778899999999999999999999999999999999


Q ss_pred             Eec
Q 043634           90 ERA   92 (121)
Q Consensus        90 ~~a   92 (121)
                      .++
T Consensus        84 ~~a   86 (97)
T 1nu4_A           84 QYA   86 (97)
T ss_dssp             EEC
T ss_pred             EEc
Confidence            999

>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=99.84  E-value=5e-20  Score=111.51  Aligned_cols=81  Identities=20%  Similarity=0.250  Sum_probs=70.8

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc---C-CCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS---A-GRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~---~-~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      ....+.++|||+|||+.+++++|+++|.+||...++++.   + +.++|||||+|.+.++|..|+ .||+..|+|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~Gi~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   88 (104)
T 1wi8_A           10 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV   88 (104)
T ss_dssp             CCSSSCEEEEEESCCSSCCHHHHHHHTTTSCEEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCcCCHHHHHHHHHHCCceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEE
Confidence            334558999999999999999999999999954455555   3 788999999999999999999 99999999999999


Q ss_pred             EecCCCC
Q 043634           90 ERASKPN   96 (121)
Q Consensus        90 ~~a~~~~   96 (121)
                      .++ .++
T Consensus        89 ~~a-~~~   94 (104)
T 1wi8_A           89 DVA-DQA   94 (104)
T ss_dssp             EEC-CCC
T ss_pred             EEc-cCC
Confidence            999 443

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

Probab=99.83  E-value=3.9e-20  Score=110.93  Aligned_cols=78  Identities=22%  Similarity=0.350  Sum_probs=71.7

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-c-cEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeE----
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-S-SVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKV----   86 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~-~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~----   86 (121)
                      ..+.++|||+|||+.+++++|+++|++||. . .++++.   ++.++|||||+|.+.++|..|+..|||..+.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            345899999999999999999999999999 6 777765   6788999999999999999999999999999999    


Q ss_pred             EEEEecC
Q 043634           87 LSVERAS   93 (121)
Q Consensus        87 l~v~~a~   93 (121)
                      |+|.+++
T Consensus        86 l~v~~a~   92 (99)
T 2div_A           86 FKLNYAT   92 (99)
T ss_dssp             CCEEETT
T ss_pred             EEEeecC
Confidence            9999993

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

Probab=99.83  E-value=3.3e-20  Score=111.07  Aligned_cols=76  Identities=28%  Similarity=0.289  Sum_probs=69.3

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc------CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS------AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~------~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      .+.++|||+|||+.+++++|+++|++||. ..++++.      ++.++|||||+|.+.++|..|+..|||..++|+.|+|
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            45899999999999999999999999999 6666664      2277899999999999999999999999999999999


Q ss_pred             Eec
Q 043634           90 ERA   92 (121)
Q Consensus        90 ~~a   92 (121)
                      .++
T Consensus        83 ~~a   85 (98)
T 2cpf_A           83 RIS   85 (98)
T ss_dssp             ECS
T ss_pred             EEc
Confidence            999

>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=99.83  E-value=4.8e-20  Score=113.91  Aligned_cols=79  Identities=28%  Similarity=0.397  Sum_probs=72.5

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ..+.++|||+|||+.+++++|+++|++||. ..+.++.  ++.++|||||+|.+.++|..|+..|||..++|+.|+|.++
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            345799999999999999999999999999 6777776  7888999999999999999999999999999999999999


Q ss_pred             CC
Q 043634           93 SK   94 (121)
Q Consensus        93 ~~   94 (121)
                      +.
T Consensus        84 ~~   85 (116)
T 2fy1_A           84 KK   85 (116)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.83  E-value=1e-19  Score=109.99  Aligned_cols=78  Identities=13%  Similarity=0.210  Sum_probs=67.4

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhc--CCeeCCeEEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLN--GLRFLGKVLSV   89 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~--g~~i~g~~l~v   89 (121)
                      .....+.++|||+|||+.+++++|+.+|++||. ..+.++..   +|||||+|.+.++|..|+..|+  +..+.|+.|.|
T Consensus         9 ~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~---kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A            9 KMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG---KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             CCCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC---CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            444556899999999999999999999999999 55555432   7999999999999999999874  67899999999


Q ss_pred             EecC
Q 043634           90 ERAS   93 (121)
Q Consensus        90 ~~a~   93 (121)
                      .+++
T Consensus        86 ~~a~   89 (101)
T 2cq1_A           86 QYSN   89 (101)
T ss_dssp             EECS
T ss_pred             EEcC
Confidence            9994

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

Probab=99.83  E-value=4.5e-20  Score=110.48  Aligned_cols=80  Identities=23%  Similarity=0.288  Sum_probs=69.6

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK   94 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   94 (121)
                      .....++|||+|||+.+++++|+++|++||...+.++ .+.++|||||+|.+.++|..|+..|||..++|+.|+|.++ .
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a-~   92 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLT-WQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA-R   92 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCCSEEE-EETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC-C
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEEEEEE-cCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc-C
Confidence            3444899999999999999999999999999323333 4567899999999999999999999999999999999999 4


Q ss_pred             CC
Q 043634           95 PN   96 (121)
Q Consensus        95 ~~   96 (121)
                      ++
T Consensus        93 ~~   94 (97)
T 2e5j_A           93 QQ   94 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.83  E-value=4.8e-20  Score=108.17  Aligned_cols=77  Identities=19%  Similarity=0.314  Sum_probs=68.5

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCC-cccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGR-LRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~-~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+++|||+|||+.+++++|+++|++||. ..+.++.   ++. ++|||||+|.+.++|..|+..|||..++|+.|+|+++
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            3689999999999999999999999999 5555555   223 7899999999999999999999999999999999999


Q ss_pred             CC
Q 043634           93 SK   94 (121)
Q Consensus        93 ~~   94 (121)
                      ..
T Consensus        83 ~~   84 (88)
T 4a8x_A           83 LA   84 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.83  E-value=2.7e-20  Score=117.12  Aligned_cols=80  Identities=25%  Similarity=0.339  Sum_probs=72.5

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      .....+.++|||+|||+.+++++|+++|++||. ..++++.   ++..+|||||+|.+.++|.+|+..|||..|+|+.|+
T Consensus        40 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~  119 (129)
T 2kxn_B           40 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR  119 (129)
T ss_dssp             SSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            344555899999999999999999999999999 6666665   578899999999999999999999999999999999


Q ss_pred             EEec
Q 043634           89 VERA   92 (121)
Q Consensus        89 v~~a   92 (121)
                      |.++
T Consensus       120 V~~a  123 (129)
T 2kxn_B          120 VDFS  123 (129)
T ss_dssp             ESCC
T ss_pred             EEEe
Confidence            9999

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

Probab=99.83  E-value=4.5e-20  Score=112.86  Aligned_cols=83  Identities=18%  Similarity=0.193  Sum_probs=68.7

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      .....+.++|||+|||+.+++++|+.+|+.||. ..++++.   +|.++|||||+|.+.++|..|+..+ +..++|+.|+
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            334445899999999999999999999999999 6677765   5888999999999999999999876 5999999999


Q ss_pred             EEecCCCCc
Q 043634           89 VERASKPNE   97 (121)
Q Consensus        89 v~~a~~~~~   97 (121)
                      |.++ .++.
T Consensus        98 V~~a-~~~~  105 (109)
T 2rs2_A           98 PKVA-FPRR  105 (109)
T ss_dssp             EEEC-CCCC
T ss_pred             EEEc-cCCC
Confidence            9999 5443

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

Probab=99.83  E-value=5.6e-21  Score=115.14  Aligned_cols=85  Identities=18%  Similarity=0.254  Sum_probs=67.1

Q ss_pred             CCCCCCCCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc----CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCe
Q 043634           10 PQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS----AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGK   85 (121)
Q Consensus        10 ~~~~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~----~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~   85 (121)
                      ..........++|||+|||+.+++++|+++|++||...++++.    +|.++|||||+|.+.++|..|+ .|||..++|+
T Consensus        10 ~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~Gi~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~   88 (100)
T 2j76_E           10 HRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNR   88 (100)
T ss_dssp             ----------CEEEESCCSSCCSSSHHHHHSCSSCEEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTB
T ss_pred             CCCcCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCe
Confidence            3344445558999999999999999999999999953455553    5778999999999999999999 8999999999


Q ss_pred             EEEEEecCCCC
Q 043634           86 VLSVERASKPN   96 (121)
Q Consensus        86 ~l~v~~a~~~~   96 (121)
                      .|+|.++ .++
T Consensus        89 ~l~V~~a-~~~   98 (100)
T 2j76_E           89 RIRVDVA-DQA   98 (100)
T ss_dssp             CCCCEEC-CCS
T ss_pred             EEEEEec-cCC
Confidence            9999999 443

>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=99.82  E-value=3.3e-20  Score=110.41  Aligned_cols=77  Identities=14%  Similarity=0.194  Sum_probs=68.1

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      .++.++|||+|||+.+++++|+++|.+||. ..+.++.   ++.++|||||+|.+.++|.+|+..||+..++|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            344799999999999999999999999999 5454443   778899999999999999999999999999999999998


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      +
T Consensus        92 a   92 (95)
T 2ek1_A           92 P   92 (95)
T ss_dssp             C
T ss_pred             c
Confidence            7

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

Probab=99.82  E-value=9.6e-20  Score=111.29  Aligned_cols=74  Identities=22%  Similarity=0.396  Sum_probs=67.1

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ....+.++|||+|||+.+++++|+++|++||. ..+.++     +|||||+|.+.++|..|+..|||..++|+.|.|.++
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-----kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  100 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-----NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS  100 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-----TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESC
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-----CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            34445899999999999999999999999999 666665     689999999999999999999999999999999999

>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=99.82  E-value=5.9e-20  Score=114.66  Aligned_cols=81  Identities=20%  Similarity=0.340  Sum_probs=72.3

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      +....+.++|||+|||+.+++++|+.+|++||. ..+.++.   ++.++|||||+|.+.++|..|+..|||..|+|+.|.
T Consensus        16 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   95 (126)
T 3ex7_B           16 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS   95 (126)
T ss_dssp             BCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            334445899999999999999999999999999 5566654   678899999999999999999999999999999999


Q ss_pred             EEecC
Q 043634           89 VERAS   93 (121)
Q Consensus        89 v~~a~   93 (121)
                      |.++.
T Consensus        96 v~~a~  100 (126)
T 3ex7_B           96 VDWCF  100 (126)
T ss_dssp             EEESE
T ss_pred             EEEec
Confidence            99993

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

Probab=99.82  E-value=1.3e-19  Score=111.31  Aligned_cols=76  Identities=20%  Similarity=0.307  Sum_probs=67.7

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhC-C-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYG-A-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G-~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ...++|||+|||+.+++++|+++|++|| . ..+.+. .+.++|||||+|.+.++|+.|+..|||..++|+.|+|.++.
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~-~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~  103 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVN-TRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDD  103 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECS-SCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEE-cCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            3479999999999999999999999999 6 444443 34678999999999999999999999999999999999994

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

Probab=99.82  E-value=3.4e-20  Score=112.12  Aligned_cols=82  Identities=18%  Similarity=0.248  Sum_probs=73.0

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhh-hCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCe-eCCeEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSH-YGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLR-FLGKVLSV   89 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~-~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~-i~g~~l~v   89 (121)
                      +..+.++|||+|||+.+++++|+++|++ ||. ..++++.  ++.++|||||+|.+.++|..|+..||+.. ++|+.|+|
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            3455899999999999999999999999 999 6666665  78889999999999999999999999999 99999999


Q ss_pred             EecCCCCc
Q 043634           90 ERASKPNE   97 (121)
Q Consensus        90 ~~a~~~~~   97 (121)
                      .++ .++.
T Consensus        85 ~~a-~~~~   91 (104)
T 2dhg_A           85 SVA-IPKA   91 (104)
T ss_dssp             CBC-CCCC
T ss_pred             EEc-cCCC
Confidence            999 4443

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

Probab=99.82  E-value=3e-20  Score=111.89  Aligned_cols=79  Identities=24%  Similarity=0.306  Sum_probs=69.2

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ...+.++|||+|||+.+++++|+.+|++||. .. .++.   ++.++|||||+|.+.++|..|+. |||..++|+.|+|.
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            3445899999999999999999999999998 44 2232   67889999999999999999998 99999999999999


Q ss_pred             ecCCCC
Q 043634           91 RASKPN   96 (121)
Q Consensus        91 ~a~~~~   96 (121)
                      ++ .++
T Consensus        91 ~a-~~~   95 (101)
T 1fj7_A           91 KP-KGR   95 (101)
T ss_dssp             CC-SCC
T ss_pred             Ec-CCC
Confidence            99 443

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

Probab=99.82  E-value=8.5e-20  Score=110.00  Aligned_cols=75  Identities=19%  Similarity=0.174  Sum_probs=66.8

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCe--eCCeEEEEEe
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLR--FLGKVLSVER   91 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~--i~g~~l~v~~   91 (121)
                      ..+|+++|||+|||+.+++++|+.+|++||. ..++++.   .+|+|||+|.+.++|..|+..|++..  +.|+.|.|.+
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~---~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~   93 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP---KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNY   93 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEE
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc---CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEe
Confidence            4456899999999999999999999999999 5555553   47999999999999999999999875  7899999999


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      +
T Consensus        94 S   94 (100)
T 3r27_A           94 S   94 (100)
T ss_dssp             C
T ss_pred             c
Confidence            9

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

Probab=99.82  E-value=2.6e-19  Score=111.56  Aligned_cols=79  Identities=19%  Similarity=0.300  Sum_probs=72.1

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ...+.++|||+|||+.+++++|+++|++||. ..++++.  +|.++|||||+|.+.++|..|+..|||..++|+.|+|.+
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            3344799999999999999999999999999 6777766  678899999999999999999999999999999999999


Q ss_pred             cC
Q 043634           92 AS   93 (121)
Q Consensus        92 a~   93 (121)
                      +.
T Consensus       111 a~  112 (124)
T 2kt5_A          111 VA  112 (124)
T ss_dssp             EC
T ss_pred             eC
Confidence            93

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

Probab=99.82  E-value=4.3e-20  Score=108.35  Aligned_cols=71  Identities=24%  Similarity=0.279  Sum_probs=65.3

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +.-|||+||++.+++++|+++|.+||+ .++++.   .++|||||+|.+.++|..|++.||+..+.|+.|+|.+|
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~---~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPY---LNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEE---TTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEc---CCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            678999999999999999999999999 444443   36899999999999999999999999999999999988

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

Probab=99.82  E-value=2e-19  Score=106.35  Aligned_cols=79  Identities=22%  Similarity=0.283  Sum_probs=70.3

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ....++|||+|||+.+++++|+++|+.|+...++++.  +|.++|||||+|.+.++|..|+. +||..++|+.|.|.++ 
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a-   84 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE-   84 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTSCCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE-
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhCCceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC-
Confidence            3448999999999999999999999999336777766  78889999999999999999999 9999999999999999 


Q ss_pred             CCC
Q 043634           94 KPN   96 (121)
Q Consensus        94 ~~~   96 (121)
                      .++
T Consensus        85 ~~~   87 (91)
T 2dgw_A           85 KSG   87 (91)
T ss_dssp             SSC
T ss_pred             CcC
Confidence            443

>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=99.82  E-value=9.7e-20  Score=106.82  Aligned_cols=77  Identities=18%  Similarity=0.283  Sum_probs=68.6

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ...+.++|||+|||+.+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|.+|+. +++..++|+.|.|+
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            3455899999999999999999999999999 6666664   68889999999999999999995 58889999999998


Q ss_pred             ec
Q 043634           91 RA   92 (121)
Q Consensus        91 ~a   92 (121)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>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=99.82  E-value=2e-19  Score=116.12  Aligned_cols=78  Identities=28%  Similarity=0.401  Sum_probs=71.6

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ..+.++|||+|||+.+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|..|+..|||..++|+.|+|.+
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            344799999999999999999999999999 6666665   688999999999999999999999999999999999999


Q ss_pred             cC
Q 043634           92 AS   93 (121)
Q Consensus        92 a~   93 (121)
                      ++
T Consensus       147 a~  148 (158)
T 2kn4_A          147 AR  148 (158)
T ss_dssp             EC
T ss_pred             CC
Confidence            94

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

Probab=99.82  E-value=7.6e-20  Score=110.82  Aligned_cols=82  Identities=18%  Similarity=0.267  Sum_probs=72.4

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      ....+.++|||+|||+.+++++|+++|.+||. ..++++.   ++.++|||||+|.+.++|..|+.. ++..|+|+.|.|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V   89 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDP   89 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEE
Confidence            34455899999999999999999999999999 6666665   678899999999999999999988 999999999999


Q ss_pred             EecCCCCc
Q 043634           90 ERASKPNE   97 (121)
Q Consensus        90 ~~a~~~~~   97 (121)
                      .++ .++.
T Consensus        90 ~~a-~~~~   96 (105)
T 2dh8_A           90 KPC-TPRG   96 (105)
T ss_dssp             CCS-CCSS
T ss_pred             EEc-cCCC
Confidence            999 5443

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

Probab=99.82  E-value=6.2e-20  Score=111.14  Aligned_cols=78  Identities=17%  Similarity=0.128  Sum_probs=67.9

Q ss_pred             CCCCCCccEEEecCCCC-CCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcC--CeeCCeEEE
Q 043634           13 KQETENLVTLLIKHLPD-AIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNG--LRFLGKVLS   88 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~-~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g--~~i~g~~l~   88 (121)
                      .....+.++|||+|||+ .+++++|+.+|++||. ..+.++.   .+|||||+|.+.++|..|+..||+  ..|.|+.|+
T Consensus         9 ~~~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~---~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A            9 KGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN---KINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECS---SSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEc---CCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            34455789999999999 9999999999999999 5566553   358999999999999999999986  459999999


Q ss_pred             EEecC
Q 043634           89 VERAS   93 (121)
Q Consensus        89 v~~a~   93 (121)
                      |.+++
T Consensus        86 V~~a~   90 (102)
T 1x4d_A           86 VHLSQ   90 (102)
T ss_dssp             EEEEC
T ss_pred             EEECC
Confidence            99994

>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=99.82  E-value=1.6e-19  Score=112.00  Aligned_cols=78  Identities=12%  Similarity=0.196  Sum_probs=68.8

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcC--CeeCCeEEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNG--LRFLGKVLSV   89 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g--~~i~g~~l~v   89 (121)
                      ....++.++|||+|||+.+++++|+++|++||. ..++++..   +|||||+|.+.++|.+|+..|++  ..+.|+.|+|
T Consensus        25 ~~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~---kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           25 RSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG---KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             TSCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG---GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC---CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            445556899999999999999999999999999 66776643   79999999999999999998874  6899999999


Q ss_pred             EecC
Q 043634           90 ERAS   93 (121)
Q Consensus        90 ~~a~   93 (121)
                      .+++
T Consensus       102 ~~a~  105 (119)
T 2ad9_A          102 QFSN  105 (119)
T ss_dssp             EECS
T ss_pred             EEcc
Confidence            9993

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

Probab=99.82  E-value=2.6e-20  Score=112.31  Aligned_cols=75  Identities=17%  Similarity=0.235  Sum_probs=70.0

Q ss_pred             CccEEEecCCCC------CCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCC-eE
Q 043634           18 NLVTLLIKHLPD------AIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLG-KV   86 (121)
Q Consensus        18 ~~~~l~V~nlp~------~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g-~~   86 (121)
                      ..++|||+|||.      .+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|.+|+..|||..+.| +.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            378999999999      9999999999999999 6666665   68899999999999999999999999999999 99


Q ss_pred             EEEEec
Q 043634           87 LSVERA   92 (121)
Q Consensus        87 l~v~~a   92 (121)
                      |+|.++
T Consensus        85 l~V~~a   90 (100)
T 3ns6_A           85 LFLYTM   90 (100)
T ss_dssp             CEEEES
T ss_pred             EEEEEC
Confidence            999998

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

Probab=99.82  E-value=7.8e-20  Score=118.45  Aligned_cols=74  Identities=14%  Similarity=0.142  Sum_probs=68.7

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhC--C-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYG--A-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G--~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .++|||+|||+.+++++|+++|++||  . ..++++.   +|.++|||||+|.+.++|.+||..|||..|+|+.|.|.++
T Consensus        55 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a  134 (156)
T 3n9u_C           55 RAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPA  134 (156)
T ss_dssp             -CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEc
Confidence            57999999999999999999999999  7 5666654   7889999999999999999999999999999999999999

>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=99.82  E-value=1.2e-19  Score=106.72  Aligned_cols=73  Identities=14%  Similarity=0.282  Sum_probs=68.1

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|.+|+ .+||..++|+.|+|.++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a   82 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPK   82 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEET
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEc
Confidence            689999999999999999999999999 6666654   6788999999999999999999 99999999999999999

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

Probab=99.82  E-value=1.2e-19  Score=110.27  Aligned_cols=76  Identities=14%  Similarity=0.312  Sum_probs=69.7

Q ss_pred             CCccEEEecCCCCCC------CHHHHHHHHhhhCC-ccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCe-EE
Q 043634           17 ENLVTLLIKHLPDAI------PQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGK-VL   87 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~------~~~~L~~~f~~~G~-~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~-~l   87 (121)
                      ...++|||+|||+.+      ++++|+.+|++||. ..+.++. +|.++|||||+|.+.++|..|+..|||..++|+ .|
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l   92 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   92 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEE
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceE
Confidence            347999999999999      78999999999999 6666665 788899999999999999999999999999998 99


Q ss_pred             EEEec
Q 043634           88 SVERA   92 (121)
Q Consensus        88 ~v~~a   92 (121)
                      +|.++
T Consensus        93 ~V~~a   97 (105)
T 2nlw_A           93 RVNLF   97 (105)
T ss_dssp             EEECS
T ss_pred             EEEEc
Confidence            99998

>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=99.82  E-value=3.6e-19  Score=108.52  Aligned_cols=76  Identities=14%  Similarity=0.163  Sum_probs=67.4

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCC-----eEEEE
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLG-----KVLSV   89 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g-----~~l~v   89 (121)
                      ....++|||+|||+.+++++|+++|.+||. ..+.++..    |||||+|.+.++|..||..||+..|+|     +.|+|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~----g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V   87 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   87 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT----TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC----CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEE
Confidence            345899999999999999999999999999 45555433    899999999999999999999999999     99999


Q ss_pred             EecCCCC
Q 043634           90 ERASKPN   96 (121)
Q Consensus        90 ~~a~~~~   96 (121)
                      .++ .++
T Consensus        88 ~~a-~~~   93 (108)
T 1x4c_A           88 KVD-GPR   93 (108)
T ss_dssp             EES-SCC
T ss_pred             EeC-CCC
Confidence            999 443

>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=99.82  E-value=3.1e-19  Score=106.73  Aligned_cols=80  Identities=18%  Similarity=0.307  Sum_probs=69.0

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeC--CeEEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFL--GKVLSV   89 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~--g~~l~v   89 (121)
                      .....+.++|||+|||+.+++++|+++|++||. ..+.++ .+  +|||||+|.+.++|..|+..||+..+.  |+.|+|
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~-~~--~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V   87 (97)
T 1why_A           11 YGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV-KG--DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEEC-SS--SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe-CC--CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEE
Confidence            334455799999999999999999999999999 444444 22  789999999999999999999999999  999999


Q ss_pred             EecCCCC
Q 043634           90 ERASKPN   96 (121)
Q Consensus        90 ~~a~~~~   96 (121)
                      .++ .++
T Consensus        88 ~~a-~~~   93 (97)
T 1why_A           88 DFA-KSG   93 (97)
T ss_dssp             EEC-CCC
T ss_pred             EEC-CCC
Confidence            999 443

>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=99.82  E-value=3.4e-19  Score=107.67  Aligned_cols=75  Identities=20%  Similarity=0.445  Sum_probs=67.1

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ....+.++|||+|||+.+++++|+++|++||. ..+.++     ++||||+|.+.++|..|+..||+..|+|+.|+|.++
T Consensus         6 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~-----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            6 SGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-----KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-----SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-----CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            34456899999999999999999999999999 445543     579999999999999999999999999999999999


Q ss_pred             C
Q 043634           93 S   93 (121)
Q Consensus        93 ~   93 (121)
                      +
T Consensus        81 ~   81 (103)
T 2dgu_A           81 K   81 (103)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=1e-19  Score=111.90  Aligned_cols=77  Identities=25%  Similarity=0.326  Sum_probs=71.2

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +.+.++|||+|||+.+++++|+.+|++||. ..+.++..+.++|||||+|.+.++|..|+..|||..++|+.|+|.++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            345799999999999999999999999999 66777667777999999999999999999999999999999999999

>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=99.82  E-value=2e-19  Score=109.32  Aligned_cols=78  Identities=12%  Similarity=0.180  Sum_probs=67.3

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCC--eeCCeEEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGL--RFLGKVLSV   89 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~--~i~g~~l~v   89 (121)
                      +....+.++|||+|||+.+++++|+++|++||. ..+.++.   .+|||||+|.+.++|..|+..|++.  .+.|+.|+|
T Consensus         9 ~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~---~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V   85 (104)
T 1wex_A            9 HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP---FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC---CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            344566899999999999999999999999999 5555543   3799999999999999999988764  599999999


Q ss_pred             EecC
Q 043634           90 ERAS   93 (121)
Q Consensus        90 ~~a~   93 (121)
                      .+++
T Consensus        86 ~~a~   89 (104)
T 1wex_A           86 NYST   89 (104)
T ss_dssp             EECS
T ss_pred             EEcc
Confidence            9994

>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=99.82  E-value=4.2e-19  Score=107.18  Aligned_cols=83  Identities=17%  Similarity=0.224  Sum_probs=71.5

Q ss_pred             CCCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEE
Q 043634           12 NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVL   87 (121)
Q Consensus        12 ~~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l   87 (121)
                      ......+.++|||+|||+.+++++|+.+|.+||. ..++++.   ++.++|||||+|.+.++|..|+.  ++..++|+.|
T Consensus         8 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l   85 (103)
T 2cqg_A            8 VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWC   85 (103)
T ss_dssp             CSCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEE
T ss_pred             CCCccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEE
Confidence            3444556899999999999999999999999999 6666655   68889999999999999999997  4779999999


Q ss_pred             EEEecCCCCc
Q 043634           88 SVERASKPNE   97 (121)
Q Consensus        88 ~v~~a~~~~~   97 (121)
                      .|.++ .++.
T Consensus        86 ~v~~a-~~~~   94 (103)
T 2cqg_A           86 DCKLP-NSKQ   94 (103)
T ss_dssp             EEECC-CTTC
T ss_pred             EEEec-CCCC
Confidence            99999 5443

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

Probab=99.82  E-value=2.5e-19  Score=113.35  Aligned_cols=78  Identities=19%  Similarity=0.309  Sum_probs=69.9

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ...+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|.+|+..|||..++|+.|+|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3445899999999999999999999999999 6666655   57889999999999999999999999999999999998


Q ss_pred             ec
Q 043634           91 RA   92 (121)
Q Consensus        91 ~a   92 (121)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            75

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

Probab=99.82  E-value=5.9e-19  Score=104.56  Aligned_cols=77  Identities=18%  Similarity=0.283  Sum_probs=68.4

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ....+.++|||+|||+.+++++|+++|++||. ..+.++     ++||||+|.+.++|..|+..|||..++|+.|+|.++
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~-----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   79 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-----KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS   79 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC-----SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEES
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE-----CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            34455899999999999999999999999999 566655     459999999999999999999999999999999999


Q ss_pred             CCCC
Q 043634           93 SKPN   96 (121)
Q Consensus        93 ~~~~   96 (121)
                       .++
T Consensus        80 -~~~   82 (92)
T 2dgt_A           80 -TSR   82 (92)
T ss_dssp             -SCC
T ss_pred             -cCC
Confidence             443

>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=99.82  E-value=2.7e-19  Score=109.93  Aligned_cols=73  Identities=27%  Similarity=0.359  Sum_probs=68.4

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .++|||+|||+.+++++|+++|+.||. ..++++.   ++.++|||||+|.+.++|..|+ .|||..|+|+.|+|.++
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEec
Confidence            589999999999999999999999999 6677765   5788999999999999999999 99999999999999998

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

Probab=99.81  E-value=5.6e-20  Score=116.45  Aligned_cols=79  Identities=28%  Similarity=0.407  Sum_probs=71.9

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ...+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+..|||..|+|+.|+|.
T Consensus        43 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  122 (135)
T 2lea_A           43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ  122 (135)
T ss_dssp             SGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3344789999999999999999999999999 6777765   67889999999999999999999999999999999999


Q ss_pred             ecC
Q 043634           91 RAS   93 (121)
Q Consensus        91 ~a~   93 (121)
                      +++
T Consensus       123 ~a~  125 (135)
T 2lea_A          123 MAR  125 (135)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            994

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

Probab=99.81  E-value=2.6e-19  Score=105.74  Aligned_cols=73  Identities=23%  Similarity=0.425  Sum_probs=66.6

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ..+.++|||+|||+.+++++|+++|++||. ..++++     ++||||+|.+.++|..|+..||+..++|+.|+|.+++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   78 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-----KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASK   78 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-----TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSS
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-----CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECC
Confidence            455899999999999999999999999999 555554     6899999999999999999999999999999999993

>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=99.81  E-value=4.1e-20  Score=111.72  Aligned_cols=75  Identities=28%  Similarity=0.494  Sum_probs=70.2

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +.++|||+|||+.+++++|+.+|++||. ..++++.   +|.++|||||+|.+.++|..|+..|||..++|+.|+|.++
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            3799999999999999999999999999 6777665   6788999999999999999999999999999999999999

>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=99.81  E-value=3.8e-19  Score=106.64  Aligned_cols=75  Identities=25%  Similarity=0.318  Sum_probs=65.8

Q ss_pred             CCCCCCccEEEecCCCC-CCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           13 KQETENLVTLLIKHLPD-AIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~-~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ....++.++|||+|||+ .+++++|+++|++||. ..+++     .+|||||+|.+.++|..|+..|||..++|+.|+|+
T Consensus        16 ~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           16 PRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-----KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             ---CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE-----CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             cCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE-----eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            33445589999999998 9999999999999999 44444     26899999999999999999999999999999999


Q ss_pred             ec
Q 043634           91 RA   92 (121)
Q Consensus        91 ~a   92 (121)
                      ++
T Consensus        91 ~a   92 (97)
T 2xnq_A           91 VS   92 (97)
T ss_dssp             EC
T ss_pred             ec
Confidence            99

>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=99.81  E-value=2e-19  Score=105.00  Aligned_cols=76  Identities=25%  Similarity=0.429  Sum_probs=67.5

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHh-cCCeeCCeEEEEEe
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQL-NGLRFLGKVLSVER   91 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l-~g~~i~g~~l~v~~   91 (121)
                      +...+.++|||+|||+.+++++|+++|++||. ..++++.   ++|||||+|.+.++|..|+..| +|..++|+.|+|.+
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~---~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~   83 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ---RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKW   83 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG---GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEE
T ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC---CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEe
Confidence            33455899999999999999999999999999 5555553   4799999999999999999988 99999999999998


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      +
T Consensus        84 a   84 (85)
T 2ytc_A           84 G   84 (85)
T ss_dssp             C
T ss_pred             c
Confidence            8

>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=99.81  E-value=1.8e-19  Score=117.47  Aligned_cols=79  Identities=18%  Similarity=0.347  Sum_probs=71.1

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ...+.++|||+|||+.+++++|+.+|++||. ..+.++.   +|.++|||||+|.+.++|..||..|||..|+|+.|.|.
T Consensus        68 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  147 (165)
T 1rk8_A           68 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  147 (165)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3444789999999999999999999999999 6666664   77889999999999999999999999999999999999


Q ss_pred             ecC
Q 043634           91 RAS   93 (121)
Q Consensus        91 ~a~   93 (121)
                      +++
T Consensus       148 ~a~  150 (165)
T 1rk8_A          148 WCF  150 (165)
T ss_dssp             ESE
T ss_pred             Eec
Confidence            994

>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=99.81  E-value=2.2e-19  Score=114.39  Aligned_cols=78  Identities=29%  Similarity=0.461  Sum_probs=70.3

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-cc--------EEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeE
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SS--------VRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKV   86 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~--------~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~   86 (121)
                      ..+.++|||+|||+.+++++|+.+|++||. ..        +++..+|.++|||||+|.+.++|..|+..|||..+.|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            455899999999999999999999999998 43        333447889999999999999999999999999999999


Q ss_pred             EEEEecC
Q 043634           87 LSVERAS   93 (121)
Q Consensus        87 l~v~~a~   93 (121)
                      |.|.+++
T Consensus       122 l~V~~a~  128 (143)
T 3egn_A          122 MVVQFAR  128 (143)
T ss_dssp             CEEEECC
T ss_pred             EEEEECC
Confidence            9999993

>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=99.81  E-value=3.1e-19  Score=107.09  Aligned_cols=77  Identities=23%  Similarity=0.408  Sum_probs=68.9

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ....+.++|||+|||+.+++++|+++|++||. ..++++.   .+|||||+|.+.++|..|+..|||..++|+.|+|.++
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~---~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpj_A           10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK---DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   86 (99)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET---TTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEec---CCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEc
Confidence            33455899999999999999999999999999 6666653   3799999999999999999999999999999999999


Q ss_pred             C
Q 043634           93 S   93 (121)
Q Consensus        93 ~   93 (121)
                      +
T Consensus        87 ~   87 (99)
T 2cpj_A           87 C   87 (99)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.81  E-value=7.3e-19  Score=107.40  Aligned_cols=74  Identities=27%  Similarity=0.443  Sum_probs=67.2

Q ss_pred             CccEEEecCCCCC-CCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 043634           18 NLVTLLIKHLPDA-IPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKP   95 (121)
Q Consensus        18 ~~~~l~V~nlp~~-~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   95 (121)
                      +.++|||+|||+. +++++|+++|++||. ..+.+     ++|||||+|.+.++|..|+..||+..++|+.|+|.+++.+
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-----~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~  100 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-----HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP  100 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-----ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-----eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            3689999999999 999999999999999 55655     5799999999999999999999999999999999999534


Q ss_pred             C
Q 043634           96 N   96 (121)
Q Consensus        96 ~   96 (121)
                      +
T Consensus       101 ~  101 (110)
T 1wf1_A          101 K  101 (110)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.81  E-value=4e-19  Score=114.71  Aligned_cols=77  Identities=17%  Similarity=0.246  Sum_probs=70.9

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+.++|||+|||+.+++++|+++|++||. ..+.++.   ++.++|||||+|.+.++|..|+..||+..|+|+.|+|.++
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45799999999999999999999999999 6666655   5788999999999999999999999999999999999999


Q ss_pred             C
Q 043634           93 S   93 (121)
Q Consensus        93 ~   93 (121)
                      +
T Consensus       117 ~  117 (156)
T 1h2v_Z          117 A  117 (156)
T ss_dssp             S
T ss_pred             C
Confidence            4

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

Probab=99.81  E-value=2e-19  Score=108.30  Aligned_cols=73  Identities=18%  Similarity=0.388  Sum_probs=67.0

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...++|||+|||..+++++|+.+|++||. ..++++   .++|||||+|.+.++|..|+..|||..++|+.|+|.++
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~---~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY---PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe---cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            34799999999999999999999999999 666665   45799999999999999999999999999999999998

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

Probab=99.81  E-value=1.1e-18  Score=104.66  Aligned_cols=79  Identities=27%  Similarity=0.428  Sum_probs=67.2

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhh--CCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHY--GASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~--G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ....+.++|||+|||+.+++++|+++|++|  |.  +..+.  ..+|||||+|.+.++|..|+..|||..++|+.|+|.+
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~--v~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpd_A           10 DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGA--VERVK--KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTL   85 (99)
T ss_dssp             SCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTC--EEEEE--ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             cccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcc--eEEEE--EeCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            344558999999999999999999999999  76  33332  1268999999999999999999999999999999999


Q ss_pred             cCCCCc
Q 043634           92 ASKPNE   97 (121)
Q Consensus        92 a~~~~~   97 (121)
                      + +++.
T Consensus        86 a-~~~~   90 (99)
T 2cpd_A           86 A-KPVD   90 (99)
T ss_dssp             C-CCCC
T ss_pred             C-CCCC
Confidence            9 5443

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

Probab=99.81  E-value=4.9e-19  Score=108.00  Aligned_cols=79  Identities=19%  Similarity=0.338  Sum_probs=69.2

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ...+.++|||+|||+.+++++|+.+|++||. ..++++..   +|||||+|.+.++|..|+..|||..++|+.|+|.++ 
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a-   96 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE---KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG-   96 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC-
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC---CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec-
Confidence            3445799999999999999999999999999 55555433   799999999999999999999999999999999999 


Q ss_pred             CCCc
Q 043634           94 KPNE   97 (121)
Q Consensus        94 ~~~~   97 (121)
                      +++.
T Consensus        97 ~~~~  100 (109)
T 1x4g_A           97 KESP  100 (109)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            4433

>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=99.81  E-value=1.5e-19  Score=109.41  Aligned_cols=78  Identities=15%  Similarity=0.146  Sum_probs=69.8

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .....++|||+|||+.+++++|+++|.+||...++++.  +++++|||||+|.+.++|.+|+ .+|+..|+|+.|.|..+
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFLN   89 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCSEEEEEESSSSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCceEEEEEECCCCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEEEC
Confidence            34558999999999999999999999999986566655  7889999999999999999999 57999999999999988


Q ss_pred             C
Q 043634           93 S   93 (121)
Q Consensus        93 ~   93 (121)
                      .
T Consensus        90 ~   90 (102)
T 1wez_A           90 S   90 (102)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.81  E-value=1.5e-19  Score=110.81  Aligned_cols=81  Identities=12%  Similarity=0.129  Sum_probs=70.6

Q ss_pred             CCCccEEEecCCCCCCCHHHHH---HHHhhhCC-ccEEEcc---C---CCcccEEEEEeCCHHHHHHHHHHhcCCeeCCe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLS---RIFSHYGA-SSVRPCS---A---GRLRNCVFVDFGNEPLASQAQMQLNGLRFLGK   85 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~---~~f~~~G~-~~~~~~~---~---~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~   85 (121)
                      ....++|||+|||+.+++++|+   ++|++||. ..+.++.   +   +.++|||||+|.+.++|.+|+..|||..|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3447999999999999999999   99999999 6666665   2   24569999999999999999999999999999


Q ss_pred             EEEEEecCCCCc
Q 043634           86 VLSVERASKPNE   97 (121)
Q Consensus        86 ~l~v~~a~~~~~   97 (121)
                      .|+|.++ .++.
T Consensus        92 ~l~V~~a-~~k~  102 (111)
T 2cpi_A           92 TLKASLG-TTKY  102 (111)
T ss_dssp             EEEEESC-CCCS
T ss_pred             EEEEEec-cccc
Confidence            9999999 5443

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

Probab=99.81  E-value=1.8e-19  Score=111.06  Aligned_cols=78  Identities=22%  Similarity=0.300  Sum_probs=70.5

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK   94 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   94 (121)
                      .++|||+|||+.+++++|+.+|.+||. ..++++.   ++.++|||||+|.+.++|..|+.. ++..|+|+.|+|.++ .
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a-~  104 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRA-V  104 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECC-S
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEEC-C
Confidence            699999999999999999999999999 6777765   578899999999999999999987 999999999999999 5


Q ss_pred             CCcc
Q 043634           95 PNEE   98 (121)
Q Consensus        95 ~~~~   98 (121)
                      ++..
T Consensus       105 ~~~~  108 (116)
T 1x4b_A          105 AREE  108 (116)
T ss_dssp             SCCC
T ss_pred             CCcc
Confidence            4433

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

Probab=99.81  E-value=2.4e-19  Score=110.20  Aligned_cols=78  Identities=27%  Similarity=0.443  Sum_probs=68.6

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccE---EEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSV---RPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~---~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ..+.++|||+|||+.+++++|+++|.+||. ..+   ..+.++.++|||||+|.+.++|..|+..|||..++|+.|+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            345799999999999999999999999998 322   1112788899999999999999999999999999999999999


Q ss_pred             cC
Q 043634           92 AS   93 (121)
Q Consensus        92 a~   93 (121)
                      ++
T Consensus       102 a~  103 (115)
T 2cpx_A          102 GK  103 (115)
T ss_dssp             CC
T ss_pred             cc
Confidence            93

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

Probab=99.81  E-value=1.7e-19  Score=109.40  Aligned_cols=75  Identities=15%  Similarity=0.177  Sum_probs=68.9

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...++|||+|||+.+++++|+.+|++||. ..++++.  .|.++|||||+|.+.++|..|+. +++..++|+.|.|.++
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            44799999999999999999999999999 6677665  57889999999999999999998 8999999999999988

>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=99.80  E-value=3.4e-19  Score=108.00  Aligned_cols=78  Identities=18%  Similarity=0.261  Sum_probs=69.4

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-cc-EEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SS-VRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~-~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      +.....++|||+|||+.+++++|+++|.+||. .. ++++.  +|.++|||||+|.+.++|..|+.. ++..++|+.|.|
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v   88 (104)
T 1wg5_A           10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEI   88 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEE
Confidence            33455899999999999999999999999998 43 55554  788899999999999999999987 999999999999


Q ss_pred             Eec
Q 043634           90 ERA   92 (121)
Q Consensus        90 ~~a   92 (121)
                      .++
T Consensus        89 ~~~   91 (104)
T 1wg5_A           89 FKS   91 (104)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            988

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

Probab=99.80  E-value=8.6e-19  Score=103.45  Aligned_cols=73  Identities=25%  Similarity=0.362  Sum_probs=66.0

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ..+.++|||+|||+.+++++|+.+|++||. ..++++     ++||||+|.+.++|..|+..|||..++|+.|+|.+++
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~-----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   79 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-----KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELST   79 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC-----SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECC
Confidence            445899999999999999999999999999 445554     4599999999999999999999999999999999993

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

Probab=99.80  E-value=9.7e-20  Score=104.05  Aligned_cols=71  Identities=15%  Similarity=0.267  Sum_probs=64.8

Q ss_pred             EEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           21 TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        21 ~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +|||+|||+.+++++|+++|++||. ..+.++.   ++.++|||||+|.+.++|.+|+. +++..++|+.|+|.+|
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            5899999999999999999999999 6666655   67889999999999999999997 9999999999999875

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

Probab=99.80  E-value=6.3e-20  Score=114.24  Aligned_cols=74  Identities=14%  Similarity=0.276  Sum_probs=68.6

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      .++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+ .|||..|+|+.|+|.+++
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            589999999999999999999999999 6666664   6888999999999999999999 899999999999999994

>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=99.80  E-value=4.2e-19  Score=105.32  Aligned_cols=76  Identities=22%  Similarity=0.354  Sum_probs=66.7

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcC-CeeCCeEEEEEecCC
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNG-LRFLGKVLSVERASK   94 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g-~~i~g~~l~v~~a~~   94 (121)
                      .+.++|||+|||+.+++++|+++|++||. .....+   .++|||||+|.+.++|..|+..||| ..++|+.|+|.++ .
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~---~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a-~   81 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL---LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYS-V   81 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE---EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEEC-C
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE---cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEc-c
Confidence            45799999999999999999999999998 443232   2468999999999999999999999 9999999999999 4


Q ss_pred             CC
Q 043634           95 PN   96 (121)
Q Consensus        95 ~~   96 (121)
                      ++
T Consensus        82 ~~   83 (93)
T 2cqh_A           82 SK   83 (93)
T ss_dssp             CC
T ss_pred             Cc
Confidence            44

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

Probab=99.80  E-value=5.1e-20  Score=106.83  Aligned_cols=71  Identities=15%  Similarity=0.368  Sum_probs=64.4

Q ss_pred             ccEEEecCCCCCC------CHHHHHHHHhhhCC-ccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCe-EEEE
Q 043634           19 LVTLLIKHLPDAI------PQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGK-VLSV   89 (121)
Q Consensus        19 ~~~l~V~nlp~~~------~~~~L~~~f~~~G~-~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~-~l~v   89 (121)
                      +++|||+|||+.+      ++++|+++|++||. ..+.++. +|.++|||||+|.+.++|..|+..|||..++|+ .|+|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            3689999999999      77999999999999 6666665 788899999999999999999999999999999 8876

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

Probab=99.80  E-value=5.6e-19  Score=109.40  Aligned_cols=77  Identities=16%  Similarity=0.139  Sum_probs=69.5

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC----ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA----SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~----~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      .....++|||+|||+.+++++|+++|+.||.    ..++++.  .|+++|||||+|.+.++|.+|+. +|+..|+|+.|.
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            3445899999999999999999999999987    4566665  68889999999999999999998 999999999999


Q ss_pred             EEec
Q 043634           89 VERA   92 (121)
Q Consensus        89 v~~a   92 (121)
                      |.++
T Consensus        92 V~~a   95 (118)
T 2db1_A           92 VFKS   95 (118)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9998

>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=99.80  E-value=5.5e-19  Score=107.62  Aligned_cols=82  Identities=18%  Similarity=0.293  Sum_probs=70.8

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC--ccEEEc-c---CCCcccEEEEEeCCHHHHHHHHHHhc--CCeeCCeEE
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA--SSVRPC-S---AGRLRNCVFVDFGNEPLASQAQMQLN--GLRFLGKVL   87 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~--~~~~~~-~---~~~~~g~afv~f~~~~~a~~ai~~l~--g~~i~g~~l   87 (121)
                      ..+.++|||+|||+.+++++|+.+|.+||.  ..+.++ .   ++.++|||||+|.+.++|..|+..|+  +..++|+.|
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            345899999999999999999999999986  456665 2   56889999999999999999999996  589999999


Q ss_pred             EEEecCCCCcc
Q 043634           88 SVERASKPNEE   98 (121)
Q Consensus        88 ~v~~a~~~~~~   98 (121)
                      +|.++ .++..
T Consensus        85 ~V~~a-~~~~~   94 (109)
T 2dis_A           85 AVDWA-EPEID   94 (109)
T ss_dssp             EEEES-CSSCS
T ss_pred             EEEEc-CCCCC
Confidence            99999 54433

>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=99.80  E-value=6.9e-19  Score=108.27  Aligned_cols=76  Identities=17%  Similarity=0.167  Sum_probs=69.1

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCCc--cEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGAS--SVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~--~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ..+.++|||+|||+.+++++|+++|..||..  .++++.  +|.++|||||+|.+.++|..|+.. |+..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            3457999999999999999999999999984  377766  788899999999999999999976 99999999999999


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      +
T Consensus        91 a   91 (114)
T 2cpy_A           91 V   91 (114)
T ss_dssp             E
T ss_pred             C
Confidence            9

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

Probab=99.80  E-value=3.9e-20  Score=108.10  Aligned_cols=76  Identities=18%  Similarity=0.270  Sum_probs=68.9

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+.++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+..|||..++|+.+++.+.
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            45899999999999999999999999999 6666654   6788999999999999999999999999999999987765

>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=99.79  E-value=9.8e-19  Score=107.33  Aligned_cols=80  Identities=19%  Similarity=0.282  Sum_probs=70.7

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCee--------C
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRF--------L   83 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i--------~   83 (121)
                      ...+.++|||+|||+.+++++|+.+|.+||. ..++++.  ++.++|||||+|.+.++|..|+..|||..+        .
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            3345799999999999999999999999999 6666665  678899999999999999999999999999        5


Q ss_pred             CeEEEEEecCCC
Q 043634           84 GKVLSVERASKP   95 (121)
Q Consensus        84 g~~l~v~~a~~~   95 (121)
                      ++.|.|.++ .|
T Consensus       101 ~~~l~v~~a-~p  111 (114)
T 1x5o_A          101 TEPLLCKFS-GP  111 (114)
T ss_dssp             SSCBEEEEC-CC
T ss_pred             CCceeEEcc-CC
Confidence            788999999 44

>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=99.79  E-value=2.5e-19  Score=111.73  Aligned_cols=75  Identities=17%  Similarity=0.177  Sum_probs=67.5

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-cc-EEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SS-VRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~-~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...++|||+|||+.+++++|+++|..||. .. +.+..  +|.++|||||+|.+.++|..||. +|+..|+|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            34799999999999999999999999999 44 33332  78899999999999999999998 9999999999999999

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

Probab=99.79  E-value=1.6e-19  Score=103.52  Aligned_cols=72  Identities=19%  Similarity=0.229  Sum_probs=66.6

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ++|||+|||+.+++++|+++|++||. ..+.++.   ++.++|||||+|.+.++|..|+..++ ..++|+.|+|+++
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            57999999999999999999999999 6777765   57889999999999999999999999 9999999999987

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

Probab=99.79  E-value=5.1e-19  Score=106.44  Aligned_cols=72  Identities=25%  Similarity=0.350  Sum_probs=66.4

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ++|||+|||+.+++++|+++|++||. ..+.++..  ++|||||+|.+.++|..|+..|||..++|+.|+|.+++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   73 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN--PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELST   73 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS--SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEcc
Confidence            58999999999999999999999999 66666544  68999999999999999999999999999999999994

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

Probab=99.79  E-value=4.6e-19  Score=108.90  Aligned_cols=75  Identities=15%  Similarity=0.244  Sum_probs=66.7

Q ss_pred             CCCCccEEEecCCCCC-CCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcC--CeeCCeEEEEE
Q 043634           15 ETENLVTLLIKHLPDA-IPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNG--LRFLGKVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~-~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g--~~i~g~~l~v~   90 (121)
                      ...+.++|||+|||+. +++++|+.+|++||. ..++++.   .+|||||+|.+.++|..|+..|++  ..|.|+.|+|.
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~---~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   97 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR---MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVD   97 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET---TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec---CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            4556899999999998 999999999999999 6666653   479999999999999999998864  56999999999


Q ss_pred             ec
Q 043634           91 RA   92 (121)
Q Consensus        91 ~a   92 (121)
                      ++
T Consensus        98 ~a   99 (112)
T 1x4f_A           98 LS   99 (112)
T ss_dssp             EE
T ss_pred             EC
Confidence            99

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

Probab=99.79  E-value=1.1e-18  Score=106.85  Aligned_cols=73  Identities=15%  Similarity=0.176  Sum_probs=67.2

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .++|||+|||+.+++++|+++|+.|+...++++.  .|+++|||||+|.+.++|.+|+ .+|+..|+|+.|.|..+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a   90 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTSCCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccCCeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            7899999999999999999999999446777775  6788999999999999999999 79999999999999888

>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=99.79  E-value=9e-20  Score=107.58  Aligned_cols=72  Identities=21%  Similarity=0.411  Sum_probs=67.8

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ++|||+|||+.+++++|+++|++||. ..++++.   +|.++|||||+|.+.+ |..|+..|||..++|+.|+|+++
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a   77 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEA   77 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEc
Confidence            68999999999999999999999999 7777776   5888999999999999 99999999999999999999999

>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=99.79  E-value=1.4e-18  Score=111.46  Aligned_cols=77  Identities=23%  Similarity=0.290  Sum_probs=68.9

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ....+.++|||+|||+.+++++|+.+|++||. ..++++..  ++|||||+|.+.++|..|+..|||..++|+.|+|.++
T Consensus        68 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  145 (150)
T 2i2y_A           68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN--PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS  145 (150)
T ss_dssp             SSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS--SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEEC
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC--CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            34455899999999999999999999999999 55555543  5799999999999999999999999999999999999

>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=99.78  E-value=9.1e-19  Score=107.37  Aligned_cols=73  Identities=23%  Similarity=0.220  Sum_probs=65.9

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ..++|||+|||+.+++++|+.+|++||. ..+.++   ..+|||||+|.+.++|..|+..|||..++|+.|.|.++.
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 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP---EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC---SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEe---CCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            3789999999999999999999999999 444443   357899999999999999999999999999999999994

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

Probab=99.78  E-value=6.5e-19  Score=105.25  Aligned_cols=73  Identities=27%  Similarity=0.318  Sum_probs=65.7

Q ss_pred             CCCccEEEecCCCC-CCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           16 TENLVTLLIKHLPD-AIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        16 ~~~~~~l~V~nlp~-~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ..+.++|||+|||+ .+++++|+.+|++||. ..+++     .+|||||+|.+.++|..|+..|||..+.|+.|+|.+++
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i-----~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   81 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-----KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSS   81 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEE-----ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE-----eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcC
Confidence            45589999999999 9999999999999999 55555     26899999999999999999999999999999999993

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

Probab=99.78  E-value=3.7e-18  Score=102.04  Aligned_cols=75  Identities=27%  Similarity=0.330  Sum_probs=65.9

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK   94 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   94 (121)
                      ..+.++|||+||  .+++++|+++|.+||. ..+.+   +.++|||||+|.+.++|..|+..|||..++|+.|+|.++ .
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i---~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a-~   85 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM---DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA-R   85 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEE---ETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECC-S
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEe---cCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC-C
Confidence            345899999996  8999999999999999 44444   456799999999999999999999999999999999999 4


Q ss_pred             CC
Q 043634           95 PN   96 (121)
Q Consensus        95 ~~   96 (121)
                      ++
T Consensus        86 ~~   87 (97)
T 1x5p_A           86 KQ   87 (97)
T ss_dssp             SC
T ss_pred             CC
Confidence            43

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

Probab=99.78  E-value=3e-18  Score=102.12  Aligned_cols=78  Identities=22%  Similarity=0.333  Sum_probs=66.8

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEE-EccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVR-PCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK   94 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~-~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   94 (121)
                      ...++|||+|||+.+++++|+.+|++||. ..++ ++. ....+.|||+|.+.++|..|+..|||..++|+.|+|.++ .
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~-~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a-~   90 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNT-DSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYI-P   90 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECC-SSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEEC-C
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeec-CCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc-C
Confidence            34799999999999999999999999999 5553 443 222345999999999999999999999999999999999 4


Q ss_pred             CC
Q 043634           95 PN   96 (121)
Q Consensus        95 ~~   96 (121)
                      ++
T Consensus        91 ~~   92 (96)
T 2e44_A           91 DE   92 (96)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>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=99.78  E-value=1.4e-18  Score=110.19  Aligned_cols=76  Identities=16%  Similarity=0.167  Sum_probs=69.0

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC----ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA----SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~----~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      ....++|||+|||+.+++++|+++|++||.    ..++++.  .|+++|||||+|.+.++|.+|+. +|+..|+|+.|.|
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V  119 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            344799999999999999999999999996    3566665  68889999999999999999998 9999999999999


Q ss_pred             Eec
Q 043634           90 ERA   92 (121)
Q Consensus        90 ~~a   92 (121)
                      .++
T Consensus       120 ~~a  122 (136)
T 2hgl_A          120 FKS  122 (136)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            988

>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=99.77  E-value=6.1e-19  Score=107.40  Aligned_cols=77  Identities=13%  Similarity=0.178  Sum_probs=69.1

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC----ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA----SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~----~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      +....++|||+|||+.+++++|+++|..||.    ..++++.  .|.++|||||+|.+.++|..|+. +|+..++|+.|.
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            3455899999999999999999999999776    4577765  67889999999999999999998 999999999999


Q ss_pred             EEec
Q 043634           89 VERA   92 (121)
Q Consensus        89 v~~a   92 (121)
                      |.++
T Consensus        86 V~~a   89 (107)
T 2lmi_A           86 VYEI   89 (107)
T ss_dssp             CEEC
T ss_pred             EEEC
Confidence            9988

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

Probab=99.77  E-value=3.9e-18  Score=112.46  Aligned_cols=77  Identities=19%  Similarity=0.306  Sum_probs=71.3

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ..+.++|||+|||+.+++++|+++|++||. ..+.++.  ++.++|||||+|.+.++|..|+..|||..|+|+.|+|.++
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            344799999999999999999999999999 6777766  6788999999999999999999999999999999999999

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

Probab=99.77  E-value=2.8e-18  Score=115.71  Aligned_cols=78  Identities=22%  Similarity=0.279  Sum_probs=70.3

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ..|.++|||+|||+.+++++|+++|++||. .+++++.   ++.++|||||+|.+.++|..|+..+|+..+.|+.|++.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            345789999999999999999999999999 6777765   788999999999999999999999999999999999998


Q ss_pred             cC
Q 043634           92 AS   93 (121)
Q Consensus        92 a~   93 (121)
                      +.
T Consensus        92 ~~   93 (213)
T 4f02_A           92 SQ   93 (213)
T ss_dssp             CC
T ss_pred             cc
Confidence            83

>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=99.77  E-value=7e-19  Score=120.29  Aligned_cols=74  Identities=16%  Similarity=0.195  Sum_probs=68.5

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhC--C-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYG--A-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G--~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .++|||+|||+.+++++|+++|++||  . ..++++.   ++.++|||||+|.+.++|.+||..||+..|+|+.|+|.++
T Consensus        68 ~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a  147 (229)
T 3q2s_C           68 RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPV  147 (229)
T ss_dssp             -CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEEC
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEEC
Confidence            57899999999999999999999999  7 5666665   7889999999999999999999999999999999999998

>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=99.77  E-value=3e-18  Score=100.82  Aligned_cols=72  Identities=22%  Similarity=0.269  Sum_probs=66.1

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...++|||+|||+.+++++|+++|++| . ..+++.   .++|||||+|.+.++|..|+..|||..++|+.|+|.++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~---~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   75 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD---RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE---GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe---CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEc
Confidence            347899999999999999999999999 7 666663   66899999999999999999999999999999999998

>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=99.77  E-value=6.6e-19  Score=100.48  Aligned_cols=71  Identities=14%  Similarity=0.223  Sum_probs=64.0

Q ss_pred             EEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           21 TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        21 ~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +|||+|||+.+++++|+++|++||. ..+.++.   ++.++|||||+|.+.++|..|+. +++..++|+.|.|.++
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            5899999999999999999999999 6666654   57889999999999999999997 4889999999999875

>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=5.3e-18  Score=100.47  Aligned_cols=75  Identities=23%  Similarity=0.308  Sum_probs=63.5

Q ss_pred             CCCccE-EEecCCCCCCCHHH----HHHHHhhhC-CccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           16 TENLVT-LLIKHLPDAIPQDT----LSRIFSHYG-ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        16 ~~~~~~-l~V~nlp~~~~~~~----L~~~f~~~G-~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      .+|..+ |||+|||+.+++++    |+++|++|| .  |..+ ++   |+|||.|.+.++|.+|++.|||..+.|+.|+|
T Consensus         5 ~~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~--Vl~V-tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v   78 (96)
T 2diu_A            5 SSGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGK--VLSI-TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIV   78 (96)
T ss_dssp             CCCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCC--EEEC-CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCe--eEEE-ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEE
Confidence            344554 99999999999987    668999995 7  4444 44   99999999999999999999999999999999


Q ss_pred             EecCCCCc
Q 043634           90 ERASKPNE   97 (121)
Q Consensus        90 ~~a~~~~~   97 (121)
                      .+| +.++
T Consensus        79 ~~A-~~~s   85 (96)
T 2diu_A           79 SFT-PKNR   85 (96)
T ss_dssp             ESS-CCSC
T ss_pred             Eec-CCCc
Confidence            999 4443

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

Probab=99.76  E-value=7.1e-19  Score=110.20  Aligned_cols=78  Identities=18%  Similarity=0.264  Sum_probs=67.9

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCCc--cEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGAS--SVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~--~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      ......++|||+|||+.+++++|+++|++|+..  .++++.  .|+++|||||+|.+.++|.+|+.. ++..|+|+.|.|
T Consensus        37 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V  115 (126)
T 2hgm_A           37 ADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEV  115 (126)
T ss_dssp             TCSSSCCEEEEECCCTTCCHHHHHHHTTTSCEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEE
Confidence            334457899999999999999999999999554  666665  678899999999999999999974 779999999999


Q ss_pred             Eec
Q 043634           90 ERA   92 (121)
Q Consensus        90 ~~a   92 (121)
                      ..+
T Consensus       116 ~~a  118 (126)
T 2hgm_A          116 FKS  118 (126)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            887

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

Probab=99.76  E-value=6.3e-18  Score=104.01  Aligned_cols=75  Identities=13%  Similarity=0.188  Sum_probs=65.3

Q ss_pred             CCCCccEEEe--cCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCee-----CCeE
Q 043634           15 ETENLVTLLI--KHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRF-----LGKV   86 (121)
Q Consensus        15 ~~~~~~~l~V--~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i-----~g~~   86 (121)
                      ...|..+|||  |||++.+++++|+++|++||. ..+.++ .  .+|||||+|.+.++|.+|+..|||..+     .|+.
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~-~--~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~   97 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-P--NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   97 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECC-T--TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEe-C--CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcE
Confidence            3455788999  779999999999999999999 444433 3  479999999999999999999999998     6889


Q ss_pred             EEEEec
Q 043634           87 LSVERA   92 (121)
Q Consensus        87 l~v~~a   92 (121)
                      |.|.++
T Consensus        98 l~v~~a  103 (114)
T 2cq2_A           98 LYLNFV  103 (114)
T ss_dssp             CEEEEE
T ss_pred             EEEEec
Confidence            999999

>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=99.76  E-value=7.9e-18  Score=109.43  Aligned_cols=76  Identities=16%  Similarity=0.337  Sum_probs=66.3

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEecC
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLG--KVLSVERAS   93 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g--~~l~v~~a~   93 (121)
                      .....|||+||++.+++++|+++|++||. ..+.+. .+..+|||||+|.+.++|..|+..|||..|.|  +.|+|++++
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~~Ak  122 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF-TKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEE-ESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEE-eCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            33678999999999999999999999999 555543 33457899999999999999999999999965  999999994

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

Probab=99.76  E-value=1.4e-17  Score=107.23  Aligned_cols=78  Identities=22%  Similarity=0.324  Sum_probs=71.3

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ...+.++|||+|||..+++++|+++|++||. ..+.++.   +|.++|+|||+|.+.++|.+|+..|||..++|+.|+|.
T Consensus        83 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  162 (166)
T 3md3_A           83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN  162 (166)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Confidence            3445899999999999999999999999999 6666654   68889999999999999999999999999999999999


Q ss_pred             ec
Q 043634           91 RA   92 (121)
Q Consensus        91 ~a   92 (121)
                      ++
T Consensus       163 ~a  164 (166)
T 3md3_A          163 WA  164 (166)
T ss_dssp             ES
T ss_pred             ec
Confidence            98

>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=99.75  E-value=1e-17  Score=108.21  Aligned_cols=76  Identities=28%  Similarity=0.386  Sum_probs=70.0

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      +.++|||+|||+.+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|..|+..|+|..++|+.|.|.++.
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            4789999999999999999999999999 5666654   67889999999999999999999999999999999999993

>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=99.75  E-value=1.3e-17  Score=107.42  Aligned_cols=75  Identities=27%  Similarity=0.416  Sum_probs=69.5

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      .++|||+|||+.+++++|+++|+.||. ..++++.   +|.++|||||+|.+.++|..|+..|+|..+.|+.|+|.++.
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            689999999999999999999999999 6666655   77888999999999999999999999999999999999993

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

Probab=99.61  E-value=6e-20  Score=113.24  Aligned_cols=80  Identities=20%  Similarity=0.374  Sum_probs=71.0

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-cc--------EEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeC
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SS--------VRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFL   83 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~--------~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~   83 (121)
                      ..+.++|||+|||+.+++++|+++|++||. ..        ++++.   ++.++|||||+|.+.++|..|+..|||..+.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            345899999999999999999999999999 44        55554   5788999999999999999999999999999


Q ss_pred             CeEEEEEecCCCC
Q 043634           84 GKVLSVERASKPN   96 (121)
Q Consensus        84 g~~l~v~~a~~~~   96 (121)
                      |+.|+|.++ .++
T Consensus        84 g~~l~V~~a-~~~   95 (116)
T 2lcw_A           84 GNPIKVSFA-TRR   95 (116)
Confidence            999999999 443

>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=99.75  E-value=7e-18  Score=98.67  Aligned_cols=72  Identities=22%  Similarity=0.433  Sum_probs=62.8

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhh----C-------CccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCe
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHY----G-------ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGK   85 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~----G-------~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~   85 (121)
                      .+.++|||+|||+.+++++|+++|++|    |       .  +..+.....+|||||+|.+.++|..|+ .|||..++|+
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~--v~~~~~~~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~   80 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNP--VLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQ   80 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCS--EEEEEECSSSSEEEEEESSHHHHHHHG-GGTTCEETTE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCc--ceEEEecCCCcEEEEEcCCHHHHHHHH-hcCCCEECCe
Confidence            458999999999999999999999999    7       5  433332344799999999999999999 9999999999


Q ss_pred             EEEEEe
Q 043634           86 VLSVER   91 (121)
Q Consensus        86 ~l~v~~   91 (121)
                      .|+|++
T Consensus        81 ~l~V~r   86 (87)
T 2hzc_A           81 SLKIRR   86 (87)
T ss_dssp             ECEEEC
T ss_pred             EEEEeC
Confidence            999874

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

Probab=99.75  E-value=2.2e-18  Score=103.86  Aligned_cols=74  Identities=20%  Similarity=0.311  Sum_probs=67.6

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+.++|||+|||+.+++++|+.+|++||. ..++++.  +|.++|||||+|.+.++|..|+.  ++..++|+.|.|.++
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            34799999999999999999999999999 6666665  77889999999999999999997  999999999999988

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

Probab=99.75  E-value=1.6e-17  Score=104.34  Aligned_cols=77  Identities=16%  Similarity=0.367  Sum_probs=66.6

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccE-EEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNC-VFVDFGNEPLASQAQMQLNGLRFLG--KVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~-afv~f~~~~~a~~ai~~l~g~~i~g--~~l~v~   90 (121)
                      .+.+...|||+||++.+++++|+++|++||. .++++..  +.+|+ |||+|.+.++|..|+..|||..|.|  +.|+|+
T Consensus        24 ~ps~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~--~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~  101 (130)
T 3zzy_A           24 GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFT--KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             -CCSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEE--ETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             CCCceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEc--CCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEE
Confidence            3445688899999999999999999999999 5565543  23577 9999999999999999999999988  899999


Q ss_pred             ecC
Q 043634           91 RAS   93 (121)
Q Consensus        91 ~a~   93 (121)
                      +++
T Consensus       102 ~ak  104 (130)
T 3zzy_A          102 FSK  104 (130)
T ss_dssp             ECS
T ss_pred             ecC
Confidence            994

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

Probab=99.74  E-value=6.6e-18  Score=113.88  Aligned_cols=77  Identities=25%  Similarity=0.366  Sum_probs=70.1

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPN   96 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~~   96 (121)
                      .++|||+|||+.+++++|+++|++||. ..++++. .+.++|||||+|.+.++|.+|+..|||..|+|+.|+|.++ .++
T Consensus       103 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a-~~~  181 (213)
T 4f02_A          103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF-KSR  181 (213)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC-CCH
T ss_pred             cccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEc-CCC
Confidence            578999999999999999999999999 6676665 5667899999999999999999999999999999999999 543

>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=99.74  E-value=1.1e-18  Score=111.12  Aligned_cols=76  Identities=14%  Similarity=0.147  Sum_probs=68.0

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ....++|||+|||+.+++++|+++|++||...++++.  .++++|||||+|.+.++|..|| .+|+..|+|+.|.|..+
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~Gi~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLN  120 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCCCSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEEC
Confidence            3447899999999999999999999999976666665  6788999999999999999999 78999999999999988

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

Probab=99.74  E-value=1.6e-17  Score=122.78  Aligned_cols=77  Identities=19%  Similarity=0.368  Sum_probs=70.9

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+.++|||+|||+.+++++|..+|++||. ..|.++.   ++.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            44689999999999999999999999999 6666664   7888999999999999999999999999999999999999


Q ss_pred             C
Q 043634           93 S   93 (121)
Q Consensus        93 ~   93 (121)
                      .
T Consensus       180 ~  180 (437)
T 3pgw_S          180 R  180 (437)
T ss_pred             C
Confidence            3

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

Probab=99.74  E-value=3.9e-17  Score=101.95  Aligned_cols=74  Identities=23%  Similarity=0.304  Sum_probs=63.9

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccE-EEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEecCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNC-VFVDFGNEPLASQAQMQLNGLRFLG--KVLSVERASK   94 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~-afv~f~~~~~a~~ai~~l~g~~i~g--~~l~v~~a~~   94 (121)
                      ...|||+||++.+++++|+.+|++||. ..+++...   .|| |||+|.+.++|..|+..|||..|.|  +.|+|.++ +
T Consensus        25 vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~---~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A-k  100 (124)
T 2e5i_A           25 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR---NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA-R  100 (124)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES---SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC-S
T ss_pred             EEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC---CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe-c
Confidence            455789999999999999999999999 55655432   386 9999999999999999999999987  68999999 4


Q ss_pred             CC
Q 043634           95 PN   96 (121)
Q Consensus        95 ~~   96 (121)
                      ++
T Consensus       101 ~~  102 (124)
T 2e5i_A          101 PT  102 (124)
T ss_dssp             CS
T ss_pred             CC
Confidence            43

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

Probab=99.74  E-value=6.6e-18  Score=105.39  Aligned_cols=75  Identities=20%  Similarity=0.224  Sum_probs=67.4

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-----ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-----SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-----~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      ...++|||+|||+.+++++|+++|++||.     ..++++.  +|+++|||||+|.+.++|..|+.. |+..++|+.|.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            44789999999999999999999999986     2566665  788999999999999999999976 999999999999


Q ss_pred             Eec
Q 043634           90 ERA   92 (121)
Q Consensus        90 ~~a   92 (121)
                      ..+
T Consensus       100 ~~a  102 (123)
T 2dha_A          100 FRS  102 (123)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            887

>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=99.74  E-value=2.1e-17  Score=97.59  Aligned_cols=75  Identities=20%  Similarity=0.398  Sum_probs=58.9

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCe--eCCeEEEEEe
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLR--FLGKVLSVER   91 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~--i~g~~l~v~~   91 (121)
                      ...+.++|||+|||+.+++++|+++|++||. ..++++.  .++|||||+|.+.++|.    .+++..  +.|+.|.|.+
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~--~srGfaFV~F~~~~~A~----~~~~~~~~~~g~~v~v~~   80 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK--PFRAFAFVTFADDKVAQ----SLCGEDLIIKGISVHISN   80 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCS--SCCSEEEEEESCHHHHH----HHTTCEEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEee--CCCCEEEEEECCHHHHH----HHcCCCcccCCEEEEEEE
Confidence            3455899999999999999999999999999 5555553  47899999999999887    356655  4599999999


Q ss_pred             cCCCC
Q 043634           92 ASKPN   96 (121)
Q Consensus        92 a~~~~   96 (121)
                      + .++
T Consensus        81 a-~~k   84 (89)
T 3d2w_A           81 A-EPK   84 (89)
T ss_dssp             C-C--
T ss_pred             c-CCC
Confidence            9 554

>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=99.74  E-value=2.2e-17  Score=111.05  Aligned_cols=74  Identities=18%  Similarity=0.271  Sum_probs=67.5

Q ss_pred             CccEEEecCCC-CCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           18 NLVTLLIKHLP-DAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        18 ~~~~l~V~nlp-~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ++++|||+||| +.+++++|+++|++||. .+++++..  .+|||||+|.+.++|..|+..|||..+.|+.|+|.+++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~--~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~   78 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS--KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSK   78 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT--STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC--CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            47899999999 89999999999999999 66666643  47999999999999999999999999999999999994

>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=99.74  E-value=2.4e-17  Score=107.40  Aligned_cols=77  Identities=23%  Similarity=0.333  Sum_probs=70.1

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKP   95 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   95 (121)
                      .+.++|||+|||+.+++++|+++|++||.  ++.+. ++.++|||||+|.+.++|.+|+..|||..++|+.|+|.++ .+
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~--v~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a-~~  173 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALE--IRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT-GE  173 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSE--EEEECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEEC-SS
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCe--EEEecCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEec-CC
Confidence            34799999999999999999999999998  55444 7888999999999999999999999999999999999999 54


Q ss_pred             C
Q 043634           96 N   96 (121)
Q Consensus        96 ~   96 (121)
                      +
T Consensus       174 k  174 (175)
T 1fje_B          174 K  174 (175)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.73  E-value=2.5e-17  Score=114.78  Aligned_cols=79  Identities=28%  Similarity=0.423  Sum_probs=72.4

Q ss_pred             CCCCccEEEecCCCCCCCHHHHH----HHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLS----RIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~----~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      +..+.++|||+|||+.+++++|+    ++|++||. ..++++.++.++|||||+|.+.++|..|+..|||..|.|+.|+|
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   84 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   84 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEE
Confidence            44568999999999999999966    89999999 66777778889999999999999999999999999999999999


Q ss_pred             EecC
Q 043634           90 ERAS   93 (121)
Q Consensus        90 ~~a~   93 (121)
                      .+++
T Consensus        85 ~~a~   88 (282)
T 3pgw_A           85 QYAK   88 (282)
T ss_pred             EEec
Confidence            9993

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

Probab=99.73  E-value=3.3e-17  Score=108.48  Aligned_cols=79  Identities=23%  Similarity=0.413  Sum_probs=71.6

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+.++|||+|||+.+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|..|+..|||..++|+.|.|.++
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            45799999999999999999999999999 5666654   6778999999999999999999999999999999999999


Q ss_pred             CCCC
Q 043634           93 SKPN   96 (121)
Q Consensus        93 ~~~~   96 (121)
                       .++
T Consensus       192 -~~~  194 (198)
T 2yh0_A          192 -SVG  194 (198)
T ss_dssp             -CCC
T ss_pred             -CCC
Confidence             544

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

Probab=99.73  E-value=3.3e-17  Score=97.38  Aligned_cols=73  Identities=18%  Similarity=0.266  Sum_probs=62.5

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...++|||+|||+.+++++|+.+|++||. ..+ +......+ ||||+|.+.++|..|+. |||..++|+.|.|.++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v-~~~~~~g~-~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV-VMDKDKGV-FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE-EECSSSCC-EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE-EEcCCCCc-EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            34689999999999999999999999999 444 22221122 99999999999999999 9999999999999988

>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=99.73  E-value=2.4e-17  Score=109.00  Aligned_cols=79  Identities=23%  Similarity=0.304  Sum_probs=70.2

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      +....+.++|||+|||+.+++++|+++|+.||. ..+.++.   +|.++|||||+|.+.++|..|+.. ++..++|+.|.
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 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVE   85 (196)
T ss_dssp             -CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEee
Confidence            334456899999999999999999999999999 6666665   678899999999999999999965 89999999999


Q ss_pred             EEec
Q 043634           89 VERA   92 (121)
Q Consensus        89 v~~a   92 (121)
                      |.++
T Consensus        86 v~~~   89 (196)
T 1l3k_A           86 PKRA   89 (196)
T ss_dssp             EEEC
T ss_pred             eecc
Confidence            9998

>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=99.73  E-value=2.9e-17  Score=106.56  Aligned_cols=76  Identities=24%  Similarity=0.419  Sum_probs=69.6

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...++|||+|||+.+++++|+++|++||. ..++++.   +|.++|+|||+|.+.++|.+|+..|||..++|+.|.|.+|
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            33799999999999999999999999999 5666554   6788999999999999999999999999999999999987

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

Probab=99.73  E-value=1.1e-17  Score=103.03  Aligned_cols=72  Identities=14%  Similarity=0.143  Sum_probs=62.2

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeE-----EEEE
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKV-----LSVE   90 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~-----l~v~   90 (121)
                      ...++|||+|||+.+++++|+++|.+||. ..+.++..    |||||+|.+.++|..||..|||..|+|+.     |+|.
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~----g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~   89 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   89 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT----SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC----CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEec
Confidence            34799999999999999999999999999 45555433    89999999999999999999999999988     7777


Q ss_pred             ec
Q 043634           91 RA   92 (121)
Q Consensus        91 ~a   92 (121)
                      .+
T Consensus        90 ~~   91 (115)
T 3beg_B           90 VD   91 (115)
T ss_dssp             EC
T ss_pred             cC
Confidence            76

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

Probab=99.72  E-value=3.8e-17  Score=105.09  Aligned_cols=74  Identities=23%  Similarity=0.326  Sum_probs=67.5

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ++|||+|||+.+++++|+++|++||. ..++++.  .+.++|||||+|.+.++|..|+..++|..+.|+.|.|.++.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~   77 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAF   77 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcC
Confidence            58999999999999999999999999 6666665  57788999999999999999999999999999999999993

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

Probab=99.71  E-value=6e-17  Score=108.50  Aligned_cols=76  Identities=16%  Similarity=0.362  Sum_probs=69.9

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      +.++|||+|||..+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.++.
T Consensus       124 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~  203 (216)
T 2qfj_A          124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV  203 (216)
T ss_dssp             TSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECS
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEec
Confidence            3589999999999999999999999999 6666665   67889999999999999999999999999999999999993

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

Probab=99.71  E-value=4.7e-17  Score=99.99  Aligned_cols=74  Identities=16%  Similarity=0.153  Sum_probs=62.8

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc---C---CCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS---A---GRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~---~---~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ...++|||+|||+.+++++|+++|++||...+.++.   +   |.++|||||+|.+.++|..|+..|+  .++|+.+.+.
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~   83 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCV   83 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCCEECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEEEEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEec
Confidence            447999999999999999999999999993355555   3   6889999999999999999999885  4778777776


Q ss_pred             ec
Q 043634           91 RA   92 (121)
Q Consensus        91 ~a   92 (121)
                      .+
T Consensus        84 ~~   85 (114)
T 2dnl_A           84 SS   85 (114)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>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=3.3e-17  Score=105.82  Aligned_cols=76  Identities=14%  Similarity=0.306  Sum_probs=69.4

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK   94 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   94 (121)
                      .++|||+|||+.+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|.+|+. ++|..++|+.|.|.++ .
T Consensus        87 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a-~  164 (167)
T 2cjk_A           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRA-E  164 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEEC-C
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeec-C
Confidence            679999999999999999999999999 6777765   68889999999999999999997 8999999999999999 5


Q ss_pred             CC
Q 043634           95 PN   96 (121)
Q Consensus        95 ~~   96 (121)
                      |+
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.70  E-value=3.7e-17  Score=95.98  Aligned_cols=76  Identities=21%  Similarity=0.364  Sum_probs=61.3

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKP   95 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   95 (121)
                      .+.++|||+|||+.+++++|+++|++||. ..++++.  .++|||||+|.+.++|++++..  ...+.|+.|.|.++ .+
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~--~~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a-~~   77 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK--PFRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNA-EP   77 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS--SCCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECC-CC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEec--CCCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEec-CC
Confidence            45799999999999999999999999999 5566553  3689999999999998754321  24558999999999 54


Q ss_pred             Cc
Q 043634           96 NE   97 (121)
Q Consensus        96 ~~   97 (121)
                      +.
T Consensus        78 ~~   79 (88)
T 1wf0_A           78 KH   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

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

Probab=99.70  E-value=4e-17  Score=101.89  Aligned_cols=73  Identities=14%  Similarity=0.183  Sum_probs=64.7

Q ss_pred             cEEEecCC----CCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCC----HHH----HHHHHH--HhcCCe
Q 043634           20 VTLLIKHL----PDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGN----EPL----ASQAQM--QLNGLR   81 (121)
Q Consensus        20 ~~l~V~nl----p~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~----~~~----a~~ai~--~l~g~~   81 (121)
                      ++|||+||    |+.+++.+|+.+|++||. .++.++.   +|.++|||||+|.+    ..+    |..|+.  .++|..
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    999999999999999999 7777666   89999999999996    322    788888  789999


Q ss_pred             eCCeEEEEEec
Q 043634           82 FLGKVLSVERA   92 (121)
Q Consensus        82 i~g~~l~v~~a   92 (121)
                      |+|+.|+|.+.
T Consensus        83 I~Gr~irV~ln   93 (136)
T 2j8a_A           83 IMGFKFEVILN   93 (136)
T ss_dssp             ETTEEEEEEEC
T ss_pred             ecCcEEEEEEC
Confidence            99999999988

>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=99.69  E-value=1.4e-16  Score=105.31  Aligned_cols=78  Identities=17%  Similarity=0.333  Sum_probs=68.2

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      +.++|||+|||+.+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|.+|+.. ++..++|+.|.|.++ 
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a-  180 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA-  180 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEEC-
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEec-
Confidence            4689999999999999999999999999 6666664   678899999999999999999976 899999999999999 


Q ss_pred             CCCc
Q 043634           94 KPNE   97 (121)
Q Consensus        94 ~~~~   97 (121)
                      .++.
T Consensus       181 ~~k~  184 (196)
T 1l3k_A          181 LSKQ  184 (196)
T ss_dssp             C---
T ss_pred             CChh
Confidence            5443

>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=99.69  E-value=1.4e-16  Score=103.37  Aligned_cols=75  Identities=21%  Similarity=0.365  Sum_probs=68.0

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeC---CeEEEEEe
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFL---GKVLSVER   91 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~---g~~l~v~~   91 (121)
                      +.++|||+|||+.+++++|+++|++||. ..++++.  +|.++|||||+|.+.++|.+|+..|||..+.   +++|.|.+
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~  173 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKF  173 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEE
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEe
Confidence            4789999999999999999999999999 6666665  6778999999999999999999999998776   49999998


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      |
T Consensus       174 a  174 (175)
T 3nmr_A          174 A  174 (175)
T ss_dssp             C
T ss_pred             c
Confidence            7

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

Probab=99.69  E-value=1.3e-16  Score=106.84  Aligned_cols=74  Identities=19%  Similarity=0.326  Sum_probs=67.3

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .++|||+|||+.+++++|+++|+.||. ..++++.   ++.++|||||+|.+.++|..|+..|++..++|+.|.|.++
T Consensus        28 ~~~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           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            689999999999999999999999999 6677765   6778999999999999999999999999999999999887

>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=99.69  E-value=9.2e-17  Score=104.60  Aligned_cols=78  Identities=24%  Similarity=0.332  Sum_probs=68.0

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-cc--EEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SS--VRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~--~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      +..+.++|||+|||+.+++++|+++|..||. ..  +....++.++|||||+|.+.++|..|+ .|||..+.|+.|.|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~   87 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEec
Confidence            4455899999999999999999999999987 33  222237888999999999999999999 5999999999999999


Q ss_pred             cC
Q 043634           92 AS   93 (121)
Q Consensus        92 a~   93 (121)
                      +.
T Consensus        88 ~~   89 (175)
T 1fje_B           88 PK   89 (175)
T ss_dssp             CC
T ss_pred             CC
Confidence            93

>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=99.69  E-value=1.9e-16  Score=102.19  Aligned_cols=76  Identities=32%  Similarity=0.435  Sum_probs=68.6

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEE
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLG--KVLSVE   90 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g--~~l~v~   90 (121)
                      .+.++|||+|||..+++++|+++|++||. ..+.++.   ++.++|+|||+|.+.++|..|+..|||..+.|  +.|+|.
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~  166 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR  166 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEE
Confidence            44789999999999999999999999999 5666555   67788999999999999999999999999988  999998


Q ss_pred             ec
Q 043634           91 RA   92 (121)
Q Consensus        91 ~a   92 (121)
                      +|
T Consensus       167 ~A  168 (168)
T 1b7f_A          167 LA  168 (168)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>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=99.68  E-value=2e-16  Score=107.64  Aligned_cols=77  Identities=21%  Similarity=0.318  Sum_probs=68.7

Q ss_pred             CCCCccEEEecCCCC-CCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           15 ETENLVTLLIKHLPD-AIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~-~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...+.++|||+|||+ .+++++|+++|++||. ..++++...  +|||||+|.+.++|..|+..|+|..+.|+.|.|.++
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~--~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  107 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS  107 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT--SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECC
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC--CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEe
Confidence            345589999999999 9999999999999999 556665432  789999999999999999999999999999999999


Q ss_pred             C
Q 043634           93 S   93 (121)
Q Consensus        93 ~   93 (121)
                      .
T Consensus       108 ~  108 (229)
T 2adc_A          108 K  108 (229)
T ss_dssp             S
T ss_pred             c
Confidence            4

>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=99.68  E-value=2.7e-16  Score=101.15  Aligned_cols=75  Identities=29%  Similarity=0.428  Sum_probs=67.0

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeE--EEEEe
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKV--LSVER   91 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~--l~v~~   91 (121)
                      +.++|||+|||..+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|.+|+..|||..+.|+.  |+|.+
T Consensus        87 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~  166 (167)
T 1fxl_A           87 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF  166 (167)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEe
Confidence            4789999999999999999999999999 5666654   6778999999999999999999999999999975  77776


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      |
T Consensus       167 A  167 (167)
T 1fxl_A          167 A  167 (167)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.67  E-value=2.9e-16  Score=104.77  Aligned_cols=73  Identities=14%  Similarity=0.158  Sum_probs=66.1

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .++|||+|||+.+++++|+.+|++||. ..++++.  ++.++|||||+|.+.++|..|+..++ ..++|+.|.|.++
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~  184 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFK  184 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEET
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEh
Confidence            589999999999999999999999999 6666665  67889999999999999999997655 5999999999988

>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=99.66  E-value=1.2e-15  Score=106.29  Aligned_cols=75  Identities=24%  Similarity=0.401  Sum_probs=66.7

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEEecC
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFL-GKVLSVERAS   93 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~-g~~l~v~~a~   93 (121)
                      .+.++|||+|||..+++++|+++|++||. ..++++..  .+|||||+|.+.++|..|+..|||..+. |+.|+|.+++
T Consensus       205 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG--RHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecC--CCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            34789999999999999999999999999 55655532  2589999999999999999999999999 9999999983

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

Probab=99.66  E-value=5.9e-16  Score=107.92  Aligned_cols=81  Identities=23%  Similarity=0.354  Sum_probs=72.6

Q ss_pred             CCCccEEEecCCCCCC-CHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAI-PQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~-~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ..+.++|||+|||+.+ ++++|+++|+.||. ..++++.  +|.++|+|||+|.+.++|..|+..|||..++|+.|+|.+
T Consensus       181 ~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  260 (284)
T 3smz_A          181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF  260 (284)
T ss_dssp             TTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEE
Confidence            3457999999999995 99999999999999 6777665  788899999999999999999999999999999999999


Q ss_pred             cCCCCc
Q 043634           92 ASKPNE   97 (121)
Q Consensus        92 a~~~~~   97 (121)
                      + .++.
T Consensus       261 a-~~~~  265 (284)
T 3smz_A          261 C-APGP  265 (284)
T ss_dssp             C-CSSS
T ss_pred             e-cCCC
Confidence            9 5443

>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=99.66  E-value=2.7e-15  Score=91.82  Aligned_cols=81  Identities=15%  Similarity=0.185  Sum_probs=67.4

Q ss_pred             CCCCccEEEecCCCCCCC-----------HHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCee
Q 043634           15 ETENLVTLLIKHLPDAIP-----------QDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRF   82 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~-----------~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i   82 (121)
                      .+.+.++|+|.||.....           +++|+.+|++||. ..+.+ ....++|||||+|.+.++|..|+..|||..+
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~   89 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDRHPDGVASVSFRDPEEADYCIQTLDGRWF   89 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETTCTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecCCCCEEEEEEECCHHHHHHHHHHcCCCEE
Confidence            445689999999954432           5799999999999 66644 3334789999999999999999999999999


Q ss_pred             CCeEEEEEecCCCCc
Q 043634           83 LGKVLSVERASKPNE   97 (121)
Q Consensus        83 ~g~~l~v~~a~~~~~   97 (121)
                      +|+.|+|.++ .++.
T Consensus        90 ~gr~l~v~~a-~~~~  103 (112)
T 2dit_A           90 GGRQITAQAW-DGTT  103 (112)
T ss_dssp             TTEECEEEEC-CSCC
T ss_pred             CCcEEEEEEe-CCCC
Confidence            9999999999 5443

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

Probab=99.66  E-value=1.9e-16  Score=108.76  Aligned_cols=74  Identities=24%  Similarity=0.347  Sum_probs=66.9

Q ss_pred             CCccEEEecCCCCCC---------CHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCee----
Q 043634           17 ENLVTLLIKHLPDAI---------PQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRF----   82 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~---------~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i----   82 (121)
                      ...++|||+||+..+         ++++|+.+|++||. ..++++.   ++|||||+|.+.++|+.|+..|+|..|    
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~---~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~  208 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE---SKNCGFVKFKYQANAEFAKEAMSNQTLLLPS  208 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG---GGTEEEEEESSHHHHHHHHHHHTTCCCCCTT
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC---CCCEEEEEeCCHHHHHHHHHHhCCCEEeccc
Confidence            347999999999998         79999999999999 5666653   479999999999999999999999999    


Q ss_pred             --------CCeEEEEEecC
Q 043634           83 --------LGKVLSVERAS   93 (121)
Q Consensus        83 --------~g~~l~v~~a~   93 (121)
                              .|+.|.|.+|+
T Consensus       209 ~~e~~~~~~gr~L~V~wA~  227 (240)
T 3u1l_A          209 DKEWDDRREGTGLLVKWAN  227 (240)
T ss_dssp             STTGGGGGGSCCCEEEECC
T ss_pred             cccccccCCCCEEEEEEcc
Confidence                    89999999993

>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=99.66  E-value=6.6e-16  Score=106.96  Aligned_cols=74  Identities=27%  Similarity=0.433  Sum_probs=67.2

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ..+.++|||+|||+.+++++|+.+|+.||. ..+.+.   .++|||||+|.+.++|..|+..++|..+.|+.|.|.++
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~---~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a   93 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN---RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEe---CCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            344799999999999999999999999999 556553   34799999999999999999999999999999999998

>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=99.65  E-value=4.6e-16  Score=100.38  Aligned_cols=73  Identities=23%  Similarity=0.362  Sum_probs=65.9

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +.++|||+|||+.+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|..|+..  +..++|+.|.|.++
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~   78 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRA   78 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccc
Confidence            4789999999999999999999999999 6666665   688899999999999999999974  67899999999888

>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=99.65  E-value=7e-16  Score=107.94  Aligned_cols=79  Identities=22%  Similarity=0.305  Sum_probs=70.1

Q ss_pred             CCCccEEEecCCCCC-CCHHHHHHHHhhhCC-ccEEEcc--C--CCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           16 TENLVTLLIKHLPDA-IPQDTLSRIFSHYGA-SSVRPCS--A--GRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~-~~~~~L~~~f~~~G~-~~~~~~~--~--~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      ..+.++|||+|||+. +++++|+++|++||. ..++++.  .  |.++|||||+|.+.++|.+|+ .|||..|+|+.|.|
T Consensus       207 ~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V  285 (292)
T 2ghp_A          207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISV  285 (292)
T ss_dssp             CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEE
T ss_pred             CCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEE
Confidence            345799999999999 999999999999999 6666665  3  788999999999999999999 99999999999999


Q ss_pred             EecCCCC
Q 043634           90 ERASKPN   96 (121)
Q Consensus        90 ~~a~~~~   96 (121)
                      .++ .++
T Consensus       286 ~~a-~~k  291 (292)
T 2ghp_A          286 SLA-DKK  291 (292)
T ss_dssp             EEC-CCC
T ss_pred             EEe-cCC
Confidence            999 443

>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=99.65  E-value=1.1e-15  Score=99.11  Aligned_cols=76  Identities=21%  Similarity=0.413  Sum_probs=66.1

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhh----CCc-----cEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEE
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHY----GAS-----SVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVL   87 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~----G~~-----~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l   87 (121)
                      .+.++|||+|||+.+++++|+++|++|    |..     .+..+..+.++|||||+|.+.++|..|+ .+||..+.|+.|
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i   80 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   80 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETTTTEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCCCCEEEEEeCCHHHHHHHH-HhCCcEecCcee
Confidence            357899999999999999999999999    520     3554555667899999999999999999 899999999999


Q ss_pred             EEEecC
Q 043634           88 SVERAS   93 (121)
Q Consensus        88 ~v~~a~   93 (121)
                      .|.++.
T Consensus        81 ~v~~~~   86 (172)
T 2g4b_A           81 KIRRPH   86 (172)
T ss_dssp             EEECCS
T ss_pred             eecCCc
Confidence            999883

>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=99.65  E-value=7.7e-16  Score=99.82  Aligned_cols=75  Identities=21%  Similarity=0.465  Sum_probs=66.0

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CC--CcccEEEEEeCCHHHHHHHHHHhcCCeeC---CeEEE
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AG--RLRNCVFVDFGNEPLASQAQMQLNGLRFL---GKVLS   88 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~--~~~g~afv~f~~~~~a~~ai~~l~g~~i~---g~~l~   88 (121)
                      ..++|||+|||+.+++++|+++|++||. ..++++.   ++  .++|||||+|.+.++|..|+..|++..+.   ++.+.
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            3689999999999999999999999999 6666665   33  78999999999999999999999998876   57778


Q ss_pred             EEec
Q 043634           89 VERA   92 (121)
Q Consensus        89 v~~a   92 (121)
                      +.++
T Consensus        82 ~~~~   85 (175)
T 3nmr_A           82 MKPA   85 (175)
T ss_dssp             EEEC
T ss_pred             Eccc
Confidence            8777

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

Probab=99.64  E-value=2.6e-15  Score=91.16  Aligned_cols=77  Identities=17%  Similarity=0.170  Sum_probs=66.6

Q ss_pred             CCCccEEEecCCCC-----CCCHHHHHHHHhhhCC-ccEEEcc----CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCe
Q 043634           16 TENLVTLLIKHLPD-----AIPQDTLSRIFSHYGA-SSVRPCS----AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGK   85 (121)
Q Consensus        16 ~~~~~~l~V~nlp~-----~~~~~~L~~~f~~~G~-~~~~~~~----~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~   85 (121)
                      ..+.++|+|+|+..     .-++++|+..|++||. .++.++.    ++.++|+|||+|.+.++|.+|+..|||..++|+
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            34578999999963     2367999999999999 6676665    257799999999999999999999999999999


Q ss_pred             EEEEEec
Q 043634           86 VLSVERA   92 (121)
Q Consensus        86 ~l~v~~a   92 (121)
                      .|.|.++
T Consensus        85 ~i~v~~a   91 (105)
T 2pe8_A           85 VVKACFY   91 (105)
T ss_dssp             ECEEEEC
T ss_pred             EEEEEEc
Confidence            9999999

>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=99.63  E-value=1.4e-15  Score=102.29  Aligned_cols=76  Identities=13%  Similarity=0.145  Sum_probs=65.0

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCCc---cEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCe----EEE
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGAS---SVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGK----VLS   88 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~---~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~----~l~   88 (121)
                      .+.++|||+|||+.+++++|+++|++||..   +++++. .+..+|+|||+|.+.++|..|+..|||..|.|+    ++.
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~  200 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYT  200 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEE
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceE
Confidence            346789999999999999999999999982   455554 445569999999999999999999999999986    577


Q ss_pred             EEec
Q 043634           89 VERA   92 (121)
Q Consensus        89 v~~a   92 (121)
                      |+++
T Consensus       201 vk~~  204 (205)
T 3tyt_A          201 LKLC  204 (205)
T ss_dssp             CEEE
T ss_pred             EEec
Confidence            7765

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

Probab=99.63  E-value=8.2e-16  Score=101.69  Aligned_cols=75  Identities=20%  Similarity=0.361  Sum_probs=65.5

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-c--------cEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-S--------SVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~--------~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      ..++|||+|||+.+++++|+++|++||. .        .+..+..+.++|||||+|.+.++|..|+ .|||..++|+.|.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~   81 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   81 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEE
Confidence            4789999999999999999999999943 1        2554556677899999999999999999 8999999999999


Q ss_pred             EEecC
Q 043634           89 VERAS   93 (121)
Q Consensus        89 v~~a~   93 (121)
                      |.++.
T Consensus        82 v~~~~   86 (198)
T 2yh0_A           82 IRRPH   86 (198)
T ss_dssp             EECCC
T ss_pred             EeCCC
Confidence            99883

>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=99.63  E-value=2.8e-15  Score=104.50  Aligned_cols=75  Identities=17%  Similarity=0.281  Sum_probs=69.6

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +.++|||+|||+.+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|..|+..|+|..++|+.|.|.++
T Consensus        94 ~~~~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           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT  172 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            4689999999999999999999999999 6666654   7888999999999999999999999999999999999999

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

Probab=99.63  E-value=3e-15  Score=99.29  Aligned_cols=74  Identities=20%  Similarity=0.298  Sum_probs=67.3

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhC-C-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYG-A-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFL-GKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G-~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~-g~~l~v~~a   92 (121)
                      .+.++|||+|||..+++++|+++|++|| . ..++++..  .+|+|||+|.+.++|..|+..|||..++ |+.|+|.++
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a  194 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK--DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS  194 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST--TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEee
Confidence            4589999999999999999999999999 7 66666543  3689999999999999999999999999 999999999

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

Probab=99.63  E-value=1.4e-15  Score=100.95  Aligned_cols=73  Identities=22%  Similarity=0.338  Sum_probs=66.6

Q ss_pred             ccEEEecCCCC-CCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           19 LVTLLIKHLPD-AIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        19 ~~~l~V~nlp~-~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      +++|||+|||+ .+++++|+++|++||. ..++++...  +|||||+|.+.++|..|+..|||..+.|+.|.|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~--~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC--SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC--CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            58999999999 9999999999999999 666666532  7899999999999999999999999999999999994

>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=99.61  E-value=4.3e-15  Score=101.03  Aligned_cols=74  Identities=20%  Similarity=0.312  Sum_probs=66.6

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhC-C-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYG-A-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFL-GKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G-~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~-g~~l~v~~a   92 (121)
                      .+.++|||+|||+.+++++|+++|++|| . ..++++.  ..+|+|||+|.+.++|..|+..|||..++ |+.|+|.++
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a  225 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ--KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS  225 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS--SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEE--CCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEe
Confidence            3479999999999999999999999999 7 5555543  24789999999999999999999999999 999999999

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

Probab=99.60  E-value=5e-15  Score=103.59  Aligned_cols=78  Identities=22%  Similarity=0.313  Sum_probs=67.5

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhC-C-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYG-A-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G-~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ..++|||+|||+.+++++|+++|..|| . ..+.++.  .|.++|||||+|.+.++|..|+..|+|..+.|+.|.|.++ 
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 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS-  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC-
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC-
Confidence            478999999999999999999999999 7 6676665  5678899999999999999999999999999999999998 


Q ss_pred             CCC
Q 043634           94 KPN   96 (121)
Q Consensus        94 ~~~   96 (121)
                      .+.
T Consensus       195 ~~~  197 (292)
T 2ghp_A          195 NPL  197 (292)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            443

>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=99.56  E-value=2.9e-14  Score=98.67  Aligned_cols=76  Identities=25%  Similarity=0.380  Sum_probs=67.0

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhc-CCeeC---CeEEEEE
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLN-GLRFL---GKVLSVE   90 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~-g~~i~---g~~l~v~   90 (121)
                      +.++|||+|||+.+++++|+++|+.||. ..+.++.  +|.++|||||+|.+.++|.+|+..|| +..+.   ++.|.|.
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~  174 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVE  174 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEe
Confidence            4689999999999999999999999999 5666655  78889999999999999999999995 55555   8999999


Q ss_pred             ecC
Q 043634           91 RAS   93 (121)
Q Consensus        91 ~a~   93 (121)
                      ++.
T Consensus       175 ~~~  177 (261)
T 3sde_A          175 PME  177 (261)
T ss_dssp             ECC
T ss_pred             ecc
Confidence            983

>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=99.54  E-value=4.1e-15  Score=90.14  Aligned_cols=69  Identities=25%  Similarity=0.424  Sum_probs=59.4

Q ss_pred             ecCCCCCCCHHHHHHHH------------hhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           24 IKHLPDAIPQDTLSRIF------------SHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        24 V~nlp~~~~~~~L~~~f------------~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      +.|||+.+++++|++.|            ++||. ..+.++.  .+.++|||||+|.+.++|.+|+..|||..++|+.|+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            56777777887777666            99999 6777776  567899999999999999999999999999999999


Q ss_pred             EEec
Q 043634           89 VERA   92 (121)
Q Consensus        89 v~~a   92 (121)
                      |.++
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9886

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

Probab=99.53  E-value=7.3e-14  Score=100.35  Aligned_cols=77  Identities=14%  Similarity=0.260  Sum_probs=63.7

Q ss_pred             CCCCCCccEEEecC--CCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeC---Ce-
Q 043634           13 KQETENLVTLLIKH--LPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFL---GK-   85 (121)
Q Consensus        13 ~~~~~~~~~l~V~n--lp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~---g~-   85 (121)
                      .....|..+|||+|  |++.+++++|+++|++||. ..+.+.   .+||||||+|.+.++|.+|++.|||..+.   |+ 
T Consensus        12 ~~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~---~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           12 ETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP---PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             CCCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECC---TTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             eecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEe---CCCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            44566789999999  5899999999999999999 444333   25799999999999999999999999883   45 


Q ss_pred             -EEEEEec
Q 043634           86 -VLSVERA   92 (121)
Q Consensus        86 -~l~v~~a   92 (121)
                       .|.|.++
T Consensus        89 ~~ly~~~~   96 (345)
T 3tht_A           89 ITLYLNFV   96 (345)
T ss_dssp             EECEEEEC
T ss_pred             eEEEEEEe
Confidence             5677777

>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=99.52  E-value=8.7e-14  Score=84.39  Aligned_cols=76  Identities=18%  Similarity=0.247  Sum_probs=64.3

Q ss_pred             CCccEEEecCC--CCCCC--------HHHHHHHHhhhCC-ccEEEcc--C---CCcccEEEEEeCCHHHHHHHHHHhcCC
Q 043634           17 ENLVTLLIKHL--PDAIP--------QDTLSRIFSHYGA-SSVRPCS--A---GRLRNCVFVDFGNEPLASQAQMQLNGL   80 (121)
Q Consensus        17 ~~~~~l~V~nl--p~~~~--------~~~L~~~f~~~G~-~~~~~~~--~---~~~~g~afv~f~~~~~a~~ai~~l~g~   80 (121)
                      .|.+.|.+.|+  |..+.        +++|+..|++||. .++.++.  .   +.++|++||+|.+.++|.+|+..|||.
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            45788899998  43443        3689999999999 6677765  1   356899999999999999999999999


Q ss_pred             eeCCeEEEEEec
Q 043634           81 RFLGKVLSVERA   92 (121)
Q Consensus        81 ~i~g~~l~v~~a   92 (121)
                      .++|+.|+|.++
T Consensus        83 ~f~GR~i~v~~~   94 (105)
T 3v4m_A           83 KFANRVVVTKYC   94 (105)
T ss_dssp             EETTEECEEEEE
T ss_pred             EeCCCEEEEEEe
Confidence            999999999988

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

Probab=99.44  E-value=4.7e-13  Score=80.50  Aligned_cols=71  Identities=17%  Similarity=0.200  Sum_probs=57.4

Q ss_pred             ccEEEecCCC-------CCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           19 LVTLLIKHLP-------DAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        19 ~~~l~V~nlp-------~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ...|-|.-..       ..+++++|+.+|++||. ..+.++  +.++|||||+|.+.++|..|+..++  .+.|+.|+|.
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~--~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l~V~   85 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS--SKKPGTAVVEFATVKAAELAVQNEV--GLVDNPLKIS   85 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE--SSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBCEEE
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc--cCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeEEEE
Confidence            4455555443       46899999999999999 555555  5778999999999999999998754  4689999999


Q ss_pred             ecC
Q 043634           91 RAS   93 (121)
Q Consensus        91 ~a~   93 (121)
                      +++
T Consensus        86 ~a~   88 (100)
T 2d9o_A           86 WLE   88 (100)
T ss_dssp             CSS
T ss_pred             Ecc
Confidence            993

>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=99.43  E-value=9.8e-13  Score=81.31  Aligned_cols=75  Identities=20%  Similarity=0.326  Sum_probs=63.9

Q ss_pred             CccEEEecCCCC--CC---CHHHHHHHHhhhCC-ccEEEcc--C-----CCcccEEEEEeCCHHHHHHHHHHhcCCeeCC
Q 043634           18 NLVTLLIKHLPD--AI---PQDTLSRIFSHYGA-SSVRPCS--A-----GRLRNCVFVDFGNEPLASQAQMQLNGLRFLG   84 (121)
Q Consensus        18 ~~~~l~V~nlp~--~~---~~~~L~~~f~~~G~-~~~~~~~--~-----~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g   84 (121)
                      +.+.|++.|+-.  .+   -+++|+..|++||. .++.++.  .     +.++|++||+|.+.++|.+|+..|||..++|
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            578999999832  22   35899999999999 6676665  2     3567999999999999999999999999999


Q ss_pred             eEEEEEec
Q 043634           85 KVLSVERA   92 (121)
Q Consensus        85 ~~l~v~~a   92 (121)
                      +.|+|.++
T Consensus        99 R~i~v~~~  106 (118)
T 3ue2_A           99 RKVVAEVY  106 (118)
T ss_dssp             EECEEEEE
T ss_pred             cEEEEEEc
Confidence            99999988

>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=99.36  E-value=1.2e-11  Score=75.89  Aligned_cols=74  Identities=15%  Similarity=0.169  Sum_probs=61.3

Q ss_pred             CccEEEecCCCCCCC----------HHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeE
Q 043634           18 NLVTLLIKHLPDAIP----------QDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKV   86 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~----------~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~   86 (121)
                      +.+.|.+.|+=..-.          +++|+..|++||. .++.+... ..+|++||+|.+.++|.+|+..|||..++|+.
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~-~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~   84 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKN-SAQGNVYVKCPSIAAAIAAVNALHGRWFAGKM   84 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTT-CTTCCEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecC-CCcEEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            466788888733221          2589999999999 77776653 24899999999999999999999999999999


Q ss_pred             EEEEec
Q 043634           87 LSVERA   92 (121)
Q Consensus        87 l~v~~a   92 (121)
                      |+|.++
T Consensus        85 i~v~~~   90 (114)
T 3s6e_A           85 ITAAYV   90 (114)
T ss_dssp             CEEEEE
T ss_pred             EEEEEE
Confidence            999998

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

Probab=99.28  E-value=2.7e-11  Score=71.05  Aligned_cols=74  Identities=20%  Similarity=0.278  Sum_probs=58.5

Q ss_pred             CCccEEEecCCCC----CCCH----HHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEE
Q 043634           17 ENLVTLLIKHLPD----AIPQ----DTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVL   87 (121)
Q Consensus        17 ~~~~~l~V~nlp~----~~~~----~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l   87 (121)
                      +|..+|+|.-.+.    ++-.    .+|.+.|++||. ..++++.     +.+||+|.+.++|.+|+. |||..++|+.|
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~-----d~~fVtF~d~~sAlaAi~-mnG~~v~Gr~L   78 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVE-----DKMWVTFLEGSSALNVLS-LNGKELLNRTI   78 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECS-----SSEEEEESSHHHHHHGGG-GTTCEETTEEE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEec-----CCEEEEECChHHHHHHHh-cCCeEeCCeEE
Confidence            4577888887662    3333    679999999998 5555553     238999999999999997 99999999999


Q ss_pred             EEEecCCCC
Q 043634           88 SVERASKPN   96 (121)
Q Consensus        88 ~v~~a~~~~   96 (121)
                      +|..++..+
T Consensus        79 kV~lkt~dW   87 (91)
T 2dnr_A           79 TIALKSPSG   87 (91)
T ss_dssp             EEEECCCSS
T ss_pred             EEEeCCCCc
Confidence            999994334

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

Probab=99.26  E-value=4.2e-11  Score=74.08  Aligned_cols=78  Identities=18%  Similarity=0.069  Sum_probs=64.4

Q ss_pred             CCCCCCccEEEecCCCCC-CCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCC-HHHHHHHHHHhc--CCeeCCeEEE
Q 043634           13 KQETENLVTLLIKHLPDA-IPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGN-EPLASQAQMQLN--GLRFLGKVLS   88 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~-~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~-~~~a~~ai~~l~--g~~i~g~~l~   88 (121)
                      +....+++.|||+||++. ++.++|+.+|++||.  |..+.--.....|||.|.+ ..+|..|+..++  +..|.|..+.
T Consensus        12 ~~~~~~G~il~v~~l~~~~~sredLke~F~~~G~--V~~Vd~~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~   89 (121)
T 1owx_A           12 SLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGE--IKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   89 (121)
T ss_dssp             CCSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCC--EEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             cccccCCeEEEEecCCCCcCCHHHHHHHHHhcCC--EEEEEEecCCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEE
Confidence            344566999999999999 999999999999999  6555511122479999999 889999999995  6889999988


Q ss_pred             EEec
Q 043634           89 VERA   92 (121)
Q Consensus        89 v~~a   92 (121)
                      ++..
T Consensus        90 ~evL   93 (121)
T 1owx_A           90 WEVL   93 (121)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            8876

>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=99.10  E-value=2.7e-10  Score=67.12  Aligned_cols=70  Identities=17%  Similarity=0.320  Sum_probs=57.4

Q ss_pred             CCccEEEecCCCCC------CCH---HHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeE
Q 043634           17 ENLVTLLIKHLPDA------IPQ---DTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKV   86 (121)
Q Consensus        17 ~~~~~l~V~nlp~~------~~~---~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~   86 (121)
                      +|..+|+|.-++..      ..+   .+|.+.|.+||. ..++++..     -+||+|.+.++|.+||+ |+|..++|+.
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d-----~~fVtF~d~~sAl~AI~-ldG~~v~Gr~   86 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-----QMLVTFADSHSALSVLD-VDGMKVKGRA   86 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-----EEEEECSCSHHHHHHHH-GGGSEETTEE
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC-----cEEEEEcChHHHHHHHh-cCCeeeCCeE
Confidence            45788999888643      232   579999999998 66666532     39999999999999998 9999999999


Q ss_pred             EEEEec
Q 043634           87 LSVERA   92 (121)
Q Consensus        87 l~v~~a   92 (121)
                      |+|.+.
T Consensus        87 L~V~~k   92 (95)
T 1ufw_A           87 VKISGP   92 (95)
T ss_dssp             EEEECC
T ss_pred             EEEecc
Confidence            999876

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

Probab=98.94  E-value=2.5e-09  Score=72.14  Aligned_cols=62  Identities=21%  Similarity=0.268  Sum_probs=54.9

Q ss_pred             CCHHHHHHHHhhhCC-ccEEEcc-------CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           31 IPQDTLSRIFSHYGA-SSVRPCS-------AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        31 ~~~~~L~~~f~~~G~-~~~~~~~-------~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      -.+++|+..|++||. .++.++.       ++.++|++||+|.+.++|.+|+..|||..++|+.|.+.+.
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~  210 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVY  210 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEc
Confidence            345789999999999 6666654       3478899999999999999999999999999999999988

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

Probab=98.46  E-value=3.5e-06  Score=50.79  Aligned_cols=72  Identities=18%  Similarity=0.249  Sum_probs=60.6

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhh-----CC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHY-----GA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~-----G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ..++|-+-|||..+++..++.+..++     |. ..+.+. ..  -+.|+|+|.|...|-+|.-.|+|..|.|++|++.-
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~-pD--H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLV-SD--FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEE-TT--TTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEe-cC--CCceEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            37889999999999999999999999     76 333332 22  36899999999999999889999999999999874


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      .
T Consensus        97 v   97 (117)
T 2l9w_A           97 I   97 (117)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=1.9e-05  Score=46.53  Aligned_cols=54  Identities=17%  Similarity=0.223  Sum_probs=47.4

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHh
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQL   77 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l   77 (121)
                      .+.+++ +.|..+...||.++|+.||...|+++..    .-|||.|.+.+.|..|+..+
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~I~WidD----TsAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQISWIDD----TSAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEEET----TEEEEECSCHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEEEEEEcC----CeEEEEecCHHHHHHHHHhc
Confidence            677777 9999999999999999999866777763    48999999999999988765

>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=98.10  E-value=1.5e-05  Score=47.67  Aligned_cols=74  Identities=20%  Similarity=0.312  Sum_probs=60.4

Q ss_pred             CCccEEEecCCCCCC-CH----HHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           17 ENLVTLLIKHLPDAI-PQ----DTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~-~~----~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ..+++|+|.||+..+ ..    +.++.+|..|+. ....++.+   -....|.|.+.++|.+|-..||+..++|+.++|.
T Consensus         3 ~~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS---FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~Y   79 (104)
T 1wey_A            3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS---FKRVRINFSNPLSAADARLRLHKTEFLGKEMKLY   79 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT---TTEEEEECSSTTHHHHHHHTSTTSEETTEECEEE
T ss_pred             CCCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc---ceEEEEEeCChHHHHHHHHHhccceecCceeEEE
Confidence            347889999998864 32    567899999998 55555543   2367899999999999999999999999999999


Q ss_pred             ecC
Q 043634           91 RAS   93 (121)
Q Consensus        91 ~a~   93 (121)
                      ++.
T Consensus        80 Fgq   82 (104)
T 1wey_A           80 FAQ   82 (104)
T ss_dssp             CCC
T ss_pred             ecC
Confidence            983

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

Probab=97.77  E-value=0.00014  Score=42.54  Aligned_cols=65  Identities=15%  Similarity=0.267  Sum_probs=51.0

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc----CC-CcccEEEEEeCCHHHHHHHHHHhcCCeeCC
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS----AG-RLRNCVFVDFGNEPLASQAQMQLNGLRFLG   84 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~----~~-~~~g~afv~f~~~~~a~~ai~~l~g~~i~g   84 (121)
                      ++|-|++||+.++++++.+.++.... .....+.    .+ .....|||.|.+.+++..-.+.++|..+.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            57899999999999999999998776 3333333    11 223689999999999999889999987653

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

Probab=97.74  E-value=0.0004  Score=41.31  Aligned_cols=72  Identities=24%  Similarity=0.317  Sum_probs=55.3

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhh---hCCccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSH---YGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~---~G~~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ....+|.|.|||+.+.++.|+-+|..   -|.-.+..+. .+   +-|+|+|.+...+++.+.. ..+.|++..|.|...
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~---~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~   81 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG---CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPA   81 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEEC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcC
Confidence            44889999999999999999999986   2332233333 22   6899999999999988853 356888888888654

>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=97.73  E-value=3.2e-05  Score=45.72  Aligned_cols=55  Identities=16%  Similarity=0.223  Sum_probs=46.4

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhc
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLN   78 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~   78 (121)
                      .+.++| +.|..+...||.++|+.||...|+++..    .-|||.|.+.+.|..|+..+.
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fggv~I~WidD----TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQISWIDD----TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSEEEEEEEEET----TEEEEEEEEECHHHHHHHHHT
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccCCEEEEEEcC----CeEEEEecCHHHHHHHHHhcc
Confidence            466777 9999999999999999999855677653    489999999999999988663

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.12  E-value=0.0037  Score=38.14  Aligned_cols=70  Identities=16%  Similarity=0.175  Sum_probs=54.6

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCC-eEEEEEec
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLG-KVLSVERA   92 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g-~~l~v~~a   92 (121)
                      ..+-|.|-+.|+.. .+.+...|.+||. .....   .....+-.|.|.+..+|++|+. .||..++| -.|-|...
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~---~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM---SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE---CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc---CCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            37889999999986 5668889999999 33333   1224699999999999999995 69999985 56777765

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

Probab=96.70  E-value=0.0018  Score=38.15  Aligned_cols=64  Identities=19%  Similarity=0.288  Sum_probs=47.1

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc--CC------CcccEEEEEeCCHHHHHHHHHHhcCCeeCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS--AG------RLRNCVFVDFGNEPLASQAQMQLNGLRFLG   84 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~--~~------~~~g~afv~f~~~~~a~~ai~~l~g~~i~g   84 (121)
                      +-+|-|+.||+.+|++++.+.++..-.  +.+..  .|      .....|||.|.+.++...=.+.++|..+.+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~--~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPA--HDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSS--EEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCc--cceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            678999999999999987766665433  32222  11      123578999999999988888999977643

>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=95.84  E-value=0.0097  Score=37.34  Aligned_cols=32  Identities=9%  Similarity=-0.013  Sum_probs=26.0

Q ss_pred             EEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcC
Q 043634           48 VRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNG   79 (121)
Q Consensus        48 ~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g   79 (121)
                      ++++. ....+|||||+|.+.++|++|+..+++
T Consensus         3 ~kl~ln~~~~~G~~fV~f~~~~~A~~al~~~~~   35 (158)
T 2kn4_A            3 YKLILNGKTLKGETTTEAVDAATAEKVFKQYAN   35 (158)
T ss_dssp             EEEEEECSSCEEEEEEECSSHHHHHHHHHHHHH
T ss_pred             EEEEecCccccchhHHHHHHHHhHHHHHHhhcc
Confidence            34444 446789999999999999999988875

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.63  E-value=0.065  Score=33.15  Aligned_cols=72  Identities=18%  Similarity=0.237  Sum_probs=51.6

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-cc-EEEcc---------------CC-CcccEEEEEeCCHHHHHHHHHHhcCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SS-VRPCS---------------AG-RLRNCVFVDFGNEPLASQAQMQLNGL   80 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~-~~~~~---------------~~-~~~g~afv~f~~~~~a~~ai~~l~g~   80 (121)
                      .+.|.|=+.|+... ..+.+.|++||. .. .....               .+ ....+-.|+|.+..+|.+|+ ..||.
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL-~~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDAL-LENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHH-TTTTC
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHH-HhCCe
Confidence            35566777766655 557788999999 32 11110               00 12468899999999999999 57999


Q ss_pred             eeCCeEEEEEec
Q 043634           81 RFLGKVLSVERA   92 (121)
Q Consensus        81 ~i~g~~l~v~~a   92 (121)
                      .++|..|.|...
T Consensus        85 ii~G~mIGV~Py   96 (132)
T 3p3d_A           85 VFNGVLLGVIPY   96 (132)
T ss_dssp             EETTEECEEEEC
T ss_pred             EeCcEEEEEEEC
Confidence            999998888877

>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=95.38  E-value=0.14  Score=38.48  Aligned_cols=55  Identities=16%  Similarity=0.226  Sum_probs=46.2

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhc
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLN   78 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~   78 (121)
                      +..++|+ +|..+...+|.++|+.||...|+++..    ..|||.|.+.+.|..++..+.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v~V~widd----t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNIQISWIDD----TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCCEEEECSS----SEEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCEEEEEEcC----CeEEEEECCHHHHHHHHHHHH
Confidence            5677777 889999999999999999855666543    479999999999999988874

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

Probab=95.31  E-value=0.0071  Score=37.77  Aligned_cols=38  Identities=16%  Similarity=0.064  Sum_probs=34.8

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHh-cCCeeCCeEEEEEec
Q 043634           54 GRLRNCVFVDFGNEPLASQAQMQL-NGLRFLGKVLSVERA   92 (121)
Q Consensus        54 ~~~~g~afv~f~~~~~a~~ai~~l-~g~~i~g~~l~v~~a   92 (121)
                      ...+|+++++|.+.+.|++|+..+ ||..++| .+.+.++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a   48 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDA   48 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETT
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccc
Confidence            355799999999999999999999 9999999 9999987

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.24  E-value=0.018  Score=42.91  Aligned_cols=53  Identities=19%  Similarity=0.302  Sum_probs=36.5

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHH
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQM   75 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~   75 (121)
                      +.|+|. .|..+++.+|.++|++||. .++.+-..  ...|+.|+|.+.+++..++.
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~--~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES--FGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS--SSEEEEEECC---CCHHHHS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc--CCeEEEEEeCCHHHHHHHHh
Confidence            789997 7999999999999999999 44443332  22699999999988876653

---

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	121
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-09
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	6e-09
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-08
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-08
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	4e-08
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-08
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	7e-08
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	7e-08
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	9e-08
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-07
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-07
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-07
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-07
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	8e-07
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-06
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-06
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-06
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-06
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-06
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	3e-06
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-06
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-06
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	5e-06
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	5e-06
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	6e-06
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	9e-06
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-05
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-05
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-05
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-05
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	4e-05
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	7e-05
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	8e-05
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-05
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-04
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	5e-04
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	5e-04
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	6e-04
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	0.001

>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 = 49.2 bits (117), Expect = 2e-09
 Identities = 20/96 (20%), Positives = 37/96 (38%), Gaps = 2/96 (2%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNG 79
            L I++LP  I  + +  IF  YG    +R  +    R   +V + +   A  A   L+G
Sbjct: 9   ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSG 68

Query: 80  LRFLGKVLSVERA-SKPNEENKHKHFEAQSISSMKE 114
                + L V    +    +      + + +  +KE
Sbjct: 69  FNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKE 104

>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 = 48.5 bits (115), Expect = 3e-09
 Identities = 21/94 (22%), Positives = 34/94 (36%), Gaps = 6/94 (6%)

Query: 10  PQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSA----GRLRNCVFVDFG 65
            + K+E E    L I  L     +++L   +  +G  +           R R   FV F 
Sbjct: 11  ERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFS 70

Query: 66  NEPLASQAQMQLNGLRFLGKVLSVERASKPNEEN 99
           +      A M        G+V+  +RA    EE+
Sbjct: 71  SMAEVDAA-MAARPHSIDGRVVEPKRA-VAREES 102

>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 = 47.3 bits (112), Expect = 6e-09
 Identities = 20/95 (21%), Positives = 39/95 (41%), Gaps = 7/95 (7%)

Query: 9  GPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVDF 64
          GP    E     T+ +  L + + +  L  +F   G        +    G+ +   FV+F
Sbjct: 1  GPI--SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 58

Query: 65 GNEPLASQAQMQLNGLRFLGKVLSVERASKPNEEN 99
           +E  A  A   ++ ++  GK + V +A   + +N
Sbjct: 59 LSEEDADYAIKIMDMIKLYGKPIRVNKA-SAHNKN 92

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

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

 Score = 45.7 bits (108), Expect = 2e-08
 Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 22 LLIKHLPDAIPQDTLSRIFSHYGASS---VRPCSAGRLRNCVFVDFGNEPLASQAQMQLN 78
          LL+ +L   +    +  +F+ +G      V    +GR      V F  +  A +A  Q N
Sbjct: 3  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 79 GLRFLGKVLSVERAS 93
          G+   G+ ++++  +
Sbjct: 63 GVPLDGRPMNIQLVT 77

>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 = 46.1 bits (109), Expect = 2e-08
 Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 4/81 (4%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLR----NCVFVDFGNEPLASQAQMQ 76
          TL + +L     ++ +  +FS  G          +++       FV++ +   A  A   
Sbjct: 9  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 77 LNGLRFLGKVLSVERASKPNE 97
          +NG R   +++  +  +   E
Sbjct: 69 INGTRLDDRIIRTDWDAGFKE 89

>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 = 45.4 bits (107), Expect = 4e-08
 Identities = 16/79 (20%), Positives = 35/79 (44%), Gaps = 2/79 (2%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGL 80
           L +++L  +  ++ + + F++            ++R+  FV F N   A +A   LNG 
Sbjct: 10 ILYVRNLMLSTSEEMIEKEFNNI--KPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGK 67

Query: 81 RFLGKVLSVERASKPNEEN 99
             G  + V  A   ++++
Sbjct: 68 VLDGSPIEVTLAKPVDKDS 86

>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 = 45.0 bits (106), Expect = 4e-08
 Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 5/79 (6%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQ 76
           L++ +LP  +    L  +F   G       +R    G      FVDF +E  + +A   
Sbjct: 4  NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 77 LNGLRFLGKVLSVERASKP 95
          LNG+    K L V  A +P
Sbjct: 64 LNGITVRNKRLKVSYA-RP 81

>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 = 44.6 bits (105), Expect = 7e-08
 Identities = 20/82 (24%), Positives = 30/82 (36%), Gaps = 7/82 (8%)

Query: 22 LLIKHLPDAIPQDTLSRIFSHYGA-------SSVRPCSAGRLRNCVFVDFGNEPLASQAQ 74
          L IK+L  +  ++TL  +FS  GA                      FV++     A +A 
Sbjct: 1  LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 75 MQLNGLRFLGKVLSVERASKPN 96
           QL G    G  L V  + +  
Sbjct: 61 KQLQGHTVDGHKLEVRISERAT 82

>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 = 44.6 bits (105), Expect = 7e-08
 Identities = 19/83 (22%), Positives = 29/83 (34%), Gaps = 5/83 (6%)

Query: 14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSA----GRLRNCVFVDFGNEPL 69
          +E E L  L I  L      ++L   F  +G  +           R R   FV +     
Sbjct: 1  KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 70 ASQAQMQLNGLRFLGKVLSVERA 92
             A M     +  G+V+  +RA
Sbjct: 61 VDAA-MNARPHKVDGRVVEPKRA 82

>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 = 44.1 bits (104), Expect = 9e-08
 Identities = 15/78 (19%), Positives = 27/78 (34%), Gaps = 4/78 (5%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQ 76
          +L +  L   + +  L   FS  G        R     R     +V+F     A +A   
Sbjct: 2  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 77 LNGLRFLGKVLSVERASK 94
          +N     GK + +  + +
Sbjct: 62 MNFDVIKGKPVRIMWSQR 79

>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 = 43.9 bits (103), Expect = 1e-07
 Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 5/80 (6%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQ 76
           L++ +LP  + Q+    +F   G       VR    G+     FV++ +   A +A   
Sbjct: 4  NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 77 LNGLRFLGKVLSVERASKPN 96
          LNGLR   K + V  A +P+
Sbjct: 64 LNGLRLQTKTIKVSYA-RPS 82

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (102), Expect = 2e-07
 Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 3/70 (4%)

Query: 24  IKHLPDAIPQDTLSRIFSHYGA-SSVRPC--SAGRLRNCVFVDFGNEPLASQAQMQLNGL 80
           ++   D   ++  + +   YG    +  C      L   V+V F  E  A +A + LN  
Sbjct: 32  MQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNR 91

Query: 81  RFLGKVLSVE 90
            F G+ +  E
Sbjct: 92  WFNGQPIHAE 101

>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 = 43.3 bits (102), Expect = 3e-07
 Identities = 21/91 (23%), Positives = 37/91 (40%), Gaps = 7/91 (7%)

Query: 8  SGPQNKQETENLVTLLIKHL-PDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGN 66
          SG  + +   +   + I +L    + +  +  IFS YG    +       +   FV + N
Sbjct: 6  SGKTDPRSMNS--RVFIGNLNTLVVKKSDVEAIFSKYG----KIVGCSVHKGFAFVQYVN 59

Query: 67 EPLASQAQMQLNGLRFLGKVLSVERASKPNE 97
          E  A  A    +G    G+VL +  A++P  
Sbjct: 60 ERNARAAVAGEDGRMIAGQVLDINLAAEPKV 90

>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 = 42.6 bits (100), Expect = 4e-07
 Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASS-----VRPCSAGRLRNCVFVDFGNEPLASQAQM 75
           +L++++P    Q  +  +FS +G         +    G  R   FVDF  +  A +A  
Sbjct: 10 KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 69

Query: 76 QL-NGLRFLGKVLSVERASK 94
           L +     G+ L +E A  
Sbjct: 70 ALCHSTHLYGRRLVLEWADS 89

>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 = 41.9 bits (98), Expect = 8e-07
 Identities = 25/78 (32%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQ 76
           L + +LP  I  D L  IF  YG     + +R    GR R   FV +     A +A   
Sbjct: 8  NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 77 LNGLRFLG--KVLSVERA 92
          LN +   G  + LSV  A
Sbjct: 68 LNNVIPEGGSQPLSVRLA 85

>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 = 41.2 bits (96), Expect = 1e-06
 Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 4/80 (5%)

Query: 22 LLIKHLPDAIPQDTL----SRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQL 77
          L I  LP+ +  D +    +        + V+  + G  +   F ++ +  +  QA   L
Sbjct: 4  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 78 NGLRFLGKVLSVERASKPNE 97
          NG++   K L V+RAS   +
Sbjct: 64 NGMQLGDKKLLVQRASVGAK 83

>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 = 41.6 bits (97), Expect = 1e-06
 Identities = 17/83 (20%), Positives = 33/83 (39%), Gaps = 1/83 (1%)

Query: 10 PQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPL 69
          P   ++     TLL K+L   I +D L  +F             G+ +   +++F +E  
Sbjct: 7  PCTSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-EIRLVSQDGKSKGIAYIEFKSEAD 65

Query: 70 ASQAQMQLNGLRFLGKVLSVERA 92
          A +   +  G    G+ +S+   
Sbjct: 66 AEKNLEEKQGAEIDGRSVSLYYT 88

>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 = 41.2 bits (96), Expect = 2e-06
 Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 3/80 (3%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGA--SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLN 78
           + IK+L  +I    L   FS +G   S    C     +   FV F  +  A +A  ++N
Sbjct: 10 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 69

Query: 79 GLRFLGKVLSVERASKPNEE 98
          G+    + + V R  K  +E
Sbjct: 70 GMLLNDRKVFVGRF-KSRKE 88

>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 = 41.1 bits (96), Expect = 2e-06
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 3/85 (3%)

Query: 13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQ 72
           Q +    T+    +   +    + + FS +G   +        +   FV F     A+ 
Sbjct: 12 NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFG--QIMEIRVFPEKGYSFVRFSTHESAAH 69

Query: 73 AQMQLNGLRFLGKVLSVERA-SKPN 96
          A + +NG    G V+        P+
Sbjct: 70 AIVSVNGTTIEGHVVKCYWGKESPD 94

>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 = 40.7 bits (95), Expect = 2e-06
 Identities = 13/75 (17%), Positives = 23/75 (30%), Gaps = 5/75 (6%)

Query: 22 LLIKHLPDAIPQDTLSRIFSHYGASSVRPCSA----GRLRNCVFVDFGNEPLASQAQMQL 77
          + I  L     Q+ L   F  +G              R R   FV F ++    +  +  
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-LAQ 61

Query: 78 NGLRFLGKVLSVERA 92
          +      K +  + A
Sbjct: 62 SRHELDSKTIDPKVA 76

>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 = 40.8 bits (95), Expect = 2e-06
 Identities = 18/92 (19%), Positives = 40/92 (43%), Gaps = 7/92 (7%)

Query: 10 PQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRL----RNCVFVDFG 65
          P  + +     T+ + +L +   +  L  +F  +G+ S    +  +     +   F+ F 
Sbjct: 1  PNRRADDNA--TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFH 58

Query: 66 NEPLASQAQMQLNGLRFLGKVLSVERASKPNE 97
              A++A   ++G  +   +L+VE A KP+ 
Sbjct: 59 RREDAARAIAGVSGFGYDHLILNVEWA-KPST 89

>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 = 40.5 bits (94), Expect = 3e-06
 Identities = 13/72 (18%), Positives = 22/72 (30%), Gaps = 3/72 (4%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGL 80
           +L+K+LP       +  +   Y           R      ++      A  A    +  
Sbjct: 7  GILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLN---GEQAQNAIQMFHQY 63

Query: 81 RFLGKVLSVERA 92
           F GK L V+  
Sbjct: 64 SFRGKDLIVQLQ 75

>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 = 40.9 bits (95), Expect = 3e-06
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 4/84 (4%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRN----CVFVDFGNEPLASQAQMQ 76
            L +++L     ++ L ++FS YG  S        L        FV F     A +A  +
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 77  LNGLRFLGKVLSVERASKPNEENK 100
           ++G  F G++L V  ++   E ++
Sbjct: 70  VDGQVFQGRMLHVLPSTIKKEASQ 93

>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 = 40.1 bits (93), Expect = 3e-06
 Identities = 17/81 (20%), Positives = 32/81 (39%), Gaps = 5/81 (6%)

Query: 22 LLIKHLPDAIPQDTLSRIFSHYGASS-----VRPCSAGRLRNCVFVDFGNEPLASQAQMQ 76
          + I +L   I +  L   FS +G        +R    G  +   F++F +   +  A   
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 77 LNGLRFLGKVLSVERASKPNE 97
          +NG     + ++V  A K + 
Sbjct: 61 MNGQYLCNRPITVSYAFKKDS 81

>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 = 39.7 bits (92), Expect = 5e-06
 Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 4/82 (4%)

Query: 12 NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASS----VRPCSAGRLRNCVFVDFGNE 67
          N+   +    L +  L     +  L  +FS YG  +    V    + R R   FV F N 
Sbjct: 2  NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 61

Query: 68 PLASQAQMQLNGLRFLGKVLSV 89
            A +A+ + NG+   G+ + V
Sbjct: 62 DDAKEAKERANGMELDGRRIRV 83

>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 = 39.7 bits (92), Expect = 5e-06
 Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 5/92 (5%)

Query: 8  SGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA--SSVRPCSAGRLRNCVFVDFG 65
          SG    + T     L + ++P       L ++F  +G         +    +   FV F 
Sbjct: 2  SGNSESKSTPK--RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFE 59

Query: 66 NEPLASQAQMQLNGLRFLGKVLSVERA-SKPN 96
          N   A +A+ +L+G    G+ + V  A ++  
Sbjct: 60 NSADADRAREKLHGTVVEGRKIEVNNATARVM 91

>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 = 39.3 bits (91), Expect = 6e-06
 Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 5/84 (5%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRL----RNCVFVDFGNEPLASQAQMQ 76
            L +  L     + +L ++FS YG  S       R     R   FV F N   A  A M 
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 77  LNGLRFLGKVLSVERASKPNEENK 100
           +NG    G+ + V++A   + +N+
Sbjct: 67  MNGKSVDGRQIRVDQA-GKSSDNR 89

>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 = 39.3 bits (91), Expect = 9e-06
 Identities = 17/82 (20%), Positives = 27/82 (32%), Gaps = 5/82 (6%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGA----SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQ 76
           L +  L + +    L   F  +G              + R   FV+F     A+ A   
Sbjct: 7  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 77 LNGLRFLGKVLSVERASKPNEE 98
          +N     G+ + V  A KP   
Sbjct: 67 MNESELFGRTIRVNLA-KPMRI 87

>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 = 38.6 bits (89), Expect = 1e-05
 Identities = 11/75 (14%), Positives = 28/75 (37%), Gaps = 5/75 (6%)

Query: 22 LLIKHLPDAIPQDTLSRIFSHYGASS----VRPCSAGRLRNCVFVDFGNEPLASQAQMQL 77
          + +  L      + +   F  +G       +   +  R R   FV F +E +  +   ++
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV-CEI 60

Query: 78 NGLRFLGKVLSVERA 92
          +      K++  ++A
Sbjct: 61 HFHEINNKMVECKKA 75

>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 = 38.1 bits (88), Expect = 2e-05
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 4/79 (5%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNG- 79
           L I +L  A+  D L ++F                    FVD+ ++  A +A   L+G 
Sbjct: 3  KLYIGNLSPAVTADDLRQLFGDRK--LPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGK 60

Query: 80 LRFLGKVLSVERASKPNEE 98
          +   GK++ V+ +    + 
Sbjct: 61 VELHGKIMEVDYS-VSKKL 78

>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 = 38.1 bits (88), Expect = 2e-05
 Identities = 15/80 (18%), Positives = 26/80 (32%), Gaps = 3/80 (3%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGL 80
            + +      + +D L   FS YG   +        R   FV F ++ +A         L
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYG-DVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDL 63

Query: 81  RFLGKVLSVERASKPNEENK 100
              G  + +  A   +  N 
Sbjct: 64  IIKGISVHISNAEPKHNSNS 83

>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 = 37.7 bits (87), Expect = 3e-05
 Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRL----RNCVFVDFGNEPLASQAQMQ 76
           L +  LP  + Q  L ++FS YG          ++    R   F+ F     A +A   
Sbjct: 8  NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 77 LNGLRFLG--KVLSVERA 92
          LNG +  G  + ++V+ A
Sbjct: 68 LNGQKPSGATEPITVKFA 85

>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 = 37.8 bits (87), Expect = 4e-05
 Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 7/86 (8%)

Query: 21  TLLIKHLPDAIPQDT-----LSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQM 75
            L+     D +  ++        +F  Y           +    V ++F N   A+ A++
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDK--DTTFQYFKSFKRVRINFSNPLSAADARL 64

Query: 76  QLNGLRFLGKVLSVERASKPNEENKH 101
           +L+   FLGK + +  A   +  + H
Sbjct: 65  RLHKTEFLGKEMKLYFAQTLHIGSSH 90

>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 = 37.0 bits (85), Expect = 7e-05
 Identities = 12/93 (12%), Positives = 32/93 (34%), Gaps = 11/93 (11%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYGASSV------RPCSAGRLRNCVFVDFGNEPLASQA- 73
            L I  +P    ++ +    +      +            + R   FV++ +   A+ A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 74  -QMQLNGLRFLGKVLSVERA---SKPNEENKHK 102
            ++    ++  G  ++V+ A      +E+    
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 95

>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 = 36.1 bits (83), Expect = 8e-05
 Identities = 10/75 (13%), Positives = 21/75 (28%), Gaps = 5/75 (6%)

Query: 22 LLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCV----FVDFGNEPLASQAQMQL 77
          + +  L    P++ +   F  +G             N      F+ F  E    +  M+ 
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI-MEK 60

Query: 78 NGLRFLGKVLSVERA 92
                     ++ A
Sbjct: 61 KYHNVGLSKCEIKVA 75

>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 = 36.1 bits (83), Expect = 9e-05
 Identities = 16/75 (21%), Positives = 24/75 (32%), Gaps = 5/75 (6%)

Query: 22 LLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRL----RNCVFVDFGNEPLASQAQMQL 77
          + I  L     +  L   FS +G           +    R   FV F       +  M  
Sbjct: 2  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKV-MDQ 60

Query: 78 NGLRFLGKVLSVERA 92
             +  GKV+  +RA
Sbjct: 61 KEHKLNGKVIDPKRA 75

>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 = 35.9 bits (82), Expect = 1e-04
 Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 10/82 (12%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASS---------VRPCSAGRLRNCVFVDFGNEPLAS 71
           L + ++P  I ++ +   F+               V      + +N  F++F +    +
Sbjct: 3  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 72 QAQMQLNGLRFLGKVLSVERAS 93
          QA M  +G+ F G+ L + R  
Sbjct: 63 QA-MAFDGIIFQGQSLKIRRPH 83

>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 = 35.4 bits (81), Expect = 3e-04
 Identities = 19/95 (20%), Positives = 33/95 (34%), Gaps = 7/95 (7%)

Query: 10  PQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYG----ASSVRPCSAGRLRNCVFVDFG 65
                E  +  T+    L   I    L   FS  G       +   ++ R +   +V+F 
Sbjct: 9   DNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC 68

Query: 66  NEPLASQAQMQLNGLRFLGKVLSVERASKPNEENK 100
                    + L G R LG  + V+ +    E+N+
Sbjct: 69  EIQSV-PLAIGLTGQRLLGVPIIVQASQA--EKNR 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 = 34.9 bits (80), Expect = 5e-04
 Identities = 10/60 (16%), Positives = 19/60 (31%)

Query: 33 QDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA 92
          ++ L    S +G                 V F +   A      L+G  F G+ ++ +  
Sbjct: 33 REDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAW 92

>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 = 34.5 bits (78), Expect = 5e-04
 Identities = 19/88 (21%), Positives = 31/88 (35%), Gaps = 4/88 (4%)

Query: 8  SGPQNKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSA---GRLRNCVFVDF 64
          S      E+     L I +L        L    S   A +         G  R   +VDF
Sbjct: 2  SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDF 61

Query: 65 GNEPLASQAQMQLNGLRFLGKVLSVERA 92
           +     +A ++L GL+  G  + +E+ 
Sbjct: 62 ESAEDLEKA-LELTGLKVFGNEIKLEKP 88

>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 = 34.8 bits (79), Expect = 6e-04
 Identities = 19/91 (20%), Positives = 30/91 (32%), Gaps = 12/91 (13%)

Query: 21  TLLIKHLPDAIPQDTLSRIFSHYG------------ASSVRPCSAGRLRNCVFVDFGNEP 68
            + ++ L D++  D L+  F   G                     G+ +    V + + P
Sbjct: 10  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 69

Query: 69  LASQAQMQLNGLRFLGKVLSVERASKPNEEN 99
            A  A    +G  F G  L V  A K    N
Sbjct: 70  TAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 100

>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 = 33.2 bits (75), Expect = 0.001
 Identities = 13/76 (17%), Positives = 22/76 (28%), Gaps = 5/76 (6%)

Query: 21 TLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRL----RNCVFVDFGNEPLASQAQMQ 76
           + +  + +   +  L   F  YG   V      R     R   FV F +   +    + 
Sbjct: 4  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD-SVDKIVI 62

Query: 77 LNGLRFLGKVLSVERA 92
                 G    V +A
Sbjct: 63 QKYHTVNGHNCEVRKA 78

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	121
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.9
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.89
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.89
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.89
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.89
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.89
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.88
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.88
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.88
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.88
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.88
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.88
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.88
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.88
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.88
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.87
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.87
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.87
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.87
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.87
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.87
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.87
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.86
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.86
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.86
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.86
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.86
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.86
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.86
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.86
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.85
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.85
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.85
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.85
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.85
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.85
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.85
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.84
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.84
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.84
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.84
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.84
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.84
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.83
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.83
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.83
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.83
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.83
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.83
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.83
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.83
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.82
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.82
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.82
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.82
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.81
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.81
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.81
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.8
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.8
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.8
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.8
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.8
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.79
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.79
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.79
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.79
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.79
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.78
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.77
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.76
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.76
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.74
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.72
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.71
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.7
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	99.63
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.62
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.58
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.55
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.53
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.52
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.36
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.84
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.81
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.63
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	97.22

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=2.1e-23  Score=125.12  Aligned_cols=81  Identities=23%  Similarity=0.338  Sum_probs=73.2

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +++++|||+|||+.+++++|+++|++||. .+++++.   +|.++|||||+|.+.++|..|+..|||..|+|+.|+|+++
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            45789999999999999999999999999 6676664   7889999999999999999999999999999999999999


Q ss_pred             CCCCcc
Q 043634           93 SKPNEE   98 (121)
Q Consensus        93 ~~~~~~   98 (121)
                       .++.+
T Consensus        96 -~~k~~  100 (102)
T d2cpza1          96 -RSKND  100 (102)
T ss_dssp             -CCSCC
T ss_pred             -CCCCC
Confidence             55543

>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=99.89  E-value=3.2e-23  Score=119.60  Aligned_cols=76  Identities=29%  Similarity=0.428  Sum_probs=70.3

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK   94 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   94 (121)
                      +++|||+|||+.+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|.+|+..|||..++|+.|+|+++ +
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a-~   80 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYA-R   80 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC-C
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEc-C
Confidence            578999999999999999999999999 6666665   7888999999999999999999999999999999999999 5


Q ss_pred             C
Q 043634           95 P   95 (121)
Q Consensus        95 ~   95 (121)
                      |
T Consensus        81 p   81 (82)
T d1b7fa1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.89  E-value=3.6e-23  Score=122.15  Aligned_cols=80  Identities=20%  Similarity=0.300  Sum_probs=72.6

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+.++|||+|||..+++++|+++|++||. .+++++.   +|.++|||||+|.+.++|+.|+..|||..++|+.|+|.+|
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34689999999999999999999999999 6677665   7889999999999999999999999999999999999999


Q ss_pred             CCCCc
Q 043634           93 SKPNE   97 (121)
Q Consensus        93 ~~~~~   97 (121)
                       .++.
T Consensus        87 -~~~~   90 (93)
T d1x5ua1          87 -SAHN   90 (93)
T ss_dssp             -TTTS
T ss_pred             -CCCC
Confidence             5543

>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=99.89  E-value=6e-23  Score=120.01  Aligned_cols=77  Identities=18%  Similarity=0.366  Sum_probs=70.8

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ...+++|||+|||+.+++++|+++|++||. .+++++.   +|.++|||||+|.+.++|..|+..|||..++|+.|+|++
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            345789999999999999999999999999 6676665   788999999999999999999999999999999999999


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      |
T Consensus        84 a   84 (88)
T d1rk8a_          84 C   84 (88)
T ss_dssp             S
T ss_pred             e
Confidence            9

>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=99.89  E-value=7.4e-23  Score=118.00  Aligned_cols=76  Identities=28%  Similarity=0.456  Sum_probs=70.1

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK   94 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   94 (121)
                      .++|||+|||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|..|+..|||..++|+.|+|.+| +
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~A-k   80 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYA-R   80 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC-C
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe-e
Confidence            468999999999999999999999999 6676664   6788999999999999999999999999999999999999 5


Q ss_pred             C
Q 043634           95 P   95 (121)
Q Consensus        95 ~   95 (121)
                      |
T Consensus        81 P   81 (82)
T d1fxla1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.89  E-value=6.2e-23  Score=120.40  Aligned_cols=80  Identities=23%  Similarity=0.436  Sum_probs=72.9

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+.++|||+|||..+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|..|+..|||..++|+.|+|+++
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            34789999999999999999999999999 6666665   6889999999999999999999999999999999999999


Q ss_pred             CCCCc
Q 043634           93 SKPNE   97 (121)
Q Consensus        93 ~~~~~   97 (121)
                       +|+.
T Consensus        86 -kp~~   89 (90)
T d2cq0a1          86 -KPST   89 (90)
T ss_dssp             -SCCC
T ss_pred             -eCCC
Confidence             6654

>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=99.88  E-value=1.9e-22  Score=119.01  Aligned_cols=77  Identities=17%  Similarity=0.246  Sum_probs=71.0

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ..+++|||+|||+.+++++|+++|++||. .++.++.   ++.++|||||+|.+.++|..|+..|||..++|+.|+|.++
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34789999999999999999999999999 6676665   7888999999999999999999999999999999999999


Q ss_pred             C
Q 043634           93 S   93 (121)
Q Consensus        93 ~   93 (121)
                      .
T Consensus        85 ~   85 (93)
T d1h2vz_          85 A   85 (93)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.88  E-value=1.4e-22  Score=118.62  Aligned_cols=77  Identities=22%  Similarity=0.345  Sum_probs=71.6

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK   94 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   94 (121)
                      .++|||+|||+.+++++|+++|++||. .+++++.   +|.++|||||+|.+.++|..|+..|||..++|+.|+|.++ .
T Consensus         5 ~~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           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA-K   83 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC-C
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe-C
Confidence            679999999999999999999999999 7777775   6889999999999999999999999999999999999999 5


Q ss_pred             CC
Q 043634           95 PN   96 (121)
Q Consensus        95 ~~   96 (121)
                      |+
T Consensus        84 p~   85 (89)
T d2cqba1          84 PM   85 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.88  E-value=2.9e-22  Score=119.36  Aligned_cols=79  Identities=23%  Similarity=0.355  Sum_probs=71.9

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...++|||+|||+.+++++|+++|.+||. ..++++.   ++.++|||||+|.+.++|..|+..||+..|+|+.|+|.++
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            44788999999999999999999999999 6676665   7888999999999999999999999999999999999999


Q ss_pred             CCCC
Q 043634           93 SKPN   96 (121)
Q Consensus        93 ~~~~   96 (121)
                       .++
T Consensus        86 -~~~   88 (99)
T d1whwa_          86 -TIK   88 (99)
T ss_dssp             -CCC
T ss_pred             -CCC
Confidence             443

>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=5.4e-22  Score=117.40  Aligned_cols=82  Identities=22%  Similarity=0.299  Sum_probs=72.6

Q ss_pred             CCCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           12 NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        12 ~~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ..+...++++|||+|||+.+++++|+++|++||. ..+.+...+..++||||+|.+.++|..||..|||..|+|+.|+|+
T Consensus         7 ~~p~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~   86 (95)
T d1x4aa1           7 RGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   86 (95)
T ss_dssp             SCCCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3344566889999999999999999999999999 555655566778999999999999999999999999999999999


Q ss_pred             ecC
Q 043634           91 RAS   93 (121)
Q Consensus        91 ~a~   93 (121)
                      +++
T Consensus        87 ~a~   89 (95)
T d1x4aa1          87 FPR   89 (95)
T ss_dssp             CCC
T ss_pred             ecc
Confidence            993

>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=99.88  E-value=6e-22  Score=116.78  Aligned_cols=83  Identities=20%  Similarity=0.306  Sum_probs=72.6

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ......++|||+|||+.+++++|+++|++||. ..++++. .+.++|||||+|.+.++|..|+..|||..++|+.|+|++
T Consensus         6 ~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   85 (93)
T d2cq3a1           6 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            33445788999999999999999999999999 6666665 445689999999999999999999999999999999999


Q ss_pred             cCCCCc
Q 043634           92 ASKPNE   97 (121)
Q Consensus        92 a~~~~~   97 (121)
                      | .++.
T Consensus        86 A-~~r~   90 (93)
T d2cq3a1          86 A-TARV   90 (93)
T ss_dssp             C-CSSC
T ss_pred             c-CcCC
Confidence            9 5543

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.88  E-value=2.7e-22  Score=115.41  Aligned_cols=75  Identities=19%  Similarity=0.300  Sum_probs=65.6

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKP   95 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   95 (121)
                      ++|||+|||+.+++++|+++|++||. ..+.++.   .|.++|||||+|.+.++|.+|+..|||..++|+.|+|+++ +|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a-~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS-NP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC-CC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc-cC
Confidence            79999999999999999999999999 5555554   6888999999999999999999999999999999999998 54

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.88  E-value=5.9e-22  Score=116.15  Aligned_cols=79  Identities=25%  Similarity=0.365  Sum_probs=69.8

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK   94 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   94 (121)
                      .++++|||+|||..+++++|+++|++||. ..++++. ....+|||||+|.+.++|..|+..|||..+.|+.|+|.+++.
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~   85 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   85 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            34789999999999999999999999999 6666665 334578999999999999999999999999999999999943


Q ss_pred             C
Q 043634           95 P   95 (121)
Q Consensus        95 ~   95 (121)
                      +
T Consensus        86 ~   86 (90)
T d2cqia1          86 P   86 (90)
T ss_dssp             T
T ss_pred             C
Confidence            3

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=2.8e-22  Score=115.83  Aligned_cols=74  Identities=27%  Similarity=0.348  Sum_probs=68.0

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSV   89 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v   89 (121)
                      +.+.++|||+|||+.+++++|+++|++||. .+++++.   ++.++|||||+|.+.++|..|+..|||..++|+.|+|
T Consensus         6 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           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            456889999999999999999999999999 6676664   6888999999999999999999999999999999987

>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=99.88  E-value=4.8e-22  Score=125.00  Aligned_cols=74  Identities=32%  Similarity=0.499  Sum_probs=69.5

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .++|||+|||+++++++|+++|++||. .+++++.   +|.++|||||+|.+.++|..|+..|||..|+|+.|+|.++
T Consensus        42 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            578999999999999999999999999 6666665   6889999999999999999999999999999999999999

>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=99.87  E-value=3.1e-22  Score=117.29  Aligned_cols=74  Identities=31%  Similarity=0.407  Sum_probs=69.0

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ..+|||+|||+.+++++|+++|++||. ..+.++.   ++.++|||||+|.+.++|+.|+..|||..++|+.|+|+++
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            677999999999999999999999999 6666665   7888999999999999999999999999999999999999

>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=99.87  E-value=4.3e-22  Score=117.64  Aligned_cols=76  Identities=28%  Similarity=0.424  Sum_probs=69.9

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc----CCCcccEEEEEeCCHHHHHHHHHHh-cCCeeCCeEEEEE
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS----AGRLRNCVFVDFGNEPLASQAQMQL-NGLRFLGKVLSVE   90 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~----~~~~~g~afv~f~~~~~a~~ai~~l-~g~~i~g~~l~v~   90 (121)
                      ...++|||+|||+.+++++|+.+|++||. ..++++.    +|.++|||||+|.+.++|..|+..| ||..++|+.|+|.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            44788999999999999999999999999 6677654    6788999999999999999999998 8999999999999


Q ss_pred             ec
Q 043634           91 RA   92 (121)
Q Consensus        91 ~a   92 (121)
                      +|
T Consensus        86 ~A   87 (94)
T d2cpha1          86 WA   87 (94)
T ss_dssp             EC
T ss_pred             Ec
Confidence            99

>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=99.87  E-value=1.2e-22  Score=118.03  Aligned_cols=77  Identities=23%  Similarity=0.414  Sum_probs=70.7

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKP   95 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   95 (121)
                      ++|||+|||+.+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|..|+..|||..++|+.|.|.++ .+
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A-~~   80 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA-SV   80 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEEC-CC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC-CC
Confidence            57999999999999999999999999 6777765   6899999999999999999999999999999999999999 54


Q ss_pred             Cc
Q 043634           96 NE   97 (121)
Q Consensus        96 ~~   97 (121)
                      ..
T Consensus        81 ~~   82 (85)
T d2u2fa_          81 GA   82 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.87  E-value=4.1e-22  Score=114.47  Aligned_cols=72  Identities=24%  Similarity=0.298  Sum_probs=68.1

Q ss_pred             EEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           21 TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        21 ~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .|||+|||+.+++++|+++|++||. .+++++.   +|.++|||||+|.+.++|..|++.|||..++|+.|+|.++
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   77 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   77 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEEC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            6999999999999999999999999 6777775   6888999999999999999999999999999999999998

>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=99.87  E-value=4e-22  Score=118.18  Aligned_cols=82  Identities=22%  Similarity=0.326  Sum_probs=72.2

Q ss_pred             CCCCCCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           12 NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        12 ~~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ......+.++|||+|||+.+++++|+++|.+||.  +..+. ++.++|||||+|.+.++|..|+..|||..|+|+.|+|.
T Consensus         9 ~~~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~--v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~   86 (96)
T d1fjca_           9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDALE--IRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEE--ECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             ccCcCCCCCEEEEeCCCCCCCHHHHHHHHHhccc--ceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3444556899999999999999999999999998  44343 78889999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 043634           91 RASKPN   96 (121)
Q Consensus        91 ~a~~~~   96 (121)
                      ++ .++
T Consensus        87 ~a-~~k   91 (96)
T d1fjca_          87 YT-GEK   91 (96)
T ss_dssp             EC-SSS
T ss_pred             Ee-CCC
Confidence            99 544

>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=99.87  E-value=4e-22  Score=116.67  Aligned_cols=77  Identities=25%  Similarity=0.366  Sum_probs=69.6

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPN   96 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~~   96 (121)
                      ..+|||+|||+.+++++|+++|++||. ..++++. .+.++|||||+|.+.++|..|+..|||..++|+.|+|.++ .++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a-~~~   86 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF-KSR   86 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEEC-CCT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC-CCC
Confidence            567999999999999999999999999 6667766 5557899999999999999999999999999999999999 443

>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=8.9e-22  Score=119.91  Aligned_cols=76  Identities=25%  Similarity=0.329  Sum_probs=70.7

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +.+++|||+|||..+++++|+++|++||. ..+++..++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34789999999999999999999999999 66776667888999999999999999999999999999999999998

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

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

Probab=99.87  E-value=1e-21  Score=112.27  Aligned_cols=72  Identities=21%  Similarity=0.356  Sum_probs=68.0

Q ss_pred             EEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           21 TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        21 ~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +|||+|||+.+++++|+++|++||. ..++++.  +|.++|||||+|.+.++|..|+..|||..++|+.|+|+++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a   76 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV   76 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            6999999999999999999999999 6677765  7888999999999999999999999999999999999988

>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=99.86  E-value=1.5e-21  Score=115.82  Aligned_cols=82  Identities=22%  Similarity=0.398  Sum_probs=70.9

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhc------CCeeCCe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLN------GLRFLGK   85 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~------g~~i~g~   85 (121)
                      ...+++|||+|||+.+++++|+.+|.+||. ..+.++.   ++.++|||||+|.+.++|..|+..+|      |..++|+
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            344789999999999999999999999999 5555554   67789999999999999999999886      6789999


Q ss_pred             EEEEEecCCCCcc
Q 043634           86 VLSVERASKPNEE   98 (121)
Q Consensus        86 ~l~v~~a~~~~~~   98 (121)
                      .|+|.++ .++.+
T Consensus        85 ~l~v~~a-~~k~~   96 (98)
T d1x4ha1          85 QLKVDLA-VTRDE   96 (98)
T ss_dssp             EEEEECC-CCCCC
T ss_pred             EEEEEEC-CCCCc
Confidence            9999999 55543

>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=99.86  E-value=1.6e-21  Score=112.61  Aligned_cols=74  Identities=20%  Similarity=0.334  Sum_probs=67.1

Q ss_pred             EEecCCCCCCCHHHHHHHHhhhCC-ccE-EEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCCCC
Q 043634           22 LLIKHLPDAIPQDTLSRIFSHYGA-SSV-RPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPN   96 (121)
Q Consensus        22 l~V~nlp~~~~~~~L~~~f~~~G~-~~~-~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~~   96 (121)
                      |||+|||+++++++|+++|++||. ..+ +++.   +|+++|||||+|.+.++|..|+..|||..++|+.|+|.++ .++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a-~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA-FKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES-CCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEe-cCC
Confidence            799999999999999999999998 443 5554   6888999999999999999999999999999999999999 443

>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=99.86  E-value=4.6e-22  Score=116.88  Aligned_cols=76  Identities=22%  Similarity=0.306  Sum_probs=68.7

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +...++|||+|||+.+++++|+++|+.||. ..+.++.  +|.++|||||+|.+.++|.+|++ |||..++|+.|+|.++
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            344789999999999999999999999998 5555544  78899999999999999999995 9999999999999998

>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=99.86  E-value=1.1e-21  Score=114.10  Aligned_cols=78  Identities=23%  Similarity=0.341  Sum_probs=67.9

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCCCCc
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKPNE   97 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~~~   97 (121)
                      ..++|||+|||+.+++++|+++|++||.  +..+..+.++|||||+|.+.++|..|+..|||..|+|+.|+|+++ +|..
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~--i~~~~~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~a-kP~~   83 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKP--GAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA-KPVD   83 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTST--TCEEEEEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC-CCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccce--eeeEEEccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEec-cCCC
Confidence            3578999999999999999999999999  323333556899999999999999999999999999999999999 5554


Q ss_pred             c
Q 043634           98 E   98 (121)
Q Consensus        98 ~   98 (121)
                      +
T Consensus        84 ~   84 (86)
T d2cpda1          84 K   84 (86)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.86  E-value=1e-21  Score=113.98  Aligned_cols=74  Identities=30%  Similarity=0.431  Sum_probs=67.5

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLG--KVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g--~~l~v~~a   92 (121)
                      +++|||+|||+.+++++|+++|++||. .+++++.   +|.++|||||+|.+.++|..|+..|||..++|  ++|.|.+|
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            678999999999999999999999999 6777765   68899999999999999999999999999998  45888875

>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=99.86  E-value=1.7e-21  Score=112.78  Aligned_cols=76  Identities=22%  Similarity=0.292  Sum_probs=68.8

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ++..++|||+|||+.+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|.+|+. +++..|+|+.|+|..
T Consensus         3 pe~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~   81 (84)
T d1l3ka1           3 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKR   81 (84)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            344689999999999999999999999999 6666665   78999999999999999999996 699999999999998


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      |
T Consensus        82 A   82 (84)
T d1l3ka1          82 A   82 (84)
T ss_dssp             C
T ss_pred             e
Confidence            7

>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=99.86  E-value=1.4e-21  Score=113.31  Aligned_cols=75  Identities=32%  Similarity=0.453  Sum_probs=68.5

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEe
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLG--KVLSVER   91 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g--~~l~v~~   91 (121)
                      ..++|||+|||+.+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|..|++.|||..+.|  ++|+|.+
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            4678999999999999999999999999 6677665   78899999999999999999999999999976  8899988


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.86  E-value=3.8e-21  Score=115.35  Aligned_cols=76  Identities=21%  Similarity=0.278  Sum_probs=66.9

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc----CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS----AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~----~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ..|.++|||+|||+.+++++|+++|+.||...++++.    ++.++|||||+|.+.++|++|+ .||+..|+|+.|+|.+
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSCEEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhccccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEE
Confidence            4567999999999999999999999999974444443    5778999999999999998776 6999999999999999


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      +
T Consensus        91 a   91 (104)
T d1wi8a_          91 A   91 (104)
T ss_dssp             C
T ss_pred             C
Confidence            9

>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=99.85  E-value=1.7e-21  Score=116.80  Aligned_cols=78  Identities=22%  Similarity=0.296  Sum_probs=69.8

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK   94 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   94 (121)
                      .++|||+|||+.+++++|+++|++||. ..+.++.   ++.++|||||+|.+.++|.+|+. +++..|+|+.|.|.+| .
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a-~   97 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRA-V   97 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECC-S
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC-c
Confidence            589999999999999999999999999 6777655   67889999999999999999984 7999999999999998 5


Q ss_pred             CCcc
Q 043634           95 PNEE   98 (121)
Q Consensus        95 ~~~~   98 (121)
                      ++.+
T Consensus        98 ~ke~  101 (103)
T d1x4ba1          98 AREE  101 (103)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            5543

>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=99.85  E-value=4.5e-21  Score=114.94  Aligned_cols=74  Identities=20%  Similarity=0.310  Sum_probs=68.1

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      .++|||+|||+.+++++|+++|++||. .+++++.   +|.++|||||+|.+.++|.+|++.+|+ .|+|+.|+|.++.
T Consensus        10 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            578999999999999999999999999 6777766   688999999999999999999998876 7999999999984

>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=99.85  E-value=5.5e-22  Score=113.17  Aligned_cols=72  Identities=18%  Similarity=0.217  Sum_probs=66.9

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      |+|||+|||+.+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|++|+. +++..++|+.|+|..|
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            68999999999999999999999999 7777765   78899999999999999999996 7999999999999887

>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=99.85  E-value=2.2e-21  Score=115.94  Aligned_cols=73  Identities=27%  Similarity=0.359  Sum_probs=68.2

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .++|||+|||+.+++++|+++|+.||. ..++++.   +|.++|||||+|.+.++|..|+ .|||..|+|+.|.|.++
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~-~l~g~~~~G~~l~V~~a   94 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS   94 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHH-HHCCCEECCEEEEEEEC
Confidence            578999999999999999999999999 6677776   6889999999999999999999 59999999999999987

>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=99.85  E-value=4.3e-21  Score=112.46  Aligned_cols=75  Identities=19%  Similarity=0.224  Sum_probs=67.4

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ....++|||+|||+.+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|.+|+...  ..|+|+.|.|.+
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~~l~Gr~i~v~~   82 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMIDGRWCDCKL   82 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEETTEEEEEEC
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--CccCCEEeEEEe
Confidence            345789999999999999999999999999 6676665   7899999999999999999999754  489999999999


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      +
T Consensus        83 a   83 (90)
T d2cqga1          83 P   83 (90)
T ss_dssp             C
T ss_pred             C
Confidence            9

>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=99.85  E-value=1.5e-21  Score=116.69  Aligned_cols=80  Identities=28%  Similarity=0.435  Sum_probs=71.2

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ..|+++|||+|||..+++++|+++|++||. ..+.++.   +|.++|||||+|.+.++|..|+..|||..|.|+.|+|.+
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            345789999999999999999999999998 5444433   788999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 043634           92 ASKPN   96 (121)
Q Consensus        92 a~~~~   96 (121)
                      + +++
T Consensus        95 a-k~k   98 (102)
T d2cpxa1          95 G-KNK   98 (102)
T ss_dssp             C-CCC
T ss_pred             C-CCc
Confidence            9 544

>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=99.85  E-value=2.6e-21  Score=112.17  Aligned_cols=71  Identities=30%  Similarity=0.346  Sum_probs=64.8

Q ss_pred             EEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CC---CcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           22 LLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AG---RLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        22 l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~---~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      |||+|||+.+++++|+++|++||. .+++++.   ++   .++|||||+|.+.++|..|+..|||..++|+.|.|+++
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a   78 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRIS   78 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECS
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            799999999999999999999999 6666665   22   45899999999999999999999999999999999998

>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=1.3e-21  Score=112.36  Aligned_cols=74  Identities=23%  Similarity=0.324  Sum_probs=64.6

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCC-eeCCeEEEEEecCCCCc
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGL-RFLGKVLSVERASKPNE   97 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~-~i~g~~l~v~~a~~~~~   97 (121)
                      .+|||+|||+.+++++|+++|++||. ...++   ...+|||||+|.+.++|..|++.|||. .++|+.|+|+++ .|+.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~---~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a-~~k~   77 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV---LLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYS-VSKK   77 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCE---EEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEEC-CCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEE---ecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEc-CCcC
Confidence            47999999999999999999999999 33333   345799999999999999999999995 799999999999 5543

>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=99.84  E-value=7.7e-21  Score=113.32  Aligned_cols=80  Identities=21%  Similarity=0.365  Sum_probs=69.0

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-cc--------EEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeC
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SS--------VRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFL   83 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~--------~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~   83 (121)
                      ....++|||+|||+.+++++|+++|.+||. ..        +....   +|.++|||||+|.+.++|..|+..|||..|+
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            344899999999999999999999999997 21        22222   5788899999999999999999999999999


Q ss_pred             CeEEEEEecCCCC
Q 043634           84 GKVLSVERASKPN   96 (121)
Q Consensus        84 g~~l~v~~a~~~~   96 (121)
                      |+.|+|+++ +++
T Consensus        85 gr~i~V~~a-~~~   96 (101)
T d2cpea1          85 GSKLKVSLA-RKK   96 (101)
T ss_dssp             TEECEEECS-SCC
T ss_pred             CEEEEEEEc-CCC
Confidence            999999999 443

>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=99.84  E-value=3.1e-21  Score=113.22  Aligned_cols=75  Identities=27%  Similarity=0.429  Sum_probs=67.6

Q ss_pred             CccEEEecCCCCCCCHHHHHH----HHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           18 NLVTLLIKHLPDAIPQDTLSR----IFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~----~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      |+++|||+|||+.+++++|++    +|++||. .++++..++.++|||||+|.+.++|..|+..+||..++|+.|+|.++
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~a   81 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA   81 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            578999999999999998864    5799999 55665557778999999999999999999999999999999999999

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.84  E-value=8.4e-21  Score=112.41  Aligned_cols=73  Identities=19%  Similarity=0.331  Sum_probs=66.7

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ++.++|||+|||..+++++|+.+|++||. .+++++.   .+|||||+|.+.++|..|+..|||..|+|+.|+|.|+
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 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP---EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   89 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEe---cceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34689999999999999999999999999 5666653   3789999999999999999999999999999999999

>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=99.84  E-value=3.2e-21  Score=115.68  Aligned_cols=74  Identities=28%  Similarity=0.496  Sum_probs=69.6

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .++|||+|||+.+++++|+++|++||. ..++++.   +|.++|||||+|.+.++|..|+..|||..++|+.|+|.++
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a   85 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            568999999999999999999999999 7777765   7889999999999999999999999999999999999998

>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=99.84  E-value=2.9e-21  Score=112.27  Aligned_cols=77  Identities=19%  Similarity=0.290  Sum_probs=65.9

Q ss_pred             CccEEEecCCCCCCC-HHHHHHHHhhhCC-ccEEEcc----CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           18 NLVTLLIKHLPDAIP-QDTLSRIFSHYGA-SSVRPCS----AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~-~~~L~~~f~~~G~-~~~~~~~----~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      .+++|||+|||+.++ +++|+++|++||. ..++++.    ++.++|||||+|.+.++|..|+. |||..++|+.|+|++
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            378999999999976 5679999999999 6666644    67889999999999999999995 999999999999999


Q ss_pred             cCCCC
Q 043634           92 ASKPN   96 (121)
Q Consensus        92 a~~~~   96 (121)
                      + .++
T Consensus        82 a-~~k   85 (86)
T d2ghpa3          82 A-DKK   85 (86)
T ss_dssp             C-CCC
T ss_pred             c-CCC
Confidence            9 443

>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=99.84  E-value=3.6e-21  Score=109.19  Aligned_cols=71  Identities=24%  Similarity=0.304  Sum_probs=64.3

Q ss_pred             EEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           21 TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        21 ~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +|||+|||+.+++++|+++|++||. ..+.++.   +++++|||||+|.+.++|+.|+. +++..|+|+.|.|..|
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            5899999999999999999999999 6666665   68899999999999999999996 7999999999998754

>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=99.84  E-value=1e-20  Score=108.15  Aligned_cols=73  Identities=16%  Similarity=0.310  Sum_probs=65.4

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .++|||+|||+.+++++|+++|++||. ..+.++.   ++.++|||||+|.+.+++.+|+ .++|..|+|+.|+|..|
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 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhCCCEECCEEEEEEEC
Confidence            468999999999999999999999999 5555554   7788999999999999999998 58999999999999876

>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=99.84  E-value=1.1e-20  Score=114.43  Aligned_cols=74  Identities=22%  Similarity=0.213  Sum_probs=66.6

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      ..++|||+|||+.+++++|+++|++||.  |..+.....+|||||+|.+.++|.+|+..|||..|.|+.|.|+++.
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 SKTVILAKNLPAGTLAAEIQETFSRFGS--LGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSC--EEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCC--ccEEEeeccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            3689999999999999999999999999  4444434567999999999999999999999999999999999994

>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=99.83  E-value=2e-20  Score=107.99  Aligned_cols=75  Identities=21%  Similarity=0.377  Sum_probs=66.4

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEEecC
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFL-GKVLSVERAS   93 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~-g~~l~v~~a~   93 (121)
                      +|+++|||+|||..+++++|..+|++||. ..++++.  ..+|||||+|.+.++|..|+..|||..+. |+.|+|.|++
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVP--NRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECT--TTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeec--ccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            45789999999999999999999999999 5666654  34689999999999999999999999885 6899999993

>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=99.83  E-value=6.6e-21  Score=107.88  Aligned_cols=71  Identities=15%  Similarity=0.267  Sum_probs=64.1

Q ss_pred             EEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           21 TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        21 ~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +|||+|||+.+++++|+++|++||. ..+.++.   ++.+++||||+|.+.++|..|++ +||..|+|+.|+|.+|
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            5899999999999999999999999 5555544   67889999999999999999995 9999999999999875

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=6.6e-21  Score=113.83  Aligned_cols=77  Identities=17%  Similarity=0.217  Sum_probs=68.3

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...+++|||+|||+.+++++|+++|++||. ..+.+..  ++.++|||||+|.+.++|.+|++.|||..|.|+++.|.++
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            334789999999999999999999999999 4454444  7788999999999999999999999999999999888766

>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=99.83  E-value=2.6e-20  Score=108.09  Aligned_cols=75  Identities=16%  Similarity=0.192  Sum_probs=67.3

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-cc-EEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SS-VRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~-~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ..++|||+|||+.+++++|+++|..||. .. +.+..  ++.++|+|||+|.+.++|..|+..||+..++|++|+|+++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3678999999999999999999999999 33 34443  7889999999999999999999999999999999999875

>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=1.4e-20  Score=111.31  Aligned_cols=80  Identities=18%  Similarity=0.276  Sum_probs=68.4

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC--ccEEEcc----CCCcccEEEEEeCCHHHHHHHHHHhcC--CeeCCeEEEEE
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA--SSVRPCS----AGRLRNCVFVDFGNEPLASQAQMQLNG--LRFLGKVLSVE   90 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~--~~~~~~~----~~~~~g~afv~f~~~~~a~~ai~~l~g--~~i~g~~l~v~   90 (121)
                      +|+|||+|||..+++++|+++|++||.  ..++++.    ++.++|||||+|.+.++|..|+..|++  ..+.|+.|+|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            478999999999999999999999996  4566654    577899999999999999999999864  56679999999


Q ss_pred             ecCCCCccc
Q 043634           91 RASKPNEEN   99 (121)
Q Consensus        91 ~a~~~~~~~   99 (121)
                      || +|+.+.
T Consensus        81 ~A-~p~~~~   88 (96)
T d2disa1          81 WA-EPEIDV   88 (96)
T ss_dssp             ES-CSSCST
T ss_pred             Ec-CCCCCC
Confidence            99 665443

>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=99.83  E-value=2.7e-20  Score=108.46  Aligned_cols=75  Identities=20%  Similarity=0.268  Sum_probs=65.8

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCee-CCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRF-LGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i-~g~~l~v~~a   92 (121)
                      +|.++|||+|||+.+++++|+++|++||. ..+... .+++++||||+|.+.++|..|+..|||..+ +|+.|+|+++
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~-~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF-FQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEE-CSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEe-eecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            45789999999999999999999999998 333322 456689999999999999999999999998 5899999999

>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=99.83  E-value=8.7e-21  Score=110.67  Aligned_cols=73  Identities=22%  Similarity=0.285  Sum_probs=65.0

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...++|||+|||+.+++++|+++|.+||...+.   .+..++||||+|.+.++|.+|+..||+..++|+.|+|+++
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G~~~~~---~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a   75 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCY---VDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSCCCCEE---EEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcCceeee---eeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            346889999999999999999999999952222   3556799999999999999999999999999999999999

>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=99.83  E-value=2.4e-20  Score=110.85  Aligned_cols=73  Identities=25%  Similarity=0.342  Sum_probs=64.2

Q ss_pred             CCccEEEecCCC-CCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCC
Q 043634           17 ENLVTLLIKHLP-DAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASK   94 (121)
Q Consensus        17 ~~~~~l~V~nlp-~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~   94 (121)
                      ...++|||+||| ..+++++|+++|++||. ..+++     ++|||||+|.+.++|.+|+..|||..|+|+.|+|.+++.
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i-----~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   87 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-----HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAE   87 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE-----ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTS
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE-----eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            346789999997 56888999999999999 44444     479999999999999999999999999999999999943

>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=99.82  E-value=5.4e-20  Score=106.82  Aligned_cols=72  Identities=25%  Similarity=0.439  Sum_probs=66.1

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ..++|||+|||+.+++++|+++|++||. ..+++..   .++||||+|.+.++|..|+..|||..|+|+.|+|++|
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~---~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A   79 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK---DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   79 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET---TTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeec---ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            3678999999999999999999999999 6666653   3689999999999999999999999999999999999

>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=99.82  E-value=2.9e-20  Score=111.13  Aligned_cols=79  Identities=15%  Similarity=0.131  Sum_probs=69.4

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      .....+.+|||+|||+.+++++|+++|..+|...++++.  .+..+|||||+|.+.++|++|+. +|+..|+|+.|+|.+
T Consensus        10 ~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~   88 (102)
T d1weza_          10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CCCSSSCEEEEESCCTTCCHHHHHHSSCSCCCSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CcCCCCCEEEEeCCCCcCCHHHHHHHHhccCcceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            344557899999999999999999999999875555555  77889999999999999999985 899999999999999


Q ss_pred             cC
Q 043634           92 AS   93 (121)
Q Consensus        92 a~   93 (121)
                      +.
T Consensus        89 s~   90 (102)
T d1weza_          89 NS   90 (102)
T ss_dssp             EC
T ss_pred             cC
Confidence            83

>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=99.82  E-value=9.1e-21  Score=107.50  Aligned_cols=71  Identities=14%  Similarity=0.223  Sum_probs=63.9

Q ss_pred             EEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           21 TLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        21 ~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +|||||||+.+++++|+++|++||. ..++++.   ++.++|||||+|.+.++|.+|++ .++..|+|+.|.|..|
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            5999999999999999999999999 6677665   78899999999999999999996 4778899999998765

>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=99.82  E-value=1.6e-20  Score=107.43  Aligned_cols=71  Identities=28%  Similarity=0.317  Sum_probs=64.1

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ..+++|||+|++  +++++|+++|++||. ..+.+.   +.++||||+|.+.++|..|+..|||..++|+.|+|.++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~---~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD---PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeec---cCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            347899999996  899999999999999 666554   34689999999999999999999999999999999999

>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=99.81  E-value=4.6e-20  Score=104.56  Aligned_cols=68  Identities=24%  Similarity=0.392  Sum_probs=62.1

Q ss_pred             EEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           22 LLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        22 l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      |||+|||+++++++|+++|++||.   ..+..+.++|||||+|.+.++|.+|+..|||..+.|++|+|+++
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g~---~~~~~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a   68 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYEL---KYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQ   68 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSCE---EEEEEETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CEEeCCCCcCCHHHHHHHHhcccc---cceeecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEe
Confidence            799999999999999999999994   23334567899999999999999999999999999999999999

>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=99.81  E-value=2.2e-20  Score=108.93  Aligned_cols=77  Identities=21%  Similarity=0.370  Sum_probs=66.0

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecCCC
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERASKP   95 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~~~   95 (121)
                      ...++|||+|||+.+++++|+++|++||. ..+++  ...+++||||+|.+.++|+.|+.  ++..|+|+.|+|.++ .+
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~--~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a-~~   77 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI--PKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA-EP   77 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEEC--CSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC-CC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEE--eeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC-CC
Confidence            44789999999999999999999999999 44443  35567999999999999999984  788999999999999 55


Q ss_pred             Ccc
Q 043634           96 NEE   98 (121)
Q Consensus        96 ~~~   98 (121)
                      +.+
T Consensus        78 k~~   80 (88)
T d1wf0a_          78 KHN   80 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            443

>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=99.81  E-value=1.3e-19  Score=104.92  Aligned_cols=73  Identities=15%  Similarity=0.187  Sum_probs=66.8

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .++|||+|||..+++++|+.+|+.||. ..+++..  +|.++|||||+|.+.++|.+|++ +++..++|+.|.|.+.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~   81 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   81 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEc
Confidence            578999999999999999999999999 6666655  78889999999999999999995 7999999999999886

>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=99.80  E-value=3.7e-19  Score=105.36  Aligned_cols=76  Identities=17%  Similarity=0.313  Sum_probs=65.9

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEe
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLG--KVLSVER   91 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g--~~l~v~~   91 (121)
                      ...|.++|||+|||+.+++++|+++|++||. ..+++.   ..++||||+|.+.++|..|+..||+..|.|  ++|+|++
T Consensus        13 ~~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~---~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV---KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEEC---SSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeee---ccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            3456799999999999999999999999999 444443   346899999999999999999999999986  5899999


Q ss_pred             cC
Q 043634           92 AS   93 (121)
Q Consensus        92 a~   93 (121)
                      ++
T Consensus        90 ak   91 (97)
T d1whya_          90 AK   91 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            93

>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=99.80  E-value=3.3e-19  Score=103.78  Aligned_cols=77  Identities=12%  Similarity=0.176  Sum_probs=66.4

Q ss_pred             CCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHh--cCCeeCCeEEEEE
Q 043634           14 QETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQL--NGLRFLGKVLSVE   90 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l--~g~~i~g~~l~v~   90 (121)
                      ...+|+++|||+|||+.+++++|+++|++||. ..+++.   ..+++|||+|.+.++|.+|+..+  ++..+.|+.|+|.
T Consensus         3 ~~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~---~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~   79 (88)
T d2cq1a1           3 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML---KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   79 (88)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEE---TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccc---ccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEE
Confidence            34567999999999999999999999999999 444443   34689999999999999999876  5678999999999


Q ss_pred             ecC
Q 043634           91 RAS   93 (121)
Q Consensus        91 ~a~   93 (121)
                      +++
T Consensus        80 ~sk   82 (88)
T d2cq1a1          80 YSN   82 (88)
T ss_dssp             ECS
T ss_pred             ECC
Confidence            993

>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=99.80  E-value=1.3e-19  Score=107.57  Aligned_cols=74  Identities=12%  Similarity=0.068  Sum_probs=65.5

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ......+|||+|||+.+++++|+++|++||. ..+.+.    .+|||||+|.+.++|..||+.|||..++|+.|+|.++
T Consensus        11 ~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~----~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          11 TRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ----KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             CCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE----TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhhccccccccc----ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            3345788999999999999999999999999 444432    2489999999999999999999999999999999998

>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=99.80  E-value=1.9e-19  Score=101.99  Aligned_cols=72  Identities=19%  Similarity=0.194  Sum_probs=63.9

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc-CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS-AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ++|||+|||+.+++++|+++|+.||. ..++++. .+..++||||+|.+.++|.+|+ .+|+..|+|+.|.|+.+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            58999999999999999999999999 6666665 4445679999999999999998 58999999999999865

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.80  E-value=3.4e-19  Score=107.37  Aligned_cols=73  Identities=22%  Similarity=0.334  Sum_probs=65.3

Q ss_pred             ccEEEecCCCC-CCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecC
Q 043634           19 LVTLLIKHLPD-AIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERAS   93 (121)
Q Consensus        19 ~~~l~V~nlp~-~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a~   93 (121)
                      +++|||+|||+ .+++++|+++|+.||. ..++++..  .+|||||+|.+.++|.+|+..|||..|+|+.|+|.+++
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 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN--KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCT--TSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEec--ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            57999999965 5999999999999999 56666543  36899999999999999999999999999999999994

>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=99.79  E-value=4.3e-19  Score=106.28  Aligned_cols=79  Identities=18%  Similarity=0.243  Sum_probs=67.7

Q ss_pred             CCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-cc-EEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           13 KQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SS-VRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        13 ~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~-~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      .+.......|||+|||+.+++++|+++|..+|. .. +.++.  ++..+|+|||+|.+.++|.+|+. +|+..|+|+.|+
T Consensus         9 ~~~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~   87 (104)
T d1wg5a_           9 SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIE   87 (104)
T ss_dssp             CSSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEE
Confidence            334445678999999999999999999999998 33 33333  77889999999999999999985 899999999999


Q ss_pred             EEec
Q 043634           89 VERA   92 (121)
Q Consensus        89 v~~a   92 (121)
                      |..+
T Consensus        88 V~~~   91 (104)
T d1wg5a_          88 IFKS   91 (104)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9999

>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=99.79  E-value=3e-20  Score=108.11  Aligned_cols=69  Identities=13%  Similarity=0.100  Sum_probs=61.9

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      .+|||+|||+.+++++|+++|++||. ..+++..    .|||||+|.+.++|..||..|||..++|+.|+|.++
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~----~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~   70 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR----DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   70 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT----TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc----cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEE
Confidence            36999999999999999999999999 4455432    389999999999999999999999999999998877

>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=99.79  E-value=3.1e-20  Score=104.38  Aligned_cols=67  Identities=21%  Similarity=0.333  Sum_probs=60.8

Q ss_pred             EEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           22 LLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        22 l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      |||+|||+.+++++|+++|++||. ..++++.   ++.++|+|||+|.+.++|.+|+..|||..++|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            799999999999999999999999 5555554   678899999999999999999999999999998763

>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=99.79  E-value=9e-20  Score=106.49  Aligned_cols=72  Identities=14%  Similarity=0.177  Sum_probs=63.1

Q ss_pred             ccEEEecCCCCCCCHHHH---HHHHhhhCC-ccEEEcc---C---CCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 043634           19 LVTLLIKHLPDAIPQDTL---SRIFSHYGA-SSVRPCS---A---GRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLS   88 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L---~~~f~~~G~-~~~~~~~---~---~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~   88 (121)
                      ...|||+|||+.+++++|   .++|++||. ..+.++.   +   +..+|||||+|.+.++|..|+..|||..++|+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            678999999999999999   678999999 6666665   2   23458999999999999999999999999999999


Q ss_pred             EE
Q 043634           89 VE   90 (121)
Q Consensus        89 v~   90 (121)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            85

>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=99.79  E-value=1.2e-18  Score=104.36  Aligned_cols=80  Identities=11%  Similarity=0.159  Sum_probs=67.7

Q ss_pred             CCCCCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHh--cCCeeCCeEEE
Q 043634           12 NKQETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQL--NGLRFLGKVLS   88 (121)
Q Consensus        12 ~~~~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l--~g~~i~g~~l~   88 (121)
                      ......+..+|||+|||+.+++++|+.+|.+||. ..+++.   ..+++|||+|.+.++|..|+..|  ++..+.|+.|+
T Consensus         8 ~~~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~---~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_           8 SHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM---PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             SCCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEE---TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             CCCcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEE---ecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            3445566899999999999999999999999999 444443   34689999999999999999988  45678899999


Q ss_pred             EEecCC
Q 043634           89 VERASK   94 (121)
Q Consensus        89 v~~a~~   94 (121)
                      |.+++.
T Consensus        85 v~~s~~   90 (104)
T d1wexa_          85 FNYSTS   90 (104)
T ss_dssp             EEECSS
T ss_pred             EEEcCC
Confidence            999943

>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=99.78  E-value=3.8e-19  Score=107.21  Aligned_cols=77  Identities=16%  Similarity=0.321  Sum_probs=66.7

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCee--CCeEEEEEec
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRF--LGKVLSVERA   92 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i--~g~~l~v~~a   92 (121)
                      ..+...|||+|||+.+++++|+++|++||. ..+.+.. .+++|+|||+|.+.++|..|+..|||..|  .|..|+|.++
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~-~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s   82 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFT-KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS   82 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEE-ETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEEC
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEe-eCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEec
Confidence            455789999999999999999999999999 4554543 34579999999999999999999999988  4788999998


Q ss_pred             C
Q 043634           93 S   93 (121)
Q Consensus        93 ~   93 (121)
                      +
T Consensus        83 ~   83 (108)
T d2adba1          83 K   83 (108)
T ss_dssp             S
T ss_pred             C
Confidence            3

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.3e-18  Score=104.00  Aligned_cols=73  Identities=19%  Similarity=0.195  Sum_probs=66.1

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-cc-EEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SS-VRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~-~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...|||+|||+.+++++|.++|..||. .. +.++.  +|.++|+|||+|.+.++|.+|+. +|+..|+|+.|.|..+
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            567999999999999999999999998 33 45544  78899999999999999999995 8999999999999987

>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=99.76  E-value=6.9e-19  Score=106.73  Aligned_cols=76  Identities=17%  Similarity=0.173  Sum_probs=66.4

Q ss_pred             CCCccEEEecCCCCCCCHHHHHHHHhhhCC-cc-EEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 043634           16 TENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SS-VRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVER   91 (121)
Q Consensus        16 ~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~-~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~   91 (121)
                      ....++|||+|||+.+++++|+++|+.||. .. +.+..  +|..+|+|||+|.+.++|.+|+. +||..|+|+.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            334789999999999999999999999998 33 33332  88899999999999999999985 899999999999988


Q ss_pred             c
Q 043634           92 A   92 (121)
Q Consensus        92 a   92 (121)
                      +
T Consensus        94 ~   94 (112)
T d1wela1          94 I   94 (112)
T ss_dssp             E
T ss_pred             c
Confidence            8

>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=99.76  E-value=3.1e-18  Score=101.67  Aligned_cols=77  Identities=16%  Similarity=0.259  Sum_probs=66.2

Q ss_pred             CCCCCccEEEecCCCCC-CCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHH--HhcCCeeCCeEEEE
Q 043634           14 QETENLVTLLIKHLPDA-IPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQM--QLNGLRFLGKVLSV   89 (121)
Q Consensus        14 ~~~~~~~~l~V~nlp~~-~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~--~l~g~~i~g~~l~v   89 (121)
                      +...++++|||+|||.. +++++|..+|++||. ..+.++.   ++|+|||+|.+.++|..|+.  .+++..++|+.|+|
T Consensus        13 ~~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~---~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V   89 (99)
T d1x4fa1          13 QKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR---MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   89 (99)
T ss_dssp             CSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET---TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             cCCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEee---cCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEE
Confidence            34455899999999985 899999999999999 6666653   36899999999999999997  56788999999999


Q ss_pred             EecC
Q 043634           90 ERAS   93 (121)
Q Consensus        90 ~~a~   93 (121)
                      .+++
T Consensus        90 ~~s~   93 (99)
T d1x4fa1          90 DLSE   93 (99)
T ss_dssp             EEEC
T ss_pred             EEcC
Confidence            9993

>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=99.74  E-value=7.8e-18  Score=98.11  Aligned_cols=76  Identities=16%  Similarity=0.123  Sum_probs=65.3

Q ss_pred             CCCCccEEEecCCCCC-CCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHh--cCCeeCCeEEEEE
Q 043634           15 ETENLVTLLIKHLPDA-IPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQL--NGLRFLGKVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~-~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l--~g~~i~g~~l~v~   90 (121)
                      ..+++.+|||+|||.. ++++||.++|++||. ..+.++.   .+++|||+|.+.++|..|+..+  ++..+.|++|+|.
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~---~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~   80 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN---KINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVH   80 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECS---SSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeec---cceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEE
Confidence            3456899999999997 889999999999999 5555543   3579999999999999999966  6788999999999


Q ss_pred             ecC
Q 043634           91 RAS   93 (121)
Q Consensus        91 ~a~   93 (121)
                      +++
T Consensus        81 ~s~   83 (89)
T d1x4da1          81 LSQ   83 (89)
T ss_dssp             EEC
T ss_pred             ECC
Confidence            994

>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=1.7e-19  Score=105.42  Aligned_cols=72  Identities=19%  Similarity=0.395  Sum_probs=62.5

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEc--------cCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPC--------SAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~--------~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ++|||+|||+.+++++|+++|+.||. ..+.+.        .++.++|||||+|.+.++|..|+ .|||..++|+.|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCcEECCEEEEEC
Confidence            58999999999999999999999997 433222        25677899999999999999998 599999999999997


Q ss_pred             ec
Q 043634           91 RA   92 (121)
Q Consensus        91 ~a   92 (121)
                      .+
T Consensus        81 r~   82 (90)
T d1u2fa_          81 RP   82 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            65

>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=99.71  E-value=1.2e-17  Score=99.96  Aligned_cols=74  Identities=20%  Similarity=0.297  Sum_probs=64.9

Q ss_pred             CCccEEEecCCCCCC-CH----HHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           17 ENLVTLLIKHLPDAI-PQ----DTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~-~~----~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      ....+|||+||+..+ ++    ++|+.+|+.||. .+++++.   +++||||+|.+.++|.+|+..|||..|+|+.|+|.
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k---~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   79 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK---SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLY   79 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET---TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEE
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec---CCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEe
Confidence            457899999999986 33    569999999999 6666653   46899999999999999999999999999999999


Q ss_pred             ecC
Q 043634           91 RAS   93 (121)
Q Consensus        91 ~a~   93 (121)
                      +++
T Consensus        80 ~a~   82 (104)
T d1weya_          80 FAQ   82 (104)
T ss_dssp             CCC
T ss_pred             ecc
Confidence            994

>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=99.70  E-value=4.2e-17  Score=105.77  Aligned_cols=80  Identities=15%  Similarity=0.287  Sum_probs=69.8

Q ss_pred             CCCCccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 043634           15 ETENLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVE   90 (121)
Q Consensus        15 ~~~~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~   90 (121)
                      .....++|||+|||+.+++++|+++|+.||. ..+.++.   ++.++|||||+|.+.++|.+|+. +++..++|+.|+|.
T Consensus        93 ~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~  171 (183)
T d1u1qa_          93 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVR  171 (183)
T ss_dssp             TTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEE
T ss_pred             cccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEE
Confidence            3444789999999999999999999999999 5555554   68889999999999999999996 78899999999999


Q ss_pred             ecCCCC
Q 043634           91 RASKPN   96 (121)
Q Consensus        91 ~a~~~~   96 (121)
                      +| .++
T Consensus       172 ~A-~~k  176 (183)
T d1u1qa_         172 KA-LSK  176 (183)
T ss_dssp             EC-CCH
T ss_pred             ec-CCc
Confidence            98 543

>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=99.63  E-value=1.4e-17  Score=99.66  Aligned_cols=73  Identities=22%  Similarity=0.375  Sum_probs=68.0

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc--CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS--AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~--~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +.++|++++..+++++|+++|++||. .+++++.  ++.++|+|||+|.+.++|.+|+..|||..++|+.|+|+++
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 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            67889999999999999999999999 7777776  7888999999999999999999999999999999999875

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=1.5e-15  Score=90.25  Aligned_cols=66  Identities=15%  Similarity=0.250  Sum_probs=55.3

Q ss_pred             CCCccEEEe--cCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeC
Q 043634           16 TENLVTLLI--KHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFL   83 (121)
Q Consensus        16 ~~~~~~l~V--~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~   83 (121)
                      ..|..++||  ||||..+++++|+++|++||.  +..+.....++||||+|.+.++|..|+..|||..+.
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~--i~~i~~~~~k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGL--VDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSC--EEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCc--ccEEeeccCccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            455677888  559999999999999999999  444443345789999999999999999999999873

>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=99.58  E-value=2.9e-15  Score=90.57  Aligned_cols=71  Identities=15%  Similarity=0.058  Sum_probs=59.7

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCH-HHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNE-PLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~-~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ...+||||||+.+|+++|+++|++||. ..+.++   ..+|||||.|.+. ++|..|+..+++..+.++.+.|.+.
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~---~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV---RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECC---TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEe---cCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            345599999999999999999999999 444444   3479999999985 6788999999999998887777776

>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=99.55  E-value=2e-14  Score=92.90  Aligned_cols=74  Identities=22%  Similarity=0.284  Sum_probs=64.7

Q ss_pred             CccEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           18 NLVTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS---AGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        18 ~~~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      ..++|||+|||+.+++++|+++|++||. ..+.++.   ++.++|||||+|.+.++|.+|+. .++..++++.+.+...
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~   82 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   82 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhh
Confidence            3689999999999999999999999999 6666654   78889999999999999999985 5677888888888766

>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=99.53  E-value=1.4e-14  Score=82.65  Aligned_cols=70  Identities=17%  Similarity=0.219  Sum_probs=58.2

Q ss_pred             ccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeE-EEEEec
Q 043634           19 LVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKV-LSVERA   92 (121)
Q Consensus        19 ~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~-l~v~~a   92 (121)
                      .+.|+|+++|+..+++.| +.|++||.  +..+..+..++||||+|.+.++|++|+. +||..++|+. |.|..+
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~--I~~~~~~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGN--ILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSC--EEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhh--hheEEecCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeC
Confidence            578999999999987655 57999999  4434445567999999999999999995 9999999975 578777

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=2.9e-14  Score=84.20  Aligned_cols=79  Identities=16%  Similarity=0.222  Sum_probs=64.7

Q ss_pred             CCCccEEEecCC--CCCCC---------HHHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeC
Q 043634           16 TENLVTLLIKHL--PDAIP---------QDTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFL   83 (121)
Q Consensus        16 ~~~~~~l~V~nl--p~~~~---------~~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~   83 (121)
                      .....+|+|.|+  |..+.         .++|+..|++||. ..+.+. .+..+|++||.|.+.++|..|+..|||..++
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~-~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~   83 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLF-DRHPDGVASVSFRDPEEADYCIQTLDGRWFG   83 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEE-TTCTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEecc-CCCCccEEEEEECCHHHHHHHHHHhCCcEEC
Confidence            345899999999  54422         2679999999999 555544 4456799999999999999999999999999


Q ss_pred             CeEEEEEecCCCC
Q 043634           84 GKVLSVERASKPN   96 (121)
Q Consensus        84 g~~l~v~~a~~~~   96 (121)
                      |+.|+|++. .++
T Consensus        84 gr~i~v~~~-~g~   95 (99)
T d2dita1          84 GRQITAQAW-DGT   95 (99)
T ss_dssp             TEECEEEEC-CSC
T ss_pred             CEEEEEEEe-CCc
Confidence            999999998 443

>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=99.36  E-value=5e-13  Score=79.43  Aligned_cols=76  Identities=18%  Similarity=0.248  Sum_probs=63.2

Q ss_pred             CCccEEEecCC--CCCCC--------HHHHHHHHhhhCC-ccEEEcc-----CCCcccEEEEEeCCHHHHHHHHHHhcCC
Q 043634           17 ENLVTLLIKHL--PDAIP--------QDTLSRIFSHYGA-SSVRPCS-----AGRLRNCVFVDFGNEPLASQAQMQLNGL   80 (121)
Q Consensus        17 ~~~~~l~V~nl--p~~~~--------~~~L~~~f~~~G~-~~~~~~~-----~~~~~g~afv~f~~~~~a~~ai~~l~g~   80 (121)
                      +|...|.|.|+  |..+.        .+||+..|++||. ..+.+.+     .....|++||.|.+.++|.+|+..|||.
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            45788999999  55543        2578999999999 6676654     2234589999999999999999999999


Q ss_pred             eeCCeEEEEEec
Q 043634           81 RFLGKVLSVERA   92 (121)
Q Consensus        81 ~i~g~~l~v~~a   92 (121)
                      .++|+.|.+.+.
T Consensus        82 ~f~gR~v~v~f~   93 (104)
T d1o0pa_          82 KFANRVVVTKYC   93 (104)
T ss_dssp             CSSSSCCEEEEE
T ss_pred             EECCeEEEEEEc
Confidence            999999999998

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.84  E-value=4.5e-05  Score=43.17  Aligned_cols=65  Identities=15%  Similarity=0.267  Sum_probs=51.7

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhhhCC-ccEEEcc----CC-CcccEEEEEeCCHHHHHHHHHHhcCCeeCC
Q 043634           20 VTLLIKHLPDAIPQDTLSRIFSHYGA-SSVRPCS----AG-RLRNCVFVDFGNEPLASQAQMQLNGLRFLG   84 (121)
Q Consensus        20 ~~l~V~nlp~~~~~~~L~~~f~~~G~-~~~~~~~----~~-~~~g~afv~f~~~~~a~~ai~~l~g~~i~g   84 (121)
                      ++|-|+.||+.++++++.+.++..|. .......    .+ .....|||.|.+.++...-.+.++|..+.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            68999999999999999999998887 4334433    12 223689999999999998889999987653

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.81  E-value=0.00015  Score=38.81  Aligned_cols=59  Identities=22%  Similarity=0.140  Sum_probs=47.2

Q ss_pred             HHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 043634           34 DTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKVLSVERA   92 (121)
Q Consensus        34 ~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~l~v~~a   92 (121)
                      +.|...|.++|. .++.+.......-.|-|...+..+|..|+..||...|++++|.|.++
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~   70 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLA   70 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEe
Confidence            346667788898 55544432223358999999999999999999999999999999987

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.63  E-value=0.00016  Score=40.53  Aligned_cols=70  Identities=17%  Similarity=0.344  Sum_probs=51.6

Q ss_pred             CCccEEEecCCCCC------CCH---HHHHHHHhhhCC-ccEEEccCCCcccEEEEEeCCHHHHHHHHHHhcCCeeCCeE
Q 043634           17 ENLVTLLIKHLPDA------IPQ---DTLSRIFSHYGA-SSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLNGLRFLGKV   86 (121)
Q Consensus        17 ~~~~~l~V~nlp~~------~~~---~~L~~~f~~~G~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~i~g~~   86 (121)
                      +|..+|.|.=..+.      ..+   .+|.+.|..||+ .-+|++     .+.-+|+|.+-.+|.+|+ .++|.+++|+.
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv-----~d~mwVTF~dG~SAL~al-~l~g~~v~G~~   86 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRIN-----QGQMLVTFADSHSALSVL-DVDGMKVKGRA   86 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEE-----TTEEEEECSCSHHHHHHH-HGGGSEETTEE
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEe-----CCeEEEEECCcHHHHHHh-ccCCeEEcceE
Confidence            34566666444322      222   468888999999 445554     257899999999999998 58999999999


Q ss_pred             EEEEec
Q 043634           87 LSVERA   92 (121)
Q Consensus        87 l~v~~a   92 (121)
                      |+|...
T Consensus        87 l~It~~   92 (95)
T d1ufwa_          87 VKISGP   92 (95)
T ss_dssp             EEEECC
T ss_pred             EEEecC
Confidence            999744

>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=97.22  E-value=0.0016  Score=36.88  Aligned_cols=58  Identities=16%  Similarity=0.198  Sum_probs=48.2

Q ss_pred             CCccEEEecCCCCCCCHHHHHHHHhhhCCccEEEccCCCcccEEEEEeCCHHHHHHHHHHhc
Q 043634           17 ENLVTLLIKHLPDAIPQDTLSRIFSHYGASSVRPCSAGRLRNCVFVDFGNEPLASQAQMQLN   78 (121)
Q Consensus        17 ~~~~~l~V~nlp~~~~~~~L~~~f~~~G~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~   78 (121)
                      +.+.-||.-..|..+...||.++|++||...|.++..    .-|||...+.+.+..++..+.
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswIdd----TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDD----TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEET----TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCcceeEEEeCCcccchhHHHHHhcCCCceEEEEecC----ceEEEEecCHHHHHHHHHHhc
Confidence            3378888889999999999999999999966666652    378999999999888876554